{
"cells": [
{
"cell_type": "code",
"execution_count": 22,
"id": "15f4833b",
"metadata": {},
"outputs": [],
"source": [
"import os\n",
"\n",
"from dotenv import load_dotenv\n",
"\n",
"from evoagentx.agents.agent_manager import AgentManager\n",
"from evoagentx.benchmark import HotPotQA\n",
"from evoagentx.core.callbacks import suppress_logger_info\n",
"from evoagentx.core.logging import logger\n",
"from evoagentx.evaluators import Evaluator\n",
"from evoagentx.models import OpenAILLM, OpenAILLMConfig\n",
"from evoagentx.optimizers import TextGradOptimizer\n",
"from evoagentx.prompts import StringTemplate\n",
"from evoagentx.workflow import SequentialWorkFlowGraph\n",
"from dotenv import load_dotenv\n",
"\n",
"from evoagentx.agents.agent_manager import AgentManager\n",
"from evoagentx.benchmark import MBPP\n",
"from evoagentx.core.callbacks import suppress_logger_info\n",
"from evoagentx.core.logging import logger\n",
"from evoagentx.evaluators import Evaluator\n",
"from evoagentx.models import OpenAILLM, OpenAILLMConfig\n",
"from evoagentx.optimizers import TextGradOptimizer\n",
"from evoagentx.prompts import StringTemplate\n",
"from evoagentx.workflow import SequentialWorkFlowGraph\n",
"\n",
"from evoagentx.models import OpenAILLMConfig, OpenAILLM\n",
"from evoagentx.workflow import SEWWorkFlowGraph, STRUCTUREWorkFlowGraph\n",
"from evoagentx.agents import AgentManager\n",
"from evoagentx.benchmark import HumanEval,AFlowMBPP\n",
"from evoagentx.evaluators import Evaluator \n",
"from evoagentx.optimizers import SEWOptimizer, STRUCTUREOptimizer\n",
"from evoagentx.optimizers.structure_optimizer import STRUCTUREWorkFlowScheme\n",
"from evoagentx.core.callbacks import suppress_logger_info\n",
"\n",
"from evoagentx.models import OpenAILLMConfig, OpenAILLM,AzureOpenAIConfig,LiteLLMConfig,LiteLLM\n",
"from evoagentx.workflow import SEWWorkFlowGraph \n",
"from evoagentx.agents import AgentManager\n",
"from evoagentx.benchmark import MBPPPLUS, AFlowMBPPPLUS\n",
"from evoagentx.evaluators import Evaluator \n",
"from evoagentx.optimizers import SEWOptimizer \n",
"from evoagentx.core.callbacks import suppress_logger_info\n",
"from evoagentx.benchmark import HumanEvalPLUS\n",
"from evoagentx.benchmark import SciCode\n",
"from evoagentx.benchmark import PertQA\n",
"from copy import deepcopy\n",
"\n",
"import nest_asyncio\n",
"nest_asyncio.apply()\n",
"\n",
"class PertQASplits(PertQA):\n",
" def _load_data(self):\n",
" # load the original test data \n",
" super()._load_data(pertdata = 'adamson')\n",
" # split the data into train, dev and test\n",
" import numpy as np \n",
" np.random.seed(42)\n",
" permutation = np.random.permutation(len(self._dev_data))\n",
" full_test_data = self._dev_data \n",
" # randomly select 10 samples for train, 40 for dev, and 100 for test\n",
" self._train_data = [full_test_data[idx] for idx in permutation[:50]]\n",
" self._dev_data = [full_test_data[idx] for idx in permutation[:50]]\n",
" self._fulldata = full_test_data\n",
"\n",
"\n",
"def collate_func(example: dict) -> dict:\n",
" problem = \"Question: {}\\n\\nAnswer:\".format(example[\"question_new\"])\n",
" return {\"question\": problem}\n",
"\n",
"\n",
"api_key = \"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\"\n",
"# Function to encode the image\n",
"import os\n",
"os.environ[\"OPENAI_API_KEY\"] = api_key\n",
"OPENAI_API_KEY = os.getenv(\"OPENAI_API_KEY\")\n",
"\n",
"\n",
"llm_config = OpenAILLMConfig(model=\"gpt-4o-mini-2024-07-18\", openai_key=OPENAI_API_KEY, top_p=0.85, temperature=0.2, frequency_penalty=0.0, presence_penalty=0.0)\n",
"llm = OpenAILLM(config=llm_config)\n",
"# os.environ[\"AZURE_OPENAI_DEPLOYMENT_NAME\"] = \"gpt-4o-mini\"\n",
"# os.environ[\"AZURE_OPENAI_ENDPOINT\"] = \"https://tianyuliu-hua-raredisea-resource.cognitiveservices.azure.com/\"\n",
"# os.environ[\"AZURE_OPENAI_KEY\"] = \"2pa9h2ZIN1lQepFWwYADlXIKIansa9KPhxMoumeGbRQ08f2uDTXiJQQJ99BKACHYHv6XJ3w3AAAAACOGsQIt\"\n",
"# os.environ[\"AZURE_OPENAI_API_VERSION\"] = \"2025-01-01-preview\"\n",
"# llm_config = LiteLLMConfig(model=\"azure/\" + os.getenv(\"AZURE_OPENAI_DEPLOYMENT_NAME\"), # Azure model format\n",
"# azure_endpoint=os.getenv(\"AZURE_OPENAI_ENDPOINT\"),\n",
"# azure_key=os.getenv(\"AZURE_OPENAI_KEY\"),\n",
"# api_version=os.getenv(\"AZURE_OPENAI_API_VERSION\", \"2024-12-01-preview\"), top_p=0.85, temperature=0.2, frequency_penalty=0.0, presence_penalty=0.0)\n",
"\n",
"# executor_llm = LiteLLM(config=llm_config)\n",
"# optimizer_llm = LiteLLM(config=llm_config)\n",
"# llm = executor_llm"
]
},
{
"cell_type": "code",
"execution_count": 23,
"id": "d954f709",
"metadata": {},
"outputs": [],
"source": [
"# hotpotqa_graph_data = {\n",
"# \"goal\": \"Provide a direct answer to the question based on the context, without including explanations or reasoning.\",\n",
"# \"tasks\": [\n",
"# {\n",
"# \"name\": \"answer_generate\",\n",
"# \"description\": \"Generate a direct answer to the question based on the context.\",\n",
"# \"inputs\": [\n",
"# {\"name\": \"question\", \"type\": \"str\", \"required\": True, \"description\": \"The question to answer directly.\"}\n",
"# ],\n",
"# \"outputs\": [\n",
"# {\"name\": \"answer\", \"type\": \"str\", \"required\": True, \"description\": \"The direct answer to the question.\"}\n",
"# ],\n",
"# \"prompt_template\": StringTemplate(instruction=\"Think step by step to answer the question. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field. You answer could be only Yes or NO.\\nFormat your output in xml format, such as xxx and xxx.\"),\n",
"# \"parse_mode\": \"xml\"\n",
"# }\n",
"# ] \n",
"# }\n",
"\n",
"#generated_workflow\n",
"hotpotqa_graph_data = {\n",
" \"goal\": \"Provide a concise answer to the question using relevant context. The answer must be straightforward and avoid unnecessary explanations.\",\n",
" \"tasks\": [\n",
" {\n",
" \"name\": \"generate_answer\",\n",
" \"description\": \"Extract and formulate an answer from the given context.\",\n",
" \"inputs\": [\n",
" {\"name\": \"question\", \"type\": \"str\", \"required\": True, \"description\": \"The question that needs to be answered.\"},\n",
" ],\n",
" \"outputs\": [\n",
" {\"name\": \"answer\", \"type\": \"str\", \"required\": True, \"description\": \"The direct answer to the question.\"}\n",
" ],\n",
" \"prompt_template\": StringTemplate(instruction=\"Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.\"),\n",
" \"parse_mode\": \"xml\"\n",
" }\n",
" ]\n",
"}"
]
},
{
"cell_type": "code",
"execution_count": 24,
"id": "a3bcfc25",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:31:56.285\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.tools.storage_handler\u001b[0m:\u001b[36m_initialize_storage\u001b[0m:\u001b[36m133\u001b[0m - \u001b[1mLocal storage initialized with base path: .\u001b[0m\n"
]
}
],
"source": [
"from evoagentx.benchmark import HotPotQA\n",
"from evoagentx.tools import ArxivToolkit\n",
"import evoagentx.tools\n",
"wiki_toolkit = evoagentx.tools.WikipediaSearchToolkit(max_summary_sentences=5)\n",
"arxiv_toolkit = evoagentx.tools.ArxivToolkit()\n",
"search_toolkit = evoagentx.tools.DDGSSearchToolkit( num_search_pages=5,\n",
" max_content_words=300,\n",
" backend=\"auto\", # Options: \"auto\", \"duckduckgo\", \"google\", \"bing\", \"brave\", \"yahoo\"\n",
" region=\"us-en\" # Language and region settings\n",
" )"
]
},
{
"cell_type": "code",
"execution_count": 25,
"id": "a962ae1e",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:31:57.083\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.benchmark.pertqa\u001b[0m:\u001b[36m_load_data_from_file\u001b[0m:\u001b[36m52\u001b[0m - \u001b[1mloading HotPotQA data from /home/tl688/pitl688/selfevolve/EvoAgentX/examples/pertqa/adamson_train.json ...\u001b[0m\n",
"\u001b[32m2026-01-01 17:31:57.084\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.benchmark.pertqa\u001b[0m:\u001b[36m_load_data_from_file\u001b[0m:\u001b[36m52\u001b[0m - \u001b[1mloading HotPotQA data from /home/tl688/pitl688/selfevolve/EvoAgentX/examples/pertqa/adamson_train.json ...\u001b[0m\n",
"\u001b[32m2026-01-01 17:31:57.085\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.benchmark.pertqa\u001b[0m:\u001b[36m_load_data_from_file\u001b[0m:\u001b[36m52\u001b[0m - \u001b[1mloading HotPotQA data from /home/tl688/pitl688/selfevolve/EvoAgentX/examples/pertqa/adamson_test.json ...\u001b[0m\n"
]
}
],
"source": [
"# llm_config = OpenAILLMConfig(model=\"gpt-4.1-mini-2025-04-14\", openai_key=OPENAI_API_KEY, top_p=0.85, temperature=0.2, frequency_penalty=0.0, presence_penalty=0.0)\n",
"# llm = OpenAILLM(config=llm_config)\n",
"\n",
"# obtain SEW workflow \n",
"# sew_graph = SEWWorkFlowGraph.from_dict(hotpotqa_graph_data)\n",
"# agent_manager = AgentManager()\n",
"# agent_manager.add_agents_from_workflow(sew_graph, executor_llm.config)\n",
"# obtain SEW workflow \n",
"# sew_graph = QASTRUCTUREWorkFlowGraph.from_dict(hotpotqa_graph_data)\n",
"benchmark = PertQA()\n",
"sew_graph = SequentialWorkFlowGraph.from_dict(hotpotqa_graph_data)\n",
"agent_manager = AgentManager(tools=[search_toolkit,wiki_toolkit,arxiv_toolkit])\n",
"agent_manager.add_agents_from_workflow(sew_graph, llm_config=llm_config)\n",
"evaluator = Evaluator(llm=llm, agent_manager=agent_manager, collate_func=collate_func, num_workers=20, verbose=True)"
]
},
{
"cell_type": "code",
"execution_count": 26,
"id": "656b3c46",
"metadata": {},
"outputs": [],
"source": [
"from evoagentx.optimizers import QASTRUCTUREOptimizer, TextGradOptimizer"
]
},
{
"cell_type": "code",
"execution_count": 27,
"id": "4318bce0",
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"# graph = QASTRUCTUREOptimizer.load_module(\"./debug/save_10_noreason.json\")\n",
"# SequentialWorkFlowGraph.from_dict(graph['graph'])"
]
},
{
"cell_type": "code",
"execution_count": 28,
"id": "eaea09d1",
"metadata": {},
"outputs": [],
"source": [
"# graph"
]
},
{
"cell_type": "code",
"execution_count": 29,
"id": "227fc475",
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"evaluator = Evaluator(llm=llm, agent_manager=agent_manager, collate_func=collate_func, num_workers=20, verbose=True)\n",
"# obtain SEWOptimizer after having more roles\n",
"optimizer = QASTRUCTUREOptimizer(\n",
" graph=sew_graph, \n",
" evaluator=evaluator, \n",
" llm=llm, \n",
" max_steps=30,\n",
" eval_rounds=1, \n",
" repr_scheme=\"python\", \n",
" optimize_mode=\"all\", \n",
" order=\"zero-order\",\n",
" max_rounds=1\n",
")\n",
"optimizer.calltime = 1\n",
"optimizer.collate_func = collate_func\n",
"\n",
"benchmark.error_list = {}\n",
"benchmark.timeout = 900\n",
"benchmark.dataname = 'pubmedxqa'"
]
},
{
"cell_type": "code",
"execution_count": 30,
"id": "019bb9e5",
"metadata": {
"scrolled": true
},
"outputs": [],
"source": [
"# optimizer.evaluator.dataname = 'hotpotqa'\n",
"# with suppress_logger_info():\n",
"# metrics = optimizer.evaluate(dataset=benchmark, eval_mode=\"test\")\n",
"# print(\"Evaluation metrics: \", metrics)"
]
},
{
"cell_type": "code",
"execution_count": 31,
"id": "3984171e",
"metadata": {},
"outputs": [],
"source": [
"# metrics\n",
"# # metrics"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "7767f030",
"metadata": {
"scrolled": true
},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 32,
"id": "c0648c81",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:32:07.755\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1011\u001b[0m - \u001b[1mOptimizing the SequentialWorkFlowGraph workflow with python representation.\u001b[0m\n",
"\u001b[32m2026-01-01 17:32:07.756\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1015\u001b[0m - \u001b[1mRun initial evaluation on the original workflow ...\u001b[0m\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Evaluating workflow: 1%|▏ | 1/80 [00:03<04:18, 3.27s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
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"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 2%|▎ | 2/80 [00:05<03:12, 2.47s/it]"
]
},
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"name": "stdout",
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
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]
},
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
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]
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]
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]
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]
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]
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:33:34.371\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1019\u001b[0m - \u001b[1mInitial metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.9125}\u001b[0m\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:33:37.530\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.760 | Total tokens: 13251421 | Current cost: $0.001 | Current tokens: 7985\u001b[0m\n",
"- The workflow lacks validation steps to ensure that the generated answers are consistent with the predictions and solutions, leading to potential discrepancies.\n",
"- There are multiple instances where the predictions and solutions are inconsistent, particularly with the questions regarding perturbations of MRGBP, SOCS1, DDIT3, and HSD17B12, indicating a failure in the computational logic or data interpretation.\n",
"- The workflow does not account for the context of each perturbation adequately, which may lead to incorrect assumptions about the significance of expression changes.\n",
"- The structure of the workflow is overly simplistic, relying solely on a single step to generate answers without considering the need for intermediate evaluations or checks.\n",
"- The repeated use of the same question format without variation may lead to ambiguity in understanding the specific context of each perturbation, potentially affecting the quality of the answers.\n",
"\u001b[32m2026-01-01 17:33:38.969\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.760 | Total tokens: 13252075 | Current cost: $0.000 | Current tokens: 654\u001b[0m\n",
"```python\n",
"steps = [\n",
" {'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
" {'name': 'validate_answer', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
" {'name': 'contextualize_answer', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, HSD17B12 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, IER3IP1 is perturbed and CLCA1 expression is measured. Determine whether CLCA1 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of TELO2, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, P4HB is perturbed and RHCE expression is measured. Determine whether RHCE exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DNAJC19 is perturbed and PHGDH expression is quantified. Does this perturbation result in a significant change in PHGDH expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: No\n",
"Solutions: Yes\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SLC35B1 and examine the expression of RHCE. Does perturbing SLC35B1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SYVN1 is perturbed and YTHDF2 expression is quantified. Does this perturbation result in a significant change in YTHDF2 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TMED2 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SCYL1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SEC63 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SRP72 and examine the expression of RPS27. Does perturbing SRP72 lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb HYOU1 and examine the expression of SNHG12. Does perturbing HYOU1 lead to a significant change in SNHG12 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, HSD17B12 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: No\n",
"Solutions: Yes\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': None, 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:33:41.840\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.761 | Total tokens: 13260089 | Current cost: $0.001 | Current tokens: 8014\u001b[0m\n",
"\u001b[32m2026-01-01 17:33:43.626\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.761 | Total tokens: 13260207 | Current cost: $0.000 | Current tokens: 118\u001b[0m\n",
"\u001b[32m2026-01-01 17:33:45.145\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.761 | Total tokens: 13260724 | Current cost: $0.000 | Current tokens: 517\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': 'Your are a task solver.', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:33:47.685\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.762 | Total tokens: 13268765 | Current cost: $0.001 | Current tokens: 8041\u001b[0m\n",
"\u001b[32m2026-01-01 17:33:48.701\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.762 | Total tokens: 13268869 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-01 17:33:50.117\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.763 | Total tokens: 13269431 | Current cost: $0.000 | Current tokens: 562\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': 'Your are a task solver.', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:33:52.565\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.764 | Total tokens: 13277480 | Current cost: $0.001 | Current tokens: 8049\u001b[0m\n",
"\u001b[32m2026-01-01 17:33:53.392\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.764 | Total tokens: 13277576 | Current cost: $0.000 | Current tokens: 96\u001b[0m\n",
"\u001b[32m2026-01-01 17:33:55.044\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.764 | Total tokens: 13278136 | Current cost: $0.000 | Current tokens: 560\u001b[0m\n",
"\u001b[32m2026-01-01 17:33:55.044\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 1 ...\u001b[0m\n"
]
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:35:13.898\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 1 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.9375}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
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"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:35:16.903\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.773 | Total tokens: 13335252 | Current cost: $0.001 | Current tokens: 8018\u001b[0m\n",
"- The workflow lacks a validation step after generating the answer, which could lead to incorrect outputs being used in subsequent steps.\n",
"- There is no explicit handling of cases where the answer may not fit the expected format ('Final Answer: Yes' or 'Final Answer: No'), which could result in ambiguous or incorrect responses.\n",
"- The control flow does not account for potential errors in the validation step, leading to unhandled cases if the answer is not validated correctly.\n",
"- The workflow assumes that all generated answers will be valid without any checks for logical consistency or relevance to the question, which may lead to misleading conclusions.\n",
"- The execution history shows multiple instances where the predictions and solutions diverge, indicating a lack of robustness in the answer generation process.\n",
"\u001b[32m2026-01-01 17:35:18.443\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.773 | Total tokens: 13335940 | Current cost: $0.000 | Current tokens: 688\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, HSD17B12 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, IER3IP1 is perturbed and CLCA1 expression is measured. Determine whether CLCA1 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of TELO2, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, P4HB is perturbed and RHCE expression is measured. Determine whether RHCE exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DNAJC19 is perturbed and PHGDH expression is quantified. Does this perturbation result in a significant change in PHGDH expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SLC35B1 and examine the expression of RHCE. Does perturbing SLC35B1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SYVN1 is perturbed and YTHDF2 expression is quantified. Does this perturbation result in a significant change in YTHDF2 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TMED2 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SCYL1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SEC63 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SRP72 and examine the expression of RPS27. Does perturbing SRP72 lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb HYOU1 and examine the expression of SNHG12. Does perturbing HYOU1 lead to a significant change in SNHG12 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, HSD17B12 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from {question} to determine the best answer. Ensure that the answer is validated for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:35:21.622\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.774 | Total tokens: 13343939 | Current cost: $0.001 | Current tokens: 7999\u001b[0m\n",
"\u001b[32m2026-01-01 17:35:23.058\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.775 | Total tokens: 13344035 | Current cost: $0.000 | Current tokens: 96\u001b[0m\n",
"\u001b[32m2026-01-01 17:35:24.410\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.775 | Total tokens: 13344593 | Current cost: $0.000 | Current tokens: 558\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy. If the answer is uncertain or ambiguous, clearly state that. After validation, generate a straightforward answer that directly addresses {question}. Format your output in XML, using to explain your reasoning and for the final response.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:35:27.532\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.776 | Total tokens: 13352662 | Current cost: $0.001 | Current tokens: 8069\u001b[0m\n",
"\u001b[32m2026-01-01 17:35:29.145\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.776 | Total tokens: 13352770 | Current cost: $0.000 | Current tokens: 108\u001b[0m\n",
"\u001b[32m2026-01-01 17:35:31.107\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.776 | Total tokens: 13353488 | Current cost: $0.000 | Current tokens: 718\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first validate the answer against the context of the question. Ensure that the answer is correct before integrating any additional context. In your thought process, consider how the context relates to the answer and clarify any assumptions made. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:35:34.398\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.777 | Total tokens: 13361565 | Current cost: $0.001 | Current tokens: 8077\u001b[0m\n",
"\u001b[32m2026-01-01 17:35:35.915\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.777 | Total tokens: 13361669 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-01 17:35:38.217\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.778 | Total tokens: 13362403 | Current cost: $0.000 | Current tokens: 734\u001b[0m\n",
"\u001b[32m2026-01-01 17:35:38.217\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 2 ...\u001b[0m\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:36:23.830\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 2 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.96}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
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"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:36:27.176\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.784 | Total tokens: 13401100 | Current cost: $0.001 | Current tokens: 8021\u001b[0m\n",
"- The workflow lacks a validation step after generating the answer, which could lead to incorrect conclusions being drawn without verification.\n",
"- There is no explicit handling of cases where the answer might be ambiguous or where data may not support a clear 'Yes' or 'No' response.\n",
"- The workflow assumes that all questions can be answered with a binary response without considering the complexity of biological data, which may not always fit this model.\n",
"- The repeated occurrence of incorrect predictions and solutions indicates a potential flaw in the underlying model or data processing, suggesting that the model may not be adequately trained for all scenarios presented.\n",
"- The control flow does not account for the possibility of conflicting results from different questions, which could lead to inconsistencies in the overall assessment of the data.\n",
"\u001b[32m2026-01-01 17:36:28.814\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.784 | Total tokens: 13401791 | Current cost: $0.000 | Current tokens: 691\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of TELO2, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, HSD17B12 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SCYL1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, P4HB is perturbed and RHCE expression is measured. Determine whether RHCE exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SEC63 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, indicate this clearly. Ensure that the answer is validated for accuracy before proceeding to the next step. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:36:31.136\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.785 | Total tokens: 13406950 | Current cost: $0.001 | Current tokens: 5159\u001b[0m\n",
"\u001b[32m2026-01-01 17:36:32.419\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.785 | Total tokens: 13407076 | Current cost: $0.000 | Current tokens: 126\u001b[0m\n",
"\u001b[32m2026-01-01 17:36:33.852\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.785 | Total tokens: 13407714 | Current cost: $0.000 | Current tokens: 638\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that. After validation, generate a straightforward answer that directly addresses {question}, considering any nuances in the data. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer reflects significant expression changes accurately and is free from oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:36:36.251\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.786 | Total tokens: 13412923 | Current cost: $0.001 | Current tokens: 5209\u001b[0m\n",
"\u001b[32m2026-01-01 17:36:37.367\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.786 | Total tokens: 13413027 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-01 17:36:38.973\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.786 | Total tokens: 13413817 | Current cost: $0.000 | Current tokens: 790\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. In your thought process, consider how the context relates to the answer and clarify any assumptions made. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:36:41.866\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.787 | Total tokens: 13419067 | Current cost: $0.001 | Current tokens: 5250\u001b[0m\n",
"\u001b[32m2026-01-01 17:36:43.377\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.787 | Total tokens: 13419172 | Current cost: $0.000 | Current tokens: 105\u001b[0m\n",
"\u001b[32m2026-01-01 17:36:45.185\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.787 | Total tokens: 13420052 | Current cost: $0.000 | Current tokens: 880\u001b[0m\n",
"\u001b[32m2026-01-01 17:36:45.185\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 3 ...\u001b[0m\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:37:33.015\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 3 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.98}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:37:36.282\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.793 | Total tokens: 13458750 | Current cost: $0.001 | Current tokens: 8018\u001b[0m\n",
"- The workflow lacks a validation step after generating the answer, which could lead to incorrect outputs being used in subsequent steps.\n",
"- There is no error handling or fallback mechanism in the workflow to address cases where the validation fails or the answer is ambiguous.\n",
"- The workflow assumes that all questions can be answered with a binary response ('Yes' or 'No') without considering the complexity or nuances of the data being analyzed.\n",
"- The execution history shows multiple instances where the solution is marked as incorrect, indicating potential flaws in the answer generation or validation processes that are not accounted for in the workflow.\n",
"- The prompts and intermediate steps do not provide sufficient context or criteria for determining what constitutes a \"significant change,\" leading to potential ambiguity in the answers.\n",
"\u001b[32m2026-01-01 17:37:37.536\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.793 | Total tokens: 13459438 | Current cost: $0.000 | Current tokens: 688\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DNAJC19 is perturbed and PHGDH expression is quantified. Does this perturbation result in a significant change in PHGDH expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of TELO2, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SEC63 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, IER3IP1 is perturbed and CLCA1 expression is measured. Determine whether CLCA1 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TMED2 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb HYOU1 and examine the expression of SNHG12. Does perturbing HYOU1 lead to a significant change in SNHG12 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SCYL1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:37:40.994\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.794 | Total tokens: 13464613 | Current cost: $0.001 | Current tokens: 5175\u001b[0m\n",
"\u001b[32m2026-01-01 17:37:42.034\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.794 | Total tokens: 13464718 | Current cost: $0.000 | Current tokens: 105\u001b[0m\n",
"\u001b[32m2026-01-01 17:37:43.084\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.794 | Total tokens: 13465404 | Current cost: $0.000 | Current tokens: 686\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:37:46.637\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.795 | Total tokens: 13470622 | Current cost: $0.001 | Current tokens: 5218\u001b[0m\n",
"\u001b[32m2026-01-01 17:37:48.165\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.795 | Total tokens: 13470726 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-01 17:37:49.935\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.795 | Total tokens: 13471645 | Current cost: $0.000 | Current tokens: 919\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:37:52.694\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.796 | Total tokens: 13476869 | Current cost: $0.001 | Current tokens: 5224\u001b[0m\n",
"\u001b[32m2026-01-01 17:37:53.590\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.796 | Total tokens: 13476965 | Current cost: $0.000 | Current tokens: 96\u001b[0m\n",
"\u001b[32m2026-01-01 17:37:55.195\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.797 | Total tokens: 13477921 | Current cost: $0.000 | Current tokens: 956\u001b[0m\n",
"\u001b[32m2026-01-01 17:37:55.195\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 4 ...\u001b[0m\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:38:41.120\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 4 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.92}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
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"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:38:44.435\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.803 | Total tokens: 13516639 | Current cost: $0.001 | Current tokens: 8012\u001b[0m\n",
"- The workflow lacks a validation step after generating the answer, which could lead to incorrect outputs being used in subsequent steps.\n",
"- There is no explicit handling of cases where the answer might be ambiguous or not strictly 'Yes' or 'No', potentially leading to misinterpretation of results.\n",
"- The workflow assumes that all questions can be answered with a binary response without considering the complexity of biological data, which may not always fit this model.\n",
"- The execution history shows multiple instances where the predicted answers were incorrect, indicating a potential flaw in the answer generation process or the underlying data interpretation.\n",
"- The workflow does not include any mechanism for addressing or correcting errors in predictions, leading to repeated inaccuracies in the final answers.\n",
"\u001b[32m2026-01-01 17:38:45.873\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.803 | Total tokens: 13517321 | Current cost: $0.000 | Current tokens: 682\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, HSD17B12 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of TELO2, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SLC35B1 and examine the expression of RHCE. Does perturbing SLC35B1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SRP72 and examine the expression of RPS27. Does perturbing SRP72 lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TMED2 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb HYOU1 and examine the expression of SNHG12. Does perturbing HYOU1 lead to a significant change in SNHG12 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SEC63 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DNAJC19 is perturbed and PHGDH expression is quantified. Does this perturbation result in a significant change in PHGDH expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, P4HB is perturbed and RHCE expression is measured. Determine whether RHCE exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:38:48.919\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.804 | Total tokens: 13522532 | Current cost: $0.001 | Current tokens: 5211\u001b[0m\n",
"\u001b[32m2026-01-01 17:38:50.383\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.804 | Total tokens: 13522651 | Current cost: $0.000 | Current tokens: 119\u001b[0m\n",
"\u001b[32m2026-01-01 17:38:51.275\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.804 | Total tokens: 13523402 | Current cost: $0.000 | Current tokens: 751\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:38:54.216\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.805 | Total tokens: 13528675 | Current cost: $0.001 | Current tokens: 5273\u001b[0m\n",
"\u001b[32m2026-01-01 17:38:55.888\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.805 | Total tokens: 13528783 | Current cost: $0.000 | Current tokens: 108\u001b[0m\n",
"\u001b[32m2026-01-01 17:38:57.879\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.805 | Total tokens: 13529836 | Current cost: $0.000 | Current tokens: 1053\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:39:00.750\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.806 | Total tokens: 13535101 | Current cost: $0.001 | Current tokens: 5265\u001b[0m\n",
"\u001b[32m2026-01-01 17:39:02.117\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.806 | Total tokens: 13535196 | Current cost: $0.000 | Current tokens: 95\u001b[0m\n",
"\u001b[32m2026-01-01 17:39:04.381\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.806 | Total tokens: 13536269 | Current cost: $0.000 | Current tokens: 1073\u001b[0m\n",
"\u001b[32m2026-01-01 17:39:04.381\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 5 ...\u001b[0m\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:39:49.122\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 5 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.98}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
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"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:39:52.288\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.812 | Total tokens: 13574984 | Current cost: $0.001 | Current tokens: 8007\u001b[0m\n",
"- The workflow lacks a validation step to ensure that the generated answer aligns with the specific format required ('Final Answer: Yes' or 'Final Answer: No'), leading to potential inconsistencies in output.\n",
"- There are multiple instances of incorrect computation results, as indicated by the execution history, suggesting that the validation step does not adequately catch errors in the answer generation process.\n",
"- The workflow does not account for the possibility of ambiguous or misleading questions, which could lead to incorrect answers being generated without proper context or clarification.\n",
"- The ordering of steps does not allow for iterative refinement; if an answer is incorrect, there is no mechanism to revisit the question or the generated answer before finalization.\n",
"\u001b[32m2026-01-01 17:39:54.231\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.812 | Total tokens: 13575661 | Current cost: $0.000 | Current tokens: 677\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of TELO2, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb HYOU1 and examine the expression of SNHG12. Does perturbing HYOU1 lead to a significant change in SNHG12 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TMED2 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SYVN1 is perturbed and YTHDF2 expression is quantified. Does this perturbation result in a significant change in YTHDF2 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DNAJC19 is perturbed and PHGDH expression is quantified. Does this perturbation result in a significant change in PHGDH expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SLC35B1 and examine the expression of RHCE. Does perturbing SLC35B1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, HSD17B12 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SCYL1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, P4HB is perturbed and RHCE expression is measured. Determine whether RHCE exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:39:57.332\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.813 | Total tokens: 13580861 | Current cost: $0.001 | Current tokens: 5200\u001b[0m\n",
"\u001b[32m2026-01-01 17:39:58.882\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.813 | Total tokens: 13580952 | Current cost: $0.000 | Current tokens: 91\u001b[0m\n",
"\u001b[32m2026-01-01 17:40:00.203\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.813 | Total tokens: 13581740 | Current cost: $0.000 | Current tokens: 788\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:40:02.474\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.814 | Total tokens: 13586971 | Current cost: $0.001 | Current tokens: 5231\u001b[0m\n",
"\u001b[32m2026-01-01 17:40:03.657\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.814 | Total tokens: 13587075 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-01 17:40:05.494\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.815 | Total tokens: 13588208 | Current cost: $0.000 | Current tokens: 1133\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:40:08.211\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.815 | Total tokens: 13593456 | Current cost: $0.001 | Current tokens: 5248\u001b[0m\n",
"\u001b[32m2026-01-01 17:40:09.733\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.815 | Total tokens: 13593560 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-01 17:40:11.502\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.816 | Total tokens: 13594748 | Current cost: $0.000 | Current tokens: 1188\u001b[0m\n",
"\u001b[32m2026-01-01 17:40:11.503\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 6 ...\u001b[0m\n"
]
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 88%|████████▊ | 44/50 [00:41<00:05, 1.01it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 90%|█████████ | 45/50 [00:42<00:04, 1.01it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 92%|█████████▏| 46/50 [00:43<00:04, 1.04s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 94%|█████████▍| 47/50 [00:44<00:03, 1.07s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 96%|█████████▌| 48/50 [00:45<00:02, 1.06s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 98%|█████████▊| 49/50 [00:46<00:01, 1.00s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Evaluating workflow: 100%|██████████| 50/50 [00:47<00:00, 1.06it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:40:58.619\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 6 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.92}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:41:01.748\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.822 | Total tokens: 13633407 | Current cost: $0.001 | Current tokens: 8002\u001b[0m\n",
"- The workflow lacks a validation step after generating the answer, which could lead to incorrect outputs being accepted without verification.\n",
"- There is an inconsistency in the execution history where multiple questions resulted in incorrect solutions despite the predictions being correct, indicating potential flaws in the answer generation or validation processes.\n",
"- The prompts for questions are overly repetitive and do not provide sufficient context or variation, which may lead to ambiguity in interpretation.\n",
"- The workflow does not account for potential edge cases or exceptions in the data, which could result in misleading conclusions.\n",
"- The control flow does not include mechanisms for handling errors or discrepancies in the predictions versus solutions, leading to unaddressed inaccuracies.\n",
"\u001b[32m2026-01-01 17:41:03.220\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.822 | Total tokens: 13634079 | Current cost: $0.000 | Current tokens: 672\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TMED2 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SYVN1 is perturbed and YTHDF2 expression is quantified. Does this perturbation result in a significant change in YTHDF2 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SCYL1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DNAJC19 is perturbed and PHGDH expression is quantified. Does this perturbation result in a significant change in PHGDH expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, IER3IP1 is perturbed and CLCA1 expression is measured. Determine whether CLCA1 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SRP72 and examine the expression of RPS27. Does perturbing SRP72 lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:41:06.369\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.823 | Total tokens: 13639244 | Current cost: $0.001 | Current tokens: 5165\u001b[0m\n",
"\u001b[32m2026-01-01 17:41:08.105\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.823 | Total tokens: 13639339 | Current cost: $0.000 | Current tokens: 95\u001b[0m\n",
"\u001b[32m2026-01-01 17:41:09.526\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.823 | Total tokens: 13640202 | Current cost: $0.000 | Current tokens: 863\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:41:12.702\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.824 | Total tokens: 13645419 | Current cost: $0.001 | Current tokens: 5217\u001b[0m\n",
"\u001b[32m2026-01-01 17:41:14.391\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.824 | Total tokens: 13645513 | Current cost: $0.000 | Current tokens: 94\u001b[0m\n",
"\u001b[32m2026-01-01 17:41:17.397\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.824 | Total tokens: 13646778 | Current cost: $0.000 | Current tokens: 1265\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:41:20.396\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.825 | Total tokens: 13652005 | Current cost: $0.001 | Current tokens: 5227\u001b[0m\n",
"\u001b[32m2026-01-01 17:41:22.055\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.825 | Total tokens: 13652109 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-01 17:41:24.939\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.825 | Total tokens: 13653443 | Current cost: $0.000 | Current tokens: 1334\u001b[0m\n",
"\u001b[32m2026-01-01 17:41:24.939\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 7 ...\u001b[0m\n"
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},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 92%|█████████▏| 46/50 [00:46<00:03, 1.11it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 94%|█████████▍| 47/50 [00:48<00:03, 1.04s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 96%|█████████▌| 48/50 [00:49<00:01, 1.03it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 98%|█████████▊| 49/50 [00:50<00:01, 1.07s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Evaluating workflow: 100%|██████████| 50/50 [00:51<00:00, 1.03s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:42:16.332\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 7 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.96}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:42:20.781\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.832 | Total tokens: 13692105 | Current cost: $0.001 | Current tokens: 7979\u001b[0m\n",
"- The workflow lacks a validation step after generating the answer, which could lead to incorrect outputs being used in subsequent steps.\n",
"- There is no explicit handling of cases where the answer might be ambiguous or unsupported by the data, potentially leading to misleading conclusions.\n",
"- The control flow does not account for scenarios where the validation of the answer fails, resulting in a lack of error handling or alternative pathways.\n",
"- The prompts and intermediate steps do not specify the criteria for determining \"significant change,\" which could lead to inconsistencies in interpretation across different questions.\n",
"\u001b[32m2026-01-01 17:42:22.100\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.832 | Total tokens: 13692754 | Current cost: $0.000 | Current tokens: 649\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TMED2 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, HSD17B12 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SRP72 and examine the expression of RPS27. Does perturbing SRP72 lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SEC63 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SCYL1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, IER3IP1 is perturbed and CLCA1 expression is measured. Determine whether CLCA1 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, P4HB is perturbed and RHCE expression is measured. Determine whether RHCE exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SYVN1 is perturbed and YTHDF2 expression is quantified. Does this perturbation result in a significant change in YTHDF2 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:42:24.794\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.832 | Total tokens: 13697938 | Current cost: $0.001 | Current tokens: 5184\u001b[0m\n",
"\u001b[32m2026-01-01 17:42:25.806\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.833 | Total tokens: 13698032 | Current cost: $0.000 | Current tokens: 94\u001b[0m\n",
"\u001b[32m2026-01-01 17:42:27.143\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.833 | Total tokens: 13698962 | Current cost: $0.000 | Current tokens: 930\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:42:29.708\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.834 | Total tokens: 13704184 | Current cost: $0.001 | Current tokens: 5222\u001b[0m\n",
"\u001b[32m2026-01-01 17:42:30.691\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.834 | Total tokens: 13704288 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-01 17:42:32.743\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.834 | Total tokens: 13705665 | Current cost: $0.000 | Current tokens: 1377\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:42:34.921\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.835 | Total tokens: 13710879 | Current cost: $0.001 | Current tokens: 5214\u001b[0m\n",
"\u001b[32m2026-01-01 17:42:36.462\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.835 | Total tokens: 13710984 | Current cost: $0.000 | Current tokens: 105\u001b[0m\n",
"\u001b[32m2026-01-01 17:42:39.321\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.835 | Total tokens: 13712420 | Current cost: $0.000 | Current tokens: 1436\u001b[0m\n",
"\u001b[32m2026-01-01 17:42:39.321\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 8 ...\u001b[0m\n"
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"text": [
"\r",
"Evaluating workflow: 92%|█████████▏| 46/50 [00:41<00:03, 1.15it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 94%|█████████▍| 47/50 [00:42<00:02, 1.19it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 96%|█████████▌| 48/50 [00:43<00:01, 1.22it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 98%|█████████▊| 49/50 [00:43<00:00, 1.23it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Evaluating workflow: 100%|██████████| 50/50 [00:44<00:00, 1.12it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:43:23.976\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 8 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.92}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:43:27.913\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.841 | Total tokens: 13751136 | Current cost: $0.001 | Current tokens: 8030\u001b[0m\n",
"- The workflow lacks a validation step after generating the answer, which could lead to incorrect outputs being used in subsequent steps.\n",
"- There is no error handling or fallback mechanism in case the validation fails or the answer is deemed invalid.\n",
"- The workflow assumes that all questions can be answered with a simple 'Yes' or 'No' without considering the complexity or variability of the underlying data.\n",
"- The execution history shows multiple instances where the predicted answers were incorrect, indicating potential flaws in the answer generation process or the underlying data analysis.\n",
"- The workflow does not specify how the answer is generated from the question, which could lead to ambiguity in understanding the basis for the answer provided.\n",
"- There is a lack of clarity on how the validation process determines the correctness of the answer, which could result in misleading outputs.\n",
"\u001b[32m2026-01-01 17:43:30.647\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.841 | Total tokens: 13751836 | Current cost: $0.000 | Current tokens: 700\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of TELO2, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SCYL1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb HYOU1 and examine the expression of SNHG12. Does perturbing HYOU1 lead to a significant change in SNHG12 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SYVN1 is perturbed and YTHDF2 expression is quantified. Does this perturbation result in a significant change in YTHDF2 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, HSD17B12 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SRP72 and examine the expression of RPS27. Does perturbing SRP72 lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, P4HB is perturbed and RHCE expression is measured. Determine whether RHCE exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:43:33.271\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.842 | Total tokens: 13757032 | Current cost: $0.001 | Current tokens: 5196\u001b[0m\n",
"\u001b[32m2026-01-01 17:43:34.782\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.842 | Total tokens: 13757129 | Current cost: $0.000 | Current tokens: 97\u001b[0m\n",
"\u001b[32m2026-01-01 17:43:35.927\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.842 | Total tokens: 13758116 | Current cost: $0.000 | Current tokens: 987\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:43:39.035\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.843 | Total tokens: 13763356 | Current cost: $0.001 | Current tokens: 5240\u001b[0m\n",
"\u001b[32m2026-01-01 17:43:40.575\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.843 | Total tokens: 13763448 | Current cost: $0.000 | Current tokens: 92\u001b[0m\n",
"\u001b[32m2026-01-01 17:43:42.210\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.844 | Total tokens: 13764936 | Current cost: $0.000 | Current tokens: 1488\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:43:44.884\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.844 | Total tokens: 13770185 | Current cost: $0.001 | Current tokens: 5249\u001b[0m\n",
"\u001b[32m2026-01-01 17:43:46.264\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.844 | Total tokens: 13770279 | Current cost: $0.000 | Current tokens: 94\u001b[0m\n",
"\u001b[32m2026-01-01 17:43:48.353\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.845 | Total tokens: 13771855 | Current cost: $0.000 | Current tokens: 1576\u001b[0m\n",
"\u001b[32m2026-01-01 17:43:48.353\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 9 ...\u001b[0m\n"
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"text": [
"\r",
"Evaluating workflow: 92%|█████████▏| 46/50 [00:43<00:03, 1.13it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 94%|█████████▍| 47/50 [00:43<00:02, 1.22it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 96%|█████████▌| 48/50 [00:44<00:01, 1.22it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 98%|█████████▊| 49/50 [00:45<00:00, 1.27it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Evaluating workflow: 100%|██████████| 50/50 [00:46<00:00, 1.08it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:44:34.678\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 9 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.94}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:44:37.975\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.851 | Total tokens: 13810525 | Current cost: $0.001 | Current tokens: 8025\u001b[0m\n",
"- The workflow lacks a validation step that checks for consistency between the predicted answer and the actual solution, leading to potential discrepancies in the final output.\n",
"- There are multiple instances of incorrect computation results that resulted in a score of 0.0, indicating a failure in the workflow to handle certain perturbation scenarios effectively.\n",
"- The workflow does not include a mechanism to address or log errors encountered during the execution, which could help in understanding the reasons behind incorrect predictions.\n",
"- The workflow assumes that all questions can be answered with a binary response without considering the complexity or nuances of the biological context, which may lead to oversimplification of the answers.\n",
"- The ordering of steps could be improved; validation should ideally occur before contextualization to ensure that only validated answers are further processed.\n",
"\u001b[32m2026-01-01 17:44:39.235\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.851 | Total tokens: 13811220 | Current cost: $0.000 | Current tokens: 695\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TMED2 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SRP72 and examine the expression of RPS27. Does perturbing SRP72 lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, HSD17B12 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DNAJC19 is perturbed and PHGDH expression is quantified. Does this perturbation result in a significant change in PHGDH expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of TELO2, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:44:42.137\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.852 | Total tokens: 13816369 | Current cost: $0.001 | Current tokens: 5149\u001b[0m\n",
"\u001b[32m2026-01-01 17:44:43.050\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.852 | Total tokens: 13816468 | Current cost: $0.000 | Current tokens: 99\u001b[0m\n",
"\u001b[32m2026-01-01 17:44:44.249\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.852 | Total tokens: 13817511 | Current cost: $0.000 | Current tokens: 1043\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:44:46.602\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.853 | Total tokens: 13822698 | Current cost: $0.001 | Current tokens: 5187\u001b[0m\n",
"\u001b[32m2026-01-01 17:44:47.499\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.853 | Total tokens: 13822801 | Current cost: $0.000 | Current tokens: 103\u001b[0m\n",
"\u001b[32m2026-01-01 17:44:49.622\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.853 | Total tokens: 13824408 | Current cost: $0.000 | Current tokens: 1607\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:44:53.013\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.854 | Total tokens: 13829602 | Current cost: $0.001 | Current tokens: 5194\u001b[0m\n",
"\u001b[32m2026-01-01 17:44:54.008\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.854 | Total tokens: 13829698 | Current cost: $0.000 | Current tokens: 96\u001b[0m\n",
"\u001b[32m2026-01-01 17:44:55.999\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.854 | Total tokens: 13831399 | Current cost: $0.000 | Current tokens: 1701\u001b[0m\n",
"\u001b[32m2026-01-01 17:44:56.000\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 10 ...\u001b[0m\n"
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"text": [
"\r",
"Evaluating workflow: 92%|█████████▏| 46/50 [00:44<00:03, 1.02it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 94%|█████████▍| 47/50 [00:45<00:02, 1.08it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 96%|█████████▌| 48/50 [00:46<00:01, 1.03it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 98%|█████████▊| 49/50 [00:48<00:01, 1.14s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Evaluating workflow: 100%|██████████| 50/50 [00:48<00:00, 1.03it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:45:44.755\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 10 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.9}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:45:48.810\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.861 | Total tokens: 13870104 | Current cost: $0.001 | Current tokens: 8025\u001b[0m\n",
"- The workflow lacks a validation step that checks for the consistency of the question and the expected answer format, which could lead to errors in interpretation.\n",
"- There are instances of incorrect computation results leading to discrepancies between predictions and solutions, indicating potential flaws in the answer generation or validation process.\n",
"- The workflow does not account for the possibility of ambiguous or poorly defined questions, which could result in misinterpretation of the required answer format.\n",
"- The control flow does not include a mechanism for handling cases where the answer is not strictly 'Yes' or 'No', which could lead to premature termination or incorrect outputs.\n",
"- The repeated occurrence of incorrect solutions suggests a systemic issue in the underlying model or data used for generating answers, indicating a need for more robust validation of the answers produced.\n",
"\u001b[32m2026-01-01 17:45:50.444\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.861 | Total tokens: 13870799 | Current cost: $0.000 | Current tokens: 695\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, P4HB is perturbed and RHCE expression is measured. Determine whether RHCE exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of TELO2, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SLC35B1 and examine the expression of RHCE. Does perturbing SLC35B1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DNAJC19 is perturbed and PHGDH expression is quantified. Does this perturbation result in a significant change in PHGDH expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: No\n",
"Solutions: Yes\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SYVN1 is perturbed and YTHDF2 expression is quantified. Does this perturbation result in a significant change in YTHDF2 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:45:53.881\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.862 | Total tokens: 13875994 | Current cost: $0.001 | Current tokens: 5195\u001b[0m\n",
"\u001b[32m2026-01-01 17:45:55.776\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.862 | Total tokens: 13876102 | Current cost: $0.000 | Current tokens: 108\u001b[0m\n",
"\u001b[32m2026-01-01 17:45:57.213\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.862 | Total tokens: 13877226 | Current cost: $0.000 | Current tokens: 1124\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:45:59.438\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.863 | Total tokens: 13882447 | Current cost: $0.001 | Current tokens: 5221\u001b[0m\n",
"\u001b[32m2026-01-01 17:46:00.526\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.863 | Total tokens: 13882542 | Current cost: $0.000 | Current tokens: 95\u001b[0m\n",
"\u001b[32m2026-01-01 17:46:02.606\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.863 | Total tokens: 13884248 | Current cost: $0.000 | Current tokens: 1706\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:46:06.008\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.864 | Total tokens: 13889519 | Current cost: $0.001 | Current tokens: 5271\u001b[0m\n",
"\u001b[32m2026-01-01 17:46:07.689\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.864 | Total tokens: 13889614 | Current cost: $0.000 | Current tokens: 95\u001b[0m\n",
"\u001b[32m2026-01-01 17:46:10.574\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.864 | Total tokens: 13891504 | Current cost: $0.000 | Current tokens: 1890\u001b[0m\n",
"\u001b[32m2026-01-01 17:46:10.574\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 11 ...\u001b[0m\n"
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"\r",
"Evaluating workflow: 92%|█████████▏| 46/50 [00:41<00:03, 1.17it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 94%|█████████▍| 47/50 [00:42<00:02, 1.18it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 96%|█████████▌| 48/50 [00:43<00:01, 1.15it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 98%|█████████▊| 49/50 [00:44<00:00, 1.18it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Evaluating workflow: 100%|██████████| 50/50 [00:45<00:00, 1.10it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:46:55.983\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 11 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.96}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:46:59.114\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.871 | Total tokens: 13930209 | Current cost: $0.001 | Current tokens: 8021\u001b[0m\n",
"- The workflow lacks a validation step for the initial question input, which could lead to processing incorrect or irrelevant questions.\n",
"- There is no error handling mechanism in place to address cases where the validation of the answer fails or where the answer generation step produces unexpected results.\n",
"- The workflow assumes that all questions will yield a binary response ('Yes' or 'No'), which may not account for ambiguous or unclear questions that require further clarification.\n",
"- The final answer is derived from a single validation step without cross-referencing or corroborating evidence from the execution history, which could lead to inconsistencies in the final output.\n",
"- The workflow does not include a mechanism to track or log the reasoning behind the answer generation, which could help in understanding discrepancies in predictions and solutions.\n",
"\u001b[32m2026-01-01 17:47:00.620\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.871 | Total tokens: 13930928 | Current cost: $0.000 | Current tokens: 719\u001b[0m\n",
"```python\n",
"steps = [\n",
" {'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
" {'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
" {'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']},\n",
" {'name': 'log_reasoning', 'args': ['question', 'validated_answer'], 'outputs': []}\n",
"]\n",
"```\n",
"Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, P4HB is perturbed and RHCE expression is measured. Determine whether RHCE exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of TELO2, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SLC35B1 and examine the expression of RHCE. Does perturbing SLC35B1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb HYOU1 and examine the expression of SNHG12. Does perturbing HYOU1 lead to a significant change in SNHG12 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, HSD17B12 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:47:03.106\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.872 | Total tokens: 13936139 | Current cost: $0.001 | Current tokens: 5211\u001b[0m\n",
"\u001b[32m2026-01-01 17:47:04.070\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.872 | Total tokens: 13936238 | Current cost: $0.000 | Current tokens: 99\u001b[0m\n",
"\u001b[32m2026-01-01 17:47:05.161\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.872 | Total tokens: 13937433 | Current cost: $0.000 | Current tokens: 1195\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:47:07.881\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.873 | Total tokens: 13942685 | Current cost: $0.001 | Current tokens: 5252\u001b[0m\n",
"\u001b[32m2026-01-01 17:47:09.599\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.873 | Total tokens: 13942780 | Current cost: $0.000 | Current tokens: 95\u001b[0m\n",
"\u001b[32m2026-01-01 17:47:12.681\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.873 | Total tokens: 13944641 | Current cost: $0.000 | Current tokens: 1861\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:47:14.826\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.874 | Total tokens: 13949893 | Current cost: $0.001 | Current tokens: 5252\u001b[0m\n",
"\u001b[32m2026-01-01 17:47:16.105\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.874 | Total tokens: 13950016 | Current cost: $0.000 | Current tokens: 123\u001b[0m\n",
"\u001b[32m2026-01-01 17:47:19.079\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.874 | Total tokens: 13952056 | Current cost: $0.000 | Current tokens: 2040\u001b[0m\n",
"{'name': 'log_reasoning483', 'description': 'Task to log_reasoning483. Takes question, validated_answer as input. ', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'Input parameter question for log_reasoning483', 'required': False}, {'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for log_reasoning483', 'required': False}], 'outputs': [], 'prompt': 'Your are a task solver.', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:47:21.810\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.875 | Total tokens: 13957341 | Current cost: $0.001 | Current tokens: 5285\u001b[0m\n",
"\u001b[32m2026-01-01 17:47:22.788\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.875 | Total tokens: 13957436 | Current cost: $0.000 | Current tokens: 95\u001b[0m\n",
"\u001b[32m2026-01-01 17:47:25.135\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.875 | Total tokens: 13958091 | Current cost: $0.000 | Current tokens: 655\u001b[0m\n",
"\u001b[32m2026-01-01 17:47:25.136\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 12 ...\u001b[0m\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:48:14.162\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 12 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.92}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
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"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:48:16.936\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.881 | Total tokens: 13996839 | Current cost: $0.001 | Current tokens: 8022\u001b[0m\n",
"- The workflow lacks a validation step after generating the answer, which could lead to unverified outputs being used in subsequent steps.\n",
"- There is an inconsistency in the execution history where multiple questions resulted in incorrect solutions despite having the same structure and format, indicating potential issues with the underlying model or data interpretation.\n",
"- The workflow does not account for potential ambiguities in the questions, which could lead to misinterpretation of the required answers.\n",
"- The control flow does not include error handling for cases where the validation fails, which could result in unhandled exceptions or incorrect outputs being presented.\n",
"- The assumption that all questions can be answered with a simple 'Yes' or 'No' may not hold true for all contexts, potentially oversimplifying complex biological scenarios.\n",
"\u001b[32m2026-01-01 17:48:18.408\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.882 | Total tokens: 13997531 | Current cost: $0.000 | Current tokens: 692\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, IER3IP1 is perturbed and CLCA1 expression is measured. Determine whether CLCA1 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SLC35B1 and examine the expression of RHCE. Does perturbing SLC35B1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DNAJC19 is perturbed and PHGDH expression is quantified. Does this perturbation result in a significant change in PHGDH expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb HYOU1 and examine the expression of SNHG12. Does perturbing HYOU1 lead to a significant change in SNHG12 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SRP72 and examine the expression of RPS27. Does perturbing SRP72 lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SEC63 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SYVN1 is perturbed and YTHDF2 expression is quantified. Does this perturbation result in a significant change in YTHDF2 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TMED2 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, HSD17B12 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:48:21.140\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.882 | Total tokens: 14002760 | Current cost: $0.001 | Current tokens: 5229\u001b[0m\n",
"\u001b[32m2026-01-01 17:48:22.206\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.882 | Total tokens: 14002864 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-01 17:48:23.498\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.883 | Total tokens: 14004096 | Current cost: $0.000 | Current tokens: 1232\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:48:25.890\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.884 | Total tokens: 14009378 | Current cost: $0.001 | Current tokens: 5282\u001b[0m\n",
"\u001b[32m2026-01-01 17:48:26.846\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.884 | Total tokens: 14009478 | Current cost: $0.000 | Current tokens: 100\u001b[0m\n",
"\u001b[32m2026-01-01 17:48:29.163\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.884 | Total tokens: 14011440 | Current cost: $0.000 | Current tokens: 1962\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:48:32.112\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.885 | Total tokens: 14016730 | Current cost: $0.001 | Current tokens: 5290\u001b[0m\n",
"\u001b[32m2026-01-01 17:48:33.260\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.885 | Total tokens: 14016830 | Current cost: $0.000 | Current tokens: 100\u001b[0m\n",
"\u001b[32m2026-01-01 17:48:35.839\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.885 | Total tokens: 14018968 | Current cost: $0.000 | Current tokens: 2138\u001b[0m\n",
"\u001b[32m2026-01-01 17:48:35.840\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 13 ...\u001b[0m\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
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"\r",
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"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:49:24.682\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 13 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.92}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:49:27.648\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.891 | Total tokens: 14057615 | Current cost: $0.001 | Current tokens: 7977\u001b[0m\n",
"- The workflow lacks a validation step after generating the answer, which could lead to incorrect outputs being used in subsequent steps.\n",
"- There is no mechanism to handle or report errors in the validation process, which may result in unhandled cases or misleading outputs.\n",
"- The workflow assumes that all generated answers are valid without any checks for consistency or correctness before proceeding to contextualization.\n",
"- The prompt and intermediate steps do not specify how to handle cases where the answer is ambiguous or not clearly defined, leading to potential misinterpretation of the question.\n",
"\u001b[32m2026-01-01 17:49:29.119\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.892 | Total tokens: 14058262 | Current cost: $0.000 | Current tokens: 647\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SEC63 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, IER3IP1 is perturbed and CLCA1 expression is measured. Determine whether CLCA1 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, HSD17B12 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SRP72 and examine the expression of RPS27. Does perturbing SRP72 lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb HYOU1 and examine the expression of SNHG12. Does perturbing HYOU1 lead to a significant change in SNHG12 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DNAJC19 is perturbed and PHGDH expression is quantified. Does this perturbation result in a significant change in PHGDH expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:49:31.566\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.892 | Total tokens: 14063432 | Current cost: $0.001 | Current tokens: 5170\u001b[0m\n",
"\u001b[32m2026-01-01 17:49:33.015\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.892 | Total tokens: 14063554 | Current cost: $0.000 | Current tokens: 122\u001b[0m\n",
"\u001b[32m2026-01-01 17:49:34.588\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.893 | Total tokens: 14064867 | Current cost: $0.000 | Current tokens: 1313\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:49:37.320\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.893 | Total tokens: 14070098 | Current cost: $0.001 | Current tokens: 5231\u001b[0m\n",
"\u001b[32m2026-01-01 17:49:38.139\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.894 | Total tokens: 14070185 | Current cost: $0.000 | Current tokens: 87\u001b[0m\n",
"\u001b[32m2026-01-01 17:49:41.047\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.894 | Total tokens: 14072255 | Current cost: $0.000 | Current tokens: 2070\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:49:43.738\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.895 | Total tokens: 14077492 | Current cost: $0.001 | Current tokens: 5237\u001b[0m\n",
"\u001b[32m2026-01-01 17:49:44.618\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.895 | Total tokens: 14077589 | Current cost: $0.000 | Current tokens: 97\u001b[0m\n",
"\u001b[32m2026-01-01 17:49:47.064\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.895 | Total tokens: 14079873 | Current cost: $0.000 | Current tokens: 2284\u001b[0m\n",
"\u001b[32m2026-01-01 17:49:47.065\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 14 ...\u001b[0m\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
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]
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]
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]
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]
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"\r",
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"output_type": "stream",
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]
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"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
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"output_type": "stream",
"text": [
"\r",
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"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
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"name": "stderr",
"output_type": "stream",
"text": [
"Evaluating workflow: 100%|██████████| 50/50 [00:46<00:00, 1.07it/s]"
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"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:50:33.676\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 14 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.9}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:50:37.715\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.901 | Total tokens: 14118617 | Current cost: $0.001 | Current tokens: 8049\u001b[0m\n",
"- The workflow lacks a validation step for the initial question input before generating an answer, which could lead to incorrect assumptions being made.\n",
"- The validation step for the answer does not specify the criteria for validation, leading to potential inconsistencies in what is considered a \"validated answer.\"\n",
"- There is no error handling or fallback mechanism in case the answer validation fails, which could result in unhandled cases or premature termination of the workflow.\n",
"- The workflow assumes that all questions can be answered with a simple 'Yes' or 'No' without considering the complexity of the underlying data, which may not always be appropriate.\n",
"- The execution history shows multiple instances where the predicted answers were incorrect, indicating a flaw in the answer generation process that is not addressed in the workflow.\n",
"- The workflow does not account for the possibility of conflicting results from the validation step, which could lead to ambiguity in the final answer.\n",
"\u001b[32m2026-01-01 17:50:40.443\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.902 | Total tokens: 14119339 | Current cost: $0.000 | Current tokens: 722\u001b[0m\n",
"```python\n",
"steps = [\n",
" {'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
" {'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
" {'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, HSD17B12 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of TELO2, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TMED2 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SCYL1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, IER3IP1 is perturbed and CLCA1 expression is measured. Determine whether CLCA1 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SRP72 and examine the expression of RPS27. Does perturbing SRP72 lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DNAJC19 is perturbed and PHGDH expression is quantified. Does this perturbation result in a significant change in PHGDH expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:50:43.915\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.902 | Total tokens: 14124569 | Current cost: $0.001 | Current tokens: 5230\u001b[0m\n",
"\u001b[32m2026-01-01 17:50:47.476\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.903 | Total tokens: 14124820 | Current cost: $0.000 | Current tokens: 251\u001b[0m\n",
"\u001b[32m2026-01-01 17:50:48.862\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.903 | Total tokens: 14126359 | Current cost: $0.000 | Current tokens: 1539\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:50:51.237\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.904 | Total tokens: 14131605 | Current cost: $0.001 | Current tokens: 5246\u001b[0m\n",
"\u001b[32m2026-01-01 17:50:52.023\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.904 | Total tokens: 14131700 | Current cost: $0.000 | Current tokens: 95\u001b[0m\n",
"\u001b[32m2026-01-01 17:50:55.196\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.904 | Total tokens: 14133880 | Current cost: $0.000 | Current tokens: 2180\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:50:58.000\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.905 | Total tokens: 14139142 | Current cost: $0.001 | Current tokens: 5262\u001b[0m\n",
"\u001b[32m2026-01-01 17:50:59.529\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.905 | Total tokens: 14139237 | Current cost: $0.000 | Current tokens: 95\u001b[0m\n",
"\u001b[32m2026-01-01 17:51:01.961\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.905 | Total tokens: 14141646 | Current cost: $0.000 | Current tokens: 2409\u001b[0m\n",
"\u001b[32m2026-01-01 17:51:01.962\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 15 ...\u001b[0m\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
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"text": [
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:51:49.847\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 15 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.88}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
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"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:51:53.575\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.912 | Total tokens: 14180373 | Current cost: $0.001 | Current tokens: 8036\u001b[0m\n",
"- The workflow lacks a step to handle cases where the answer is not straightforward or requires additional context, leading to potential oversights in complex scenarios.\n",
"- There is no validation step to ensure that the generated answer aligns with the expected format ('Final Answer: Yes' or 'Final Answer: No'), which could result in format inconsistencies.\n",
"- The workflow does not include error handling for cases where the validation of the answer fails, leading to unaddressed discrepancies in the final output.\n",
"- The assumption that all questions can be answered with a simple 'Yes' or 'No' may not hold true for all perturbation experiments, indicating a lack of flexibility in the workflow.\n",
"- The execution history shows multiple instances where the predicted answers were correct, but the solutions were marked incorrect, suggesting a flaw in the validation or scoring mechanism.\n",
"\u001b[32m2026-01-01 17:51:54.880\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.912 | Total tokens: 14181079 | Current cost: $0.000 | Current tokens: 706\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['answer', 'question'], 'outputs': ['final_answer']},\n",
"{'name': 'validate_answer2087', 'args': ['final_answer'], 'outputs': ['validated_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SRP72 and examine the expression of RPS27. Does perturbing SRP72 lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SEC63 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TMED2 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DNAJC19 is perturbed and PHGDH expression is quantified. Does this perturbation result in a significant change in PHGDH expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SCYL1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: No\n",
"Solutions: Yes\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SLC35B1 and examine the expression of RHCE. Does perturbing SLC35B1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, HSD17B12 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:51:58.332\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.913 | Total tokens: 14186298 | Current cost: $0.001 | Current tokens: 5219\u001b[0m\n",
"\u001b[32m2026-01-01 17:52:00.056\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.913 | Total tokens: 14186401 | Current cost: $0.000 | Current tokens: 103\u001b[0m\n",
"\u001b[32m2026-01-01 17:52:01.923\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.913 | Total tokens: 14187841 | Current cost: $0.000 | Current tokens: 1440\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:52:04.376\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.914 | Total tokens: 14193092 | Current cost: $0.001 | Current tokens: 5251\u001b[0m\n",
"\u001b[32m2026-01-01 17:52:05.230\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.914 | Total tokens: 14193187 | Current cost: $0.000 | Current tokens: 95\u001b[0m\n",
"\u001b[32m2026-01-01 17:52:07.762\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.914 | Total tokens: 14195716 | Current cost: $0.000 | Current tokens: 2529\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:52:10.116\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.915 | Total tokens: 14200974 | Current cost: $0.001 | Current tokens: 5258\u001b[0m\n",
"\u001b[32m2026-01-01 17:52:10.951\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.915 | Total tokens: 14201073 | Current cost: $0.000 | Current tokens: 99\u001b[0m\n",
"\u001b[32m2026-01-01 17:52:13.823\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.915 | Total tokens: 14203385 | Current cost: $0.000 | Current tokens: 2312\u001b[0m\n",
"\u001b[32m2026-01-01 17:52:13.824\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 16 ...\u001b[0m\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
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"text": [
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:53:02.994\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 16 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.94}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
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"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:53:05.982\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.922 | Total tokens: 14242159 | Current cost: $0.001 | Current tokens: 8030\u001b[0m\n",
"- The workflow lacks a validation step to ensure that the initial predictions align with the expected format of 'Final Answer: Yes' or 'Final Answer: No', which could lead to incorrect outputs being accepted as valid.\n",
"- There are multiple instances of incorrect computation results leading to discrepancies between predictions and solutions, indicating a failure in the validation or computation process.\n",
"- The workflow does not include any error handling or mechanisms to address cases where the predictions do not match the solutions, which could result in unhandled exceptions or misleading outputs.\n",
"- The prompt structure for questions is overly repetitive and does not account for variations in phrasing or context, potentially leading to ambiguity in interpretation.\n",
"- The control flow does not account for the possibility of conflicting results from different questions, which could undermine the reliability of the overall workflow.\n",
"\u001b[32m2026-01-01 17:53:07.363\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.922 | Total tokens: 14242862 | Current cost: $0.000 | Current tokens: 703\u001b[0m\n",
"```python\n",
"steps = [\n",
" {'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
" {'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
" {'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SYVN1 is perturbed and YTHDF2 expression is quantified. Does this perturbation result in a significant change in YTHDF2 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, HSD17B12 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DNAJC19 is perturbed and PHGDH expression is quantified. Does this perturbation result in a significant change in PHGDH expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SLC35B1 and examine the expression of RHCE. Does perturbing SLC35B1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TMED2 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, HSD17B12 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:53:10.750\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.923 | Total tokens: 14248104 | Current cost: $0.001 | Current tokens: 5242\u001b[0m\n",
"\u001b[32m2026-01-01 17:53:12.166\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.923 | Total tokens: 14248199 | Current cost: $0.000 | Current tokens: 95\u001b[0m\n",
"\u001b[32m2026-01-01 17:53:13.535\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.923 | Total tokens: 14249673 | Current cost: $0.000 | Current tokens: 1474\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:53:16.542\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.924 | Total tokens: 14254982 | Current cost: $0.001 | Current tokens: 5309\u001b[0m\n",
"\u001b[32m2026-01-01 17:53:17.588\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.924 | Total tokens: 14255086 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-01 17:53:19.409\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.924 | Total tokens: 14257529 | Current cost: $0.000 | Current tokens: 2443\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:53:22.714\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.925 | Total tokens: 14262837 | Current cost: $0.001 | Current tokens: 5308\u001b[0m\n",
"\u001b[32m2026-01-01 17:53:24.190\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.925 | Total tokens: 14262934 | Current cost: $0.000 | Current tokens: 97\u001b[0m\n",
"\u001b[32m2026-01-01 17:53:26.723\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.926 | Total tokens: 14265612 | Current cost: $0.000 | Current tokens: 2678\u001b[0m\n",
"\u001b[32m2026-01-01 17:53:26.723\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 17 ...\u001b[0m\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:54:14.303\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 17 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.98}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:54:17.325\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.932 | Total tokens: 14304310 | Current cost: $0.001 | Current tokens: 8029\u001b[0m\n",
"- The workflow lacks a validation step to ensure that the generated answer aligns with the specific format required ('Final Answer: Yes' or 'Final Answer: No'), which could lead to incorrect outputs.\n",
"- There are multiple instances of incorrect computation results leading to discrepancies between predictions and solutions, indicating potential flaws in the answer generation or validation processes.\n",
"- The workflow does not account for the possibility of ambiguous or conflicting data in the input questions, which could lead to misleading answers.\n",
"- The execution history shows several cases where the final answer was marked as correct despite the underlying computations being incorrect, suggesting a lack of robust error handling or validation mechanisms.\n",
"- The workflow assumes that all questions can be answered with a binary response without considering the context or complexity of the underlying data, which may not always be valid.\n",
"\u001b[32m2026-01-01 17:54:18.603\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.932 | Total tokens: 14305012 | Current cost: $0.000 | Current tokens: 702\u001b[0m\n",
"```python\n",
"steps = [\n",
" {'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
" {'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
" {'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SEC63 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, HSD17B12 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TMED2 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of TELO2, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, P4HB is perturbed and RHCE expression is measured. Determine whether RHCE exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, HSD17B12 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SCYL1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:54:21.708\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.933 | Total tokens: 14310187 | Current cost: $0.001 | Current tokens: 5175\u001b[0m\n",
"\u001b[32m2026-01-01 17:54:22.588\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.933 | Total tokens: 14310290 | Current cost: $0.000 | Current tokens: 103\u001b[0m\n",
"\u001b[32m2026-01-01 17:54:23.646\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.933 | Total tokens: 14311848 | Current cost: $0.000 | Current tokens: 1558\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:54:26.480\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.934 | Total tokens: 14317053 | Current cost: $0.001 | Current tokens: 5205\u001b[0m\n",
"\u001b[32m2026-01-01 17:54:28.104\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.934 | Total tokens: 14317157 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-01 17:54:30.332\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.934 | Total tokens: 14319695 | Current cost: $0.000 | Current tokens: 2538\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:54:33.635\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.935 | Total tokens: 14324901 | Current cost: $0.001 | Current tokens: 5206\u001b[0m\n",
"\u001b[32m2026-01-01 17:54:34.597\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.935 | Total tokens: 14325004 | Current cost: $0.000 | Current tokens: 103\u001b[0m\n",
"\u001b[32m2026-01-01 17:54:36.971\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.936 | Total tokens: 14327805 | Current cost: $0.000 | Current tokens: 2801\u001b[0m\n",
"\u001b[32m2026-01-01 17:54:36.972\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 18 ...\u001b[0m\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:55:22.874\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 18 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.92}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:55:26.747\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.942 | Total tokens: 14366511 | Current cost: $0.001 | Current tokens: 8019\u001b[0m\n",
"- The workflow lacks a validation step after generating the answer, which could lead to incorrect outputs being used in subsequent steps.\n",
"- The control flow does not account for potential errors or inconsistencies in the answer validation process, leading to unhandled cases where the answer may not be valid.\n",
"- There is an assumption that all generated answers will be valid without any checks for logical consistency or correctness before moving to contextualization.\n",
"- The execution history shows multiple instances where the predictions and solutions do not align, indicating a failure in the validation process that should have caught these discrepancies.\n",
"- The final answer format is strictly defined, yet the workflow does not ensure that all intermediate outputs conform to this format, which could lead to ambiguity in the final presentation of answers.\n",
"\u001b[32m2026-01-01 17:55:27.885\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.942 | Total tokens: 14367200 | Current cost: $0.000 | Current tokens: 689\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, HSD17B12 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DNAJC19 is perturbed and PHGDH expression is quantified. Does this perturbation result in a significant change in PHGDH expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SEC63 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, IER3IP1 is perturbed and CLCA1 expression is measured. Determine whether CLCA1 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, P4HB is perturbed and RHCE expression is measured. Determine whether RHCE exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: No\n",
"Solutions: Yes\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SCYL1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TMED2 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:55:30.402\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.943 | Total tokens: 14372378 | Current cost: $0.001 | Current tokens: 5178\u001b[0m\n",
"\u001b[32m2026-01-01 17:55:31.324\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.943 | Total tokens: 14372482 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-01 17:55:32.735\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.943 | Total tokens: 14374074 | Current cost: $0.000 | Current tokens: 1592\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:55:35.336\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.944 | Total tokens: 14379306 | Current cost: $0.001 | Current tokens: 5232\u001b[0m\n",
"\u001b[32m2026-01-01 17:55:36.919\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.944 | Total tokens: 14379410 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-01 17:55:38.760\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.945 | Total tokens: 14382064 | Current cost: $0.000 | Current tokens: 2654\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:55:41.281\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.945 | Total tokens: 14387310 | Current cost: $0.001 | Current tokens: 5246\u001b[0m\n",
"\u001b[32m2026-01-01 17:55:42.586\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.945 | Total tokens: 14387404 | Current cost: $0.000 | Current tokens: 94\u001b[0m\n",
"\u001b[32m2026-01-01 17:55:44.997\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.946 | Total tokens: 14390336 | Current cost: $0.000 | Current tokens: 2932\u001b[0m\n",
"\u001b[32m2026-01-01 17:55:44.998\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 19 ...\u001b[0m\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
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"text": [
"\r",
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:56:35.531\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 19 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.92}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:56:38.438\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.952 | Total tokens: 14429035 | Current cost: $0.001 | Current tokens: 8012\u001b[0m\n",
"- The workflow lacks a validation step after generating the answer, which could lead to incorrect outputs being processed further without verification.\n",
"- There is no explicit handling of cases where the answer might be ambiguous or require additional context, leading to potential misinterpretation of the results.\n",
"- The assumption that all questions can be answered with a simple 'Yes' or 'No' may not hold true for all scenarios, risking oversimplification of complex biological data.\n",
"- The workflow does not include a mechanism for addressing or logging errors encountered during execution, which could help in identifying patterns of failure.\n",
"- The control flow does not account for potential contradictions between the predictions and solutions, which could lead to confusion in the final output.\n",
"\u001b[32m2026-01-01 17:56:41.756\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.952 | Total tokens: 14429717 | Current cost: $0.000 | Current tokens: 682\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb HYOU1 and examine the expression of SNHG12. Does perturbing HYOU1 lead to a significant change in SNHG12 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, HSD17B12 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SEC63 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SYVN1 is perturbed and YTHDF2 expression is quantified. Does this perturbation result in a significant change in YTHDF2 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, HSD17B12 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:56:45.344\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.953 | Total tokens: 14434904 | Current cost: $0.001 | Current tokens: 5187\u001b[0m\n",
"\u001b[32m2026-01-01 17:56:46.899\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.953 | Total tokens: 14435007 | Current cost: $0.000 | Current tokens: 103\u001b[0m\n",
"\u001b[32m2026-01-01 17:56:48.929\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.953 | Total tokens: 14436670 | Current cost: $0.000 | Current tokens: 1663\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:56:51.911\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.954 | Total tokens: 14441920 | Current cost: $0.001 | Current tokens: 5250\u001b[0m\n",
"\u001b[32m2026-01-01 17:56:52.954\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.954 | Total tokens: 14442027 | Current cost: $0.000 | Current tokens: 107\u001b[0m\n",
"\u001b[32m2026-01-01 17:56:55.796\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.955 | Total tokens: 14444821 | Current cost: $0.000 | Current tokens: 2794\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:56:58.147\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.956 | Total tokens: 14450057 | Current cost: $0.001 | Current tokens: 5236\u001b[0m\n",
"\u001b[32m2026-01-01 17:56:59.113\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.956 | Total tokens: 14450153 | Current cost: $0.000 | Current tokens: 96\u001b[0m\n",
"\u001b[32m2026-01-01 17:57:02.000\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.956 | Total tokens: 14453212 | Current cost: $0.001 | Current tokens: 3059\u001b[0m\n",
"\u001b[32m2026-01-01 17:57:02.000\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 20 ...\u001b[0m\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
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"output_type": "stream",
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n",
"\u001b[32m2026-01-01 17:57:47.794\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 20 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.92}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:57:51.436\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.962 | Total tokens: 14491942 | Current cost: $0.001 | Current tokens: 8043\u001b[0m\n",
"- The workflow lacks a validation step for the initial question input, which could lead to incorrect assumptions being made about the context or requirements of the question.\n",
"- There is no explicit handling of cases where the answer might be ambiguous or where the data may not support a clear 'Yes' or 'No' response, leading to potential misinterpretation of results.\n",
"- The control flow does not account for scenarios where the validation of the answer fails, as there is no mechanism to revisit or adjust the answer based on validation feedback.\n",
"- The workflow assumes that all questions are straightforward and can be answered with a binary response, which may not hold true for all perturbation experiments, potentially oversimplifying complex biological data.\n",
"- The execution history shows multiple instances where the predicted answers were incorrect, indicating a potential flaw in the answer generation process that is not addressed in the workflow.\n",
"\u001b[32m2026-01-01 17:57:52.764\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.963 | Total tokens: 14492655 | Current cost: $0.000 | Current tokens: 713\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TMED2 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, HSD17B12 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SLC35B1 and examine the expression of RHCE. Does perturbing SLC35B1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of TELO2, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SCYL1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SRP72 and examine the expression of RPS27. Does perturbing SRP72 lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, IER3IP1 is perturbed and CLCA1 expression is measured. Determine whether CLCA1 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DNAJC19 is perturbed and PHGDH expression is quantified. Does this perturbation result in a significant change in PHGDH expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:57:55.175\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.963 | Total tokens: 14497818 | Current cost: $0.001 | Current tokens: 5163\u001b[0m\n",
"\u001b[32m2026-01-01 17:57:56.827\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.963 | Total tokens: 14497940 | Current cost: $0.000 | Current tokens: 122\u001b[0m\n",
"\u001b[32m2026-01-01 17:57:58.574\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.964 | Total tokens: 14499657 | Current cost: $0.000 | Current tokens: 1717\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:58:00.890\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.965 | Total tokens: 14504896 | Current cost: $0.001 | Current tokens: 5239\u001b[0m\n",
"\u001b[32m2026-01-01 17:58:02.937\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.965 | Total tokens: 14505001 | Current cost: $0.000 | Current tokens: 105\u001b[0m\n",
"\u001b[32m2026-01-01 17:58:05.693\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.965 | Total tokens: 14507901 | Current cost: $0.000 | Current tokens: 2900\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:58:08.285\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.966 | Total tokens: 14513144 | Current cost: $0.001 | Current tokens: 5243\u001b[0m\n",
"\u001b[32m2026-01-01 17:58:09.687\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.966 | Total tokens: 14513240 | Current cost: $0.000 | Current tokens: 96\u001b[0m\n",
"\u001b[32m2026-01-01 17:58:11.989\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.967 | Total tokens: 14516441 | Current cost: $0.001 | Current tokens: 3201\u001b[0m\n",
"\u001b[32m2026-01-01 17:58:11.990\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 21 ...\u001b[0m\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 17:58:57.642\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 21 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.92}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:58:59.757\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.973 | Total tokens: 14555129 | Current cost: $0.001 | Current tokens: 7990\u001b[0m\n",
"- The workflow lacks a validation step after generating the answer, which could lead to incorrect outputs being accepted without verification.\n",
"- The control flow does not account for potential errors in the answer generation or validation steps, leading to unhandled cases where the answer may be incorrect.\n",
"- There is an inconsistency in the execution history where multiple instances show incorrect predictions and solutions, indicating a failure to adequately address or learn from errors in prior steps.\n",
"- The prompts and intermediate steps do not specify how to handle cases where the expression change is ambiguous or not statistically significant, leading to potential misinterpretation of results.\n",
"\u001b[32m2026-01-01 17:59:01.511\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.973 | Total tokens: 14555789 | Current cost: $0.000 | Current tokens: 660\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SYVN1 is perturbed and YTHDF2 expression is quantified. Does this perturbation result in a significant change in YTHDF2 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SRP72 and examine the expression of RPS27. Does perturbing SRP72 lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SLC35B1 and examine the expression of RHCE. Does perturbing SLC35B1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TMED2 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb HYOU1 and examine the expression of SNHG12. Does perturbing HYOU1 lead to a significant change in SNHG12 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, HSD17B12 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: No\n",
"Solutions: Yes\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, P4HB is perturbed and RHCE expression is measured. Determine whether RHCE exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:59:04.234\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.974 | Total tokens: 14560988 | Current cost: $0.001 | Current tokens: 5199\u001b[0m\n",
"\u001b[32m2026-01-01 17:59:05.106\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.974 | Total tokens: 14561083 | Current cost: $0.000 | Current tokens: 95\u001b[0m\n",
"\u001b[32m2026-01-01 17:59:06.266\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.974 | Total tokens: 14562858 | Current cost: $0.000 | Current tokens: 1775\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:59:08.733\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.975 | Total tokens: 14568103 | Current cost: $0.001 | Current tokens: 5245\u001b[0m\n",
"\u001b[32m2026-01-01 17:59:09.646\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.975 | Total tokens: 14568208 | Current cost: $0.000 | Current tokens: 105\u001b[0m\n",
"\u001b[32m2026-01-01 17:59:11.803\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.975 | Total tokens: 14571222 | Current cost: $0.001 | Current tokens: 3014\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 17:59:14.404\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.976 | Total tokens: 14576455 | Current cost: $0.001 | Current tokens: 5233\u001b[0m\n",
"\u001b[32m2026-01-01 17:59:15.418\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.976 | Total tokens: 14576550 | Current cost: $0.000 | Current tokens: 95\u001b[0m\n",
"\u001b[32m2026-01-01 17:59:17.965\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.977 | Total tokens: 14579864 | Current cost: $0.001 | Current tokens: 3314\u001b[0m\n",
"\u001b[32m2026-01-01 17:59:17.965\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 22 ...\u001b[0m\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 18:00:04.675\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 22 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.96}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
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"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 18:00:07.425\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.983 | Total tokens: 14618573 | Current cost: $0.001 | Current tokens: 8006\u001b[0m\n",
"- The workflow lacks a step to handle potential errors or inconsistencies in the predictions and solutions, leading to unhandled cases where the computation result is incorrect.\n",
"- There is no validation step to ensure that the generated answer aligns with the strict format required ('Final Answer: Yes' or 'Final Answer: No'), which could lead to ambiguous outputs.\n",
"- The control flow does not account for scenarios where the validation of the answer fails, resulting in premature termination of the workflow without addressing the issue.\n",
"- The assumption that all questions can be answered with a simple 'Yes' or 'No' may not hold true for all cases, leading to potential oversights in more complex queries.\n",
"\u001b[32m2026-01-01 18:00:09.545\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.983 | Total tokens: 14619272 | Current cost: $0.000 | Current tokens: 699\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']},\n",
"{'name': 'error_handling', 'args': ['validated_answer'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SLC35B1 and examine the expression of RHCE. Does perturbing SLC35B1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb HYOU1 and examine the expression of SNHG12. Does perturbing HYOU1 lead to a significant change in SNHG12 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TMED2 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, HSD17B12 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SRP72 and examine the expression of RPS27. Does perturbing SRP72 lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DNAJC19 is perturbed and PHGDH expression is quantified. Does this perturbation result in a significant change in PHGDH expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, P4HB is perturbed and RHCE expression is measured. Determine whether RHCE exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, HSD17B12 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 18:00:11.877\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.984 | Total tokens: 14624485 | Current cost: $0.001 | Current tokens: 5213\u001b[0m\n",
"\u001b[32m2026-01-01 18:00:13.184\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.984 | Total tokens: 14624588 | Current cost: $0.000 | Current tokens: 103\u001b[0m\n",
"\u001b[32m2026-01-01 18:00:14.492\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.984 | Total tokens: 14626446 | Current cost: $0.000 | Current tokens: 1858\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 18:00:17.147\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.985 | Total tokens: 14631725 | Current cost: $0.001 | Current tokens: 5279\u001b[0m\n",
"\u001b[32m2026-01-01 18:00:18.977\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.985 | Total tokens: 14631844 | Current cost: $0.000 | Current tokens: 119\u001b[0m\n",
"\u001b[32m2026-01-01 18:00:22.349\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.986 | Total tokens: 14635028 | Current cost: $0.001 | Current tokens: 3184\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 18:00:25.615\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.987 | Total tokens: 14640301 | Current cost: $0.001 | Current tokens: 5273\u001b[0m\n",
"\u001b[32m2026-01-01 18:00:27.700\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.987 | Total tokens: 14640396 | Current cost: $0.000 | Current tokens: 95\u001b[0m\n",
"\u001b[32m2026-01-01 18:00:30.603\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.987 | Total tokens: 14643876 | Current cost: $0.001 | Current tokens: 3480\u001b[0m\n",
"{'name': 'error_handling3683', 'description': 'Task to error_handling3683. Takes validated_answer as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for error_handling3683', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from error_handling3683', 'required': True}], 'prompt': 'Your are a task solver.', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 18:00:32.921\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.988 | Total tokens: 14649130 | Current cost: $0.001 | Current tokens: 5254\u001b[0m\n",
"\u001b[32m2026-01-01 18:00:34.508\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.988 | Total tokens: 14649259 | Current cost: $0.000 | Current tokens: 129\u001b[0m\n",
"\u001b[32m2026-01-01 18:00:36.711\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.988 | Total tokens: 14649908 | Current cost: $0.000 | Current tokens: 649\u001b[0m\n",
"\u001b[32m2026-01-01 18:00:36.712\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 23 ...\u001b[0m\n"
]
},
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 18:01:28.180\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 23 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.92}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
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"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 18:01:31.024\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.995 | Total tokens: 14688609 | Current cost: $0.001 | Current tokens: 8015\u001b[0m\n",
"- The workflow lacks a validation step after generating the answer, which could lead to incorrect outputs being used in subsequent steps without verification.\n",
"- There are multiple instances of incorrect predictions leading to incorrect solutions, indicating a failure in the computational logic or data processing that was not addressed in the workflow.\n",
"- The workflow does not account for potential contradictions in the answers derived from different questions, which could lead to inconsistencies in the final outputs.\n",
"- The prompts and intermediate steps do not specify the criteria for determining \"significant change,\" which may lead to ambiguity in the interpretation of results.\n",
"- The control flow does not include error handling for cases where the validation fails, which could result in unhandled exceptions or incorrect final answers being presented.\n",
"\u001b[32m2026-01-01 18:01:32.316\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.995 | Total tokens: 14689294 | Current cost: $0.000 | Current tokens: 685\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SLC35B1 and examine the expression of RHCE. Does perturbing SLC35B1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, HSD17B12 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb HYOU1 and examine the expression of SNHG12. Does perturbing HYOU1 lead to a significant change in SNHG12 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, P4HB is perturbed and RHCE expression is measured. Determine whether RHCE exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SRP72 and examine the expression of RPS27. Does perturbing SRP72 lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SYVN1 is perturbed and YTHDF2 expression is quantified. Does this perturbation result in a significant change in YTHDF2 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SEC63 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, IER3IP1 is perturbed and CLCA1 expression is measured. Determine whether CLCA1 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, HSD17B12 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 18:01:35.956\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.995 | Total tokens: 14694478 | Current cost: $0.001 | Current tokens: 5184\u001b[0m\n",
"\u001b[32m2026-01-01 18:01:37.185\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.996 | Total tokens: 14694600 | Current cost: $0.000 | Current tokens: 122\u001b[0m\n",
"\u001b[32m2026-01-01 18:01:38.800\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.996 | Total tokens: 14696520 | Current cost: $0.000 | Current tokens: 1920\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 18:01:41.269\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.997 | Total tokens: 14701747 | Current cost: $0.001 | Current tokens: 5227\u001b[0m\n",
"\u001b[32m2026-01-01 18:01:43.229\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.997 | Total tokens: 14701851 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-01 18:01:45.048\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.997 | Total tokens: 14705096 | Current cost: $0.001 | Current tokens: 3245\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 18:01:48.393\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.998 | Total tokens: 14710317 | Current cost: $0.001 | Current tokens: 5221\u001b[0m\n",
"\u001b[32m2026-01-01 18:01:49.291\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.998 | Total tokens: 14710417 | Current cost: $0.000 | Current tokens: 100\u001b[0m\n",
"\u001b[32m2026-01-01 18:01:51.961\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $2.999 | Total tokens: 14713990 | Current cost: $0.001 | Current tokens: 3573\u001b[0m\n",
"\u001b[32m2026-01-01 18:01:51.962\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 24 ...\u001b[0m\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 18:02:48.863\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 24 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.96}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
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"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 18:02:51.807\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.005 | Total tokens: 14752644 | Current cost: $0.001 | Current tokens: 8009\u001b[0m\n",
"- The workflow lacks a validation step before generating the answer, which could lead to incorrect outputs being processed further.\n",
"- The validation step is not clearly defined, which raises concerns about its effectiveness and reliability in ensuring the correctness of the answer.\n",
"- There is no mechanism to handle cases where the answer cannot be determined or is ambiguous, leading to potential premature termination of the workflow.\n",
"- The workflow assumes that all questions can be answered with a binary response ('Yes' or 'No'), which may not be applicable for all scenarios, potentially leading to misleading conclusions.\n",
"- The execution history shows multiple instances where the predicted answers were incorrect, indicating a failure in the underlying model or data used for generating predictions.\n",
"\u001b[32m2026-01-01 18:02:53.810\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.005 | Total tokens: 14753323 | Current cost: $0.000 | Current tokens: 679\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, P4HB is perturbed and RHCE expression is measured. Determine whether RHCE exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SYVN1 is perturbed and YTHDF2 expression is quantified. Does this perturbation result in a significant change in YTHDF2 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SCYL1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: No\n",
"Solutions: Yes\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of TELO2, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, HSD17B12 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, IER3IP1 is perturbed and CLCA1 expression is measured. Determine whether CLCA1 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 18:02:57.165\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.006 | Total tokens: 14758464 | Current cost: $0.001 | Current tokens: 5141\u001b[0m\n",
"\u001b[32m2026-01-01 18:02:58.213\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.006 | Total tokens: 14758569 | Current cost: $0.000 | Current tokens: 105\u001b[0m\n",
"\u001b[32m2026-01-01 18:02:59.410\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.006 | Total tokens: 14760538 | Current cost: $0.000 | Current tokens: 1969\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 18:03:03.185\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.007 | Total tokens: 14765697 | Current cost: $0.001 | Current tokens: 5159\u001b[0m\n",
"\u001b[32m2026-01-01 18:03:04.215\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.007 | Total tokens: 14765800 | Current cost: $0.000 | Current tokens: 103\u001b[0m\n",
"\u001b[32m2026-01-01 18:03:06.276\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.008 | Total tokens: 14769144 | Current cost: $0.001 | Current tokens: 3344\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 18:03:09.265\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.008 | Total tokens: 14774320 | Current cost: $0.001 | Current tokens: 5176\u001b[0m\n",
"\u001b[32m2026-01-01 18:03:10.806\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.009 | Total tokens: 14774417 | Current cost: $0.000 | Current tokens: 97\u001b[0m\n",
"\u001b[32m2026-01-01 18:03:13.031\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.009 | Total tokens: 14778122 | Current cost: $0.001 | Current tokens: 3705\u001b[0m\n",
"\u001b[32m2026-01-01 18:03:13.031\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 25 ...\u001b[0m\n"
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 18:04:06.066\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 25 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.92}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
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"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 18:04:09.589\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.015 | Total tokens: 14816803 | Current cost: $0.001 | Current tokens: 8017\u001b[0m\n",
"- The workflow lacks a validation step to ensure that the generated answer aligns with the specific format required ('Final Answer: Yes' or 'Final Answer: No'), which could lead to incorrect outputs.\n",
"- There are multiple instances of incorrect computation results leading to mismatches between predictions and solutions, indicating potential flaws in the answer generation or validation processes.\n",
"- The workflow does not account for the possibility of ambiguous or contradictory questions, which could result in misleading answers.\n",
"- The control flow does not include error handling for cases where the validation fails, leading to unaddressed discrepancies in the output.\n",
"- The assumption that all questions can be answered with a binary response may not hold true for all experimental contexts, potentially oversimplifying complex biological scenarios.\n",
"\u001b[32m2026-01-01 18:04:13.622\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.015 | Total tokens: 14817490 | Current cost: $0.000 | Current tokens: 687\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SRP72 and examine the expression of RPS27. Does perturbing SRP72 lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SYVN1 is perturbed and YTHDF2 expression is quantified. Does this perturbation result in a significant change in YTHDF2 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SLC35B1 and examine the expression of RHCE. Does perturbing SLC35B1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 18:04:16.941\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.016 | Total tokens: 14822663 | Current cost: $0.001 | Current tokens: 5173\u001b[0m\n",
"\u001b[32m2026-01-01 18:04:18.747\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.016 | Total tokens: 14822764 | Current cost: $0.000 | Current tokens: 101\u001b[0m\n",
"\u001b[32m2026-01-01 18:04:20.020\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.017 | Total tokens: 14824794 | Current cost: $0.000 | Current tokens: 2030\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 18:04:22.863\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.018 | Total tokens: 14830014 | Current cost: $0.001 | Current tokens: 5220\u001b[0m\n",
"\u001b[32m2026-01-01 18:04:24.159\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.018 | Total tokens: 14830118 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-01 18:04:27.186\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.018 | Total tokens: 14833619 | Current cost: $0.001 | Current tokens: 3501\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 18:04:30.214\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.019 | Total tokens: 14838850 | Current cost: $0.001 | Current tokens: 5231\u001b[0m\n",
"\u001b[32m2026-01-01 18:04:31.707\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.019 | Total tokens: 14838958 | Current cost: $0.000 | Current tokens: 108\u001b[0m\n",
"\u001b[32m2026-01-01 18:04:36.876\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.020 | Total tokens: 14842833 | Current cost: $0.001 | Current tokens: 3875\u001b[0m\n",
"\u001b[32m2026-01-01 18:04:36.877\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 26 ...\u001b[0m\n"
]
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]
},
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 18:05:33.468\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 26 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.94}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 18:05:36.979\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.026 | Total tokens: 14881558 | Current cost: $0.001 | Current tokens: 8033\u001b[0m\n",
"- The workflow lacks a validation step after generating the answer, which could lead to incorrect outputs being used in subsequent steps without verification.\n",
"- There is no explicit handling of cases where the generated answer may not conform to the required format ('Final Answer: Yes' or 'Final Answer: No'), which could result in ambiguous or incorrect responses.\n",
"- The control flow does not account for potential errors in the validation step, which could lead to the propagation of incorrect answers without any corrective action.\n",
"- The execution history shows multiple instances where the predicted answers were correct, but the solutions were marked incorrect, indicating a potential flaw in the validation logic or criteria used for correctness assessment.\n",
"- The workflow does not specify how to handle conflicting results between predictions and solutions, which could lead to confusion or misinterpretation of the final answer.\n",
"\u001b[32m2026-01-01 18:05:38.403\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.026 | Total tokens: 14882261 | Current cost: $0.000 | Current tokens: 703\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, HSD17B12 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, IER3IP1 is perturbed and CLCA1 expression is measured. Determine whether CLCA1 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLC35B1 is perturbed and the expression of FCER1G is measured. Does this perturbation cause a significant change in FCER1G expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SRP72 and examine the expression of RPS27. Does perturbing SRP72 lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb NEDD8 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SEC63 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of TELO2, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SYVN1 is perturbed and YTHDF2 expression is quantified. Does this perturbation result in a significant change in YTHDF2 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 18:05:41.594\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.027 | Total tokens: 14887453 | Current cost: $0.001 | Current tokens: 5192\u001b[0m\n",
"\u001b[32m2026-01-01 18:05:42.769\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.027 | Total tokens: 14887572 | Current cost: $0.000 | Current tokens: 119\u001b[0m\n",
"\u001b[32m2026-01-01 18:05:44.394\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.027 | Total tokens: 14889675 | Current cost: $0.000 | Current tokens: 2103\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 18:05:47.273\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.028 | Total tokens: 14894899 | Current cost: $0.001 | Current tokens: 5224\u001b[0m\n",
"\u001b[32m2026-01-01 18:05:48.129\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.028 | Total tokens: 14894995 | Current cost: $0.000 | Current tokens: 96\u001b[0m\n",
"\u001b[32m2026-01-01 18:05:51.561\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.029 | Total tokens: 14898587 | Current cost: $0.001 | Current tokens: 3592\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 18:05:55.076\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.030 | Total tokens: 14903815 | Current cost: $0.001 | Current tokens: 5228\u001b[0m\n",
"\u001b[32m2026-01-01 18:05:56.257\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.030 | Total tokens: 14903923 | Current cost: $0.000 | Current tokens: 108\u001b[0m\n",
"\u001b[32m2026-01-01 18:05:59.778\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.030 | Total tokens: 14907900 | Current cost: $0.001 | Current tokens: 3977\u001b[0m\n",
"\u001b[32m2026-01-01 18:05:59.778\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 27 ...\u001b[0m\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
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"output_type": "stream",
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]
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"\r",
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 18:06:52.069\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 27 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.94}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
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"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 18:06:55.470\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.036 | Total tokens: 14946586 | Current cost: $0.001 | Current tokens: 8001\u001b[0m\n",
"- The workflow lacks a validation step to ensure that the generated answer aligns with the expected format ('Final Answer: Yes' or 'Final Answer: No') before proceeding to contextualization, which could lead to incorrect outputs.\n",
"- There are multiple instances of incorrect computation results leading to discrepancies between predictions and solutions, indicating potential flaws in the answer generation or validation logic.\n",
"- The workflow does not account for the possibility of ambiguous or contradictory questions, which may lead to misinterpretation of the required answer format.\n",
"- The execution history shows several cases where the final answer was marked as correct despite the underlying computations being incorrect, suggesting inadequate error handling or validation mechanisms.\n",
"\u001b[32m2026-01-01 18:06:57.242\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.037 | Total tokens: 14947257 | Current cost: $0.000 | Current tokens: 671\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SEC63 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, HSD17B12 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SLC35B1 and examine the expression of RHCE. Does perturbing SLC35B1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb HYOU1 and examine the expression of SNHG12. Does perturbing HYOU1 lead to a significant change in SNHG12 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of RHCE is measured. Determine whether RHCE shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SAMM50 and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of TELO2, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SEC63 is perturbed and CD52 expression is measured. Determine whether CD52 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SAMM50, does the expression profile of FCGR2A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 18:06:59.991\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.037 | Total tokens: 14952423 | Current cost: $0.001 | Current tokens: 5166\u001b[0m\n",
"\u001b[32m2026-01-01 18:07:00.909\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.037 | Total tokens: 14952527 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-01 18:07:02.541\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.038 | Total tokens: 14954656 | Current cost: $0.000 | Current tokens: 2129\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 18:07:05.887\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.039 | Total tokens: 14959896 | Current cost: $0.001 | Current tokens: 5240\u001b[0m\n",
"\u001b[32m2026-01-01 18:07:07.292\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.039 | Total tokens: 14959991 | Current cost: $0.000 | Current tokens: 95\u001b[0m\n",
"\u001b[32m2026-01-01 18:07:09.260\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.039 | Total tokens: 14963726 | Current cost: $0.001 | Current tokens: 3735\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 18:07:12.192\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.040 | Total tokens: 14968959 | Current cost: $0.001 | Current tokens: 5233\u001b[0m\n",
"\u001b[32m2026-01-01 18:07:13.620\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.040 | Total tokens: 14969060 | Current cost: $0.000 | Current tokens: 101\u001b[0m\n",
"\u001b[32m2026-01-01 18:07:16.165\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.041 | Total tokens: 14973177 | Current cost: $0.001 | Current tokens: 4117\u001b[0m\n",
"\u001b[32m2026-01-01 18:07:16.166\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 28 ...\u001b[0m\n"
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"name": "stderr",
"output_type": "stream",
"text": [
"\r",
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]
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{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
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"\r",
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
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]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
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]
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"output_type": "stream",
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 18:08:13.495\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 28 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.94}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 18:08:16.646\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.047 | Total tokens: 15011873 | Current cost: $0.001 | Current tokens: 8018\u001b[0m\n",
"- The workflow lacks a validation step to ensure that the generated answer aligns with the specific format required ('Final Answer: Yes' or 'Final Answer: No'), leading to potential inconsistencies in output.\n",
"- There are multiple instances of incorrect computation results, indicating a failure in the validation process or the underlying logic used to derive answers, as seen in questions regarding MRGBP, PPWD1, SOCS1, and others.\n",
"- The workflow does not account for the possibility of ambiguous or contradictory questions, which could lead to misinterpretation and incorrect answers.\n",
"- The execution history shows that the same question structure is used repeatedly without adapting to the specific context of each perturbation, which may lead to oversights in unique biological nuances.\n",
"\u001b[32m2026-01-01 18:08:19.464\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.047 | Total tokens: 15012561 | Current cost: $0.000 | Current tokens: 688\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['answer', 'question'], 'outputs': ['final_answer']},\n",
"{'name': 'validate_answer2087', 'args': ['final_answer'], 'outputs': ['validated_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PPWD1 is perturbed and CLCA1 expression is observed. Does this perturbation lead to a significant difference in CLCA1 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to UFL1 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of GMPPB, does the expression profile of RHCE indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, NEDD8 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which ATP5B is perturbed and FCER1G expression is observed. Does this perturbation lead to a significant difference in FCER1G expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SCYL1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, PDIA6 is perturbed and SNHG12 expression is measured. Determine whether SNHG12 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of ARHGAP22, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to MRGBP and then measure expression of RPS27. Does this perturbation cause a significant change in RPS27 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb HYOU1 and examine the expression of SNHG12. Does perturbing HYOU1 lead to a significant change in SNHG12 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, P4HB is perturbed and RHCE expression is measured. Determine whether RHCE exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SEC63 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DAD1 and examine the expression of CLCA1. Does perturbing DAD1 lead to a significant change in CLCA1 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, HSD17B12 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SLC35B1 and examine the expression of RHCE. Does perturbing SLC35B1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPZ1, does the expression profile of SH3BGRL3 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, CHERP is perturbed and NPL expression is quantified. Does this perturbation result in a significant change in NPL expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of PPWD1 is associated with a significant change in CD52 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to TIMM23 and then measure expression of SH3BGRL3. Does this perturbation cause a significant change in SH3BGRL3 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SLMO2 and then measure expression of PHGDH. Does this perturbation cause a significant change in PHGDH expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb TTI1 and examine the expression of RHCE. Does perturbing TTI1 lead to a significant change in RHCE expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, IER3IP1 is perturbed and CLCA1 expression is measured. Determine whether CLCA1 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, SOCS1 is perturbed and RPS27 expression is measured. Determine whether RPS27 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb DDIT3 and examine the expression of RGS16. Does perturbing DDIT3 lead to a significant change in RGS16 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SYVN1 is perturbed and YTHDF2 expression is quantified. Does this perturbation result in a significant change in YTHDF2 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 18:08:22.815\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.048 | Total tokens: 15017748 | Current cost: $0.001 | Current tokens: 5187\u001b[0m\n",
"\u001b[32m2026-01-01 18:08:23.984\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.048 | Total tokens: 15017847 | Current cost: $0.000 | Current tokens: 99\u001b[0m\n",
"\u001b[32m2026-01-01 18:08:25.226\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.048 | Total tokens: 15020062 | Current cost: $0.000 | Current tokens: 2215\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 18:08:27.886\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.049 | Total tokens: 15025280 | Current cost: $0.001 | Current tokens: 5218\u001b[0m\n",
"\u001b[32m2026-01-01 18:08:29.344\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.049 | Total tokens: 15025375 | Current cost: $0.000 | Current tokens: 95\u001b[0m\n",
"\u001b[32m2026-01-01 18:08:33.967\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.050 | Total tokens: 15029613 | Current cost: $0.001 | Current tokens: 4238\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 18:08:36.841\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.051 | Total tokens: 15034857 | Current cost: $0.001 | Current tokens: 5244\u001b[0m\n",
"\u001b[32m2026-01-01 18:08:37.637\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.051 | Total tokens: 15034952 | Current cost: $0.000 | Current tokens: 95\u001b[0m\n",
"\u001b[32m2026-01-01 18:08:40.591\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.052 | Total tokens: 15038817 | Current cost: $0.001 | Current tokens: 3865\u001b[0m\n",
"\u001b[32m2026-01-01 18:08:40.592\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 29 ...\u001b[0m\n"
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"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 92%|█████████▏| 46/50 [00:47<00:05, 1.29s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 94%|█████████▍| 47/50 [00:48<00:03, 1.26s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 96%|█████████▌| 48/50 [00:49<00:02, 1.12s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 98%|█████████▊| 49/50 [00:50<00:01, 1.01s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Evaluating workflow: 100%|██████████| 50/50 [00:51<00:00, 1.02s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"\u001b[32m2026-01-01 18:09:31.815\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 29 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.96}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 18:09:34.764\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.058 | Total tokens: 15077516 | Current cost: $0.001 | Current tokens: 8017\u001b[0m\n",
"- The workflow lacks a validation step to ensure that the generated answer aligns with the specific format required ('Final Answer: Yes' or 'Final Answer: No'), which could lead to incorrect outputs.\n",
"- There are multiple instances of incorrect computation results leading to discrepancies between predictions and solutions, indicating potential flaws in the answer generation or validation process.\n",
"- The workflow does not account for the possibility of ambiguous or contradictory questions, which could result in misleading answers.\n",
"- The control flow does not include error handling for cases where the validation step fails, leading to unhandled cases in the output.\n",
"- The assumption that all questions can be answered with a binary response may not hold true for all contexts, indicating a lack of flexibility in the workflow design.\n",
"\u001b[32m2026-01-01 18:09:36.253\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.058 | Total tokens: 15078203 | Current cost: $0.000 | Current tokens: 687\u001b[0m\n",
"```python\n",
"steps = [\n",
"{'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
"{'name': 'validate_answer2087', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
"{'name': 'contextualize_answer4593', 'args': ['validated_answer', 'question'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb SAMM50 and examine the expression of FCGR2A. Does perturbing SAMM50 lead to a significant change in FCGR2A expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, GBF1 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ZNF326 is associated with a significant change in RGS16 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of TELO2, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of HARS, does the expression profile of PHGDH indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IDH3A is perturbed and SNHG12 expression is observed. Does this perturbation lead to a significant difference in SNHG12 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of SEL1L is associated with a significant change in TXNIP expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SPCS2 is perturbed and the expression of SH3BGRL3 is measured. Determine whether SH3BGRL3 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SRP68 and then measure expression of PPCS. Does this perturbation cause a significant change in PPCS expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TIMM23 is perturbed and the expression of CLCA1 is measured. Determine whether CLCA1 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DAD1 and monitor SNHG12 expression. Decide whether this perturbation leads to a significant alteration in SNHG12 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, KCTD16 is perturbed and the expression of SNHG12 is measured. Does this perturbation cause a significant change in SNHG12 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to DERL2 and then measure expression of FCER1G. Does this perturbation cause a significant change in FCER1G expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb PSMD4 and monitor PSMD4 expression. Decide whether this perturbation leads to a significant alteration in PSMD4 expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, DDIT3 is perturbed and RPS27 expression is quantified. Does this perturbation result in a significant change in RPS27 expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb HYOU1 and examine the expression of SNHG12. Does perturbing HYOU1 lead to a significant change in SNHG12 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, CARS is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SEC63 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb FARSB and monitor FCGR2A expression. Decide whether this perturbation leads to a significant alteration in FCGR2A expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, ARHGAP22 is perturbed and the expression of SH3BGRL3 is measured. Does this perturbation cause a significant change in SH3BGRL3 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which IER3IP1 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, STT3A is perturbed and the expression of FCER1G is measured. Determine whether FCER1G shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, ZNF326 is perturbed and ZNF326 expression is measured. Determine whether ZNF326 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, TMEM167A is perturbed and the expression of CD52 is measured. Does this perturbation cause a significant change in CD52 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of IER3IP1, does the expression profile of FCER1G indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which TIMM23 is perturbed and SH3BGRL3 expression is observed. Does this perturbation lead to a significant difference in SH3BGRL3 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb IER3IP1 and monitor FCER1G expression. Decide whether this perturbation leads to a significant alteration in FCER1G expression. Answer only in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of COPB1, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which PDIA6 is perturbed and YTHDF2 expression is observed. Does this perturbation lead to a significant difference in YTHDF2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, P4HB is perturbed and RHCE expression is measured. Determine whether RHCE exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, TTI1 is perturbed and the expression of CD52 is measured. Determine whether CD52 shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to CARS and then measure expression of FCGR2A. Does this perturbation cause a significant change in FCGR2A expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, IER3IP1 is perturbed and CLCA1 expression is measured. Determine whether CLCA1 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, SRP68 is perturbed and FCER1G expression is quantified. Does this perturbation result in a significant change in FCER1G expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, P4HB is perturbed and RHCE expression is quantified. Does this perturbation result in a significant change in RHCE expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are assisting with the interpretation of perturbation-based expression data. In K562 cells, HSD17B12 is perturbed and FCGR2A expression is quantified. Does this perturbation result in a significant change in FCGR2A expression compared with control cells? Respond exactly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to SYVN1 and then measure expression of CD52. Does this perturbation cause a significant change in CD52 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of MARS, does the expression profile of FAM129A indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, UFM1 is perturbed and the expression of CLCA1 is measured. Does this perturbation cause a significant change in CLCA1 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which AMIGO3 is perturbed and TXNIP expression is observed. Does this perturbation lead to a significant difference in TXNIP expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a domain expert in functional genomics. For experiments carried out in K562 cells, we perturb MRGBP and examine the expression of RPS27. Does perturbing MRGBP lead to a significant change in RPS27 expression? Reply only with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which BHLHE40 is perturbed and SESN2 expression is observed. Does this perturbation lead to a significant difference in SESN2 expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, SLMO2 is perturbed and the expression of FCGR2A is measured. Does this perturbation cause a significant change in FCGR2A expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, IARS2 is perturbed and the expression of PHGDH is measured. Determine whether PHGDH shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, EIF2B2 is perturbed and FCGR2A expression is measured. Determine whether FCGR2A exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in regulatory genomics. Consider data from K562 cells in which SRPRB is perturbed and PPCS expression is observed. Does this perturbation lead to a significant difference in PPCS expression relative to control conditions? Answer strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene expression analysis. For K562 cells, assess whether perturbation of ASCC3 is associated with a significant change in SH3BGRL3 expression compared with unperturbed controls. Answer strictly as 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SPCS3, does the expression profile of CD52 indicate a significant change relative to control conditions? Reply strictly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a genomics expert evaluating perturbation experiments. In K562 cells, SRPRB is perturbed and the expression of PPCS is measured. Determine whether PPCS shows a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are an expert in gene regulation studies. For experiments performed in K562 cells, BHLHE40 is perturbed and SESN2 expression is measured. Determine whether SESN2 exhibits a significant expression change under this perturbation. Respond exactly with 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: Yes\n",
"Solutions: Yes\n",
"Score: 1.0\n",
"The solution is correct.\n",
"{'name': 'generate_answer', 'description': 'Extract and formulate an answer from the given context.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'prompt': '\"\"\"\\nUse the context from `{question}` to determine the best answer. If the answer is uncertain or conflicting, clearly indicate this. Ensure that the answer is validated against reliable sources for accuracy before proceeding. Provide your final answer in a clear format, without extra commentary or reasoning.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': 'Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.'}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 18:09:39.365\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.059 | Total tokens: 15083389 | Current cost: $0.001 | Current tokens: 5186\u001b[0m\n",
"\u001b[32m2026-01-01 18:09:40.267\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.059 | Total tokens: 15083491 | Current cost: $0.000 | Current tokens: 102\u001b[0m\n",
"\u001b[32m2026-01-01 18:09:41.425\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.059 | Total tokens: 15085768 | Current cost: $0.000 | Current tokens: 2277\u001b[0m\n",
"{'name': 'validate_answer2087', 'description': 'Task to validate_answer2087. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer2087', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer2087', 'required': True}], 'prompt': '\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. First, validate the context to ensure accuracy and relevance. If the answer is uncertain or ambiguous, clearly state that uncertainty. After validation, generate a straightforward answer that directly addresses {question}, considering any relevant nuances. Format your output in XML, using to explain your reasoning and for the final response. Ensure that the answer is concise and reflects any significant changes accurately, avoiding oversimplification.\\n\"\"\"', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 18:09:43.954\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.060 | Total tokens: 15090996 | Current cost: $0.001 | Current tokens: 5228\u001b[0m\n",
"\u001b[32m2026-01-01 18:09:44.789\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.060 | Total tokens: 15091093 | Current cost: $0.000 | Current tokens: 97\u001b[0m\n",
"\u001b[32m2026-01-01 18:09:46.819\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.061 | Total tokens: 15095063 | Current cost: $0.001 | Current tokens: 3970\u001b[0m\n",
"{'name': 'contextualize_answer4593', 'description': 'Task to contextualize_answer4593. Takes validated_answer, question as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for contextualize_answer4593', 'required': False}, {'name': 'question', 'type': 'str', 'description': 'Input parameter question for contextualize_answer4593', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from contextualize_answer4593', 'required': True}], 'prompt': '```xml\\n\"\"\"\\nTo answer the question accurately, first generate an answer based on the provided {question}. Validate the generated answer by ensuring it aligns with the context of the {question} and meets the criteria for a \"validated answer,\" which includes correctness and relevance. If the generated answer does not significantly change the context or is incorrect, indicate this in your validation. In your thought process, clarify any assumptions made and how the context relates to the answer. Ensure that the final answer is presented in the format \\'Final Answer: Yes\\' or \\'Final Answer: No\\'. Provide your reasoning in the field and the final validated answer in the field.\\n\"\"\"\\n```', 'prompt_template': {'class_name': 'StringTemplate', 'instruction': \"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\"}, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}\n",
"\u001b[32m2026-01-01 18:09:49.409\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.061 | Total tokens: 15100284 | Current cost: $0.001 | Current tokens: 5221\u001b[0m\n",
"\u001b[32m2026-01-01 18:09:50.896\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.062 | Total tokens: 15100405 | Current cost: $0.000 | Current tokens: 121\u001b[0m\n",
"\u001b[32m2026-01-01 18:09:52.946\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $3.062 | Total tokens: 15104807 | Current cost: $0.001 | Current tokens: 4402\u001b[0m\n",
"\u001b[32m2026-01-01 18:09:52.946\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1049\u001b[0m - \u001b[1mEvaluate the workflow at step 30 ...\u001b[0m\n"
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"\u001b[32m2026-01-01 18:10:44.622\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1052\u001b[0m - \u001b[1mStep 30 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.92}\u001b[0m\n",
"randomly update dataset\n",
"\u001b[32m2026-01-01 18:10:44.622\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1059\u001b[0m - \u001b[1mReach the maximum number of steps 30. Stop the optimization.\u001b[0m\n",
"\u001b[32m2026-01-01 18:10:44.622\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1062\u001b[0m - \u001b[1mRestore the best graph from the snapshot ...\u001b[0m\n",
"\u001b[32m2026-01-01 18:10:44.623\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36mrestore_best_graph\u001b[0m:\u001b[36m1211\u001b[0m - \u001b[1mRestore the best graph from snapshot with metrics {'f1': 0.0, 'em': 0.0, 'acc': 0.98} ...\u001b[0m\n",
"\u001b[32m2026-01-01 18:10:44.624\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36mrestore_best_graph\u001b[0m:\u001b[36m1211\u001b[0m - \u001b[1mRestore the best graph from snapshot with metrics {'f1': 0.0, 'em': 0.0, 'acc': 0.98} ...\u001b[0m\n",
"\u001b[32m2026-01-01 18:10:44.624\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.workflow.workflow_graph\u001b[0m:\u001b[36msave_module\u001b[0m:\u001b[36m1201\u001b[0m - \u001b[1mSaving SequentialWorkFlowGraph to ./debug/save_30_noreason.json\u001b[0m\n",
"\u001b[32m2026-01-01 18:10:44.631\u001b[0m | \u001b[33m\u001b[1mWARNING \u001b[0m | \u001b[36mevoagentx.agents.customize_agent\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m92\u001b[0m - \u001b[33m\u001b[1mBoth `prompt` and `prompt_template` are provided in `CustomizeAgent`. `prompt_template` will be used.\u001b[0m\n",
"\u001b[32m2026-01-01 18:10:44.651\u001b[0m | \u001b[33m\u001b[1mWARNING \u001b[0m | \u001b[36mevoagentx.agents.customize_agent\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m92\u001b[0m - \u001b[33m\u001b[1mBoth `prompt` and `prompt_template` are provided in `CustomizeAgent`. `prompt_template` will be used.\u001b[0m\n"
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{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 1.0, 'em': 1.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▊| 2465/2500 [3:13:57<02:33, 4.37s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▊| 2466/2500 [3:14:00<02:14, 3.96s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 1.0, 'em': 1.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▊| 2467/2500 [3:14:05<02:21, 4.30s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▊| 2468/2500 [3:14:09<02:16, 4.25s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2469/2500 [3:14:16<02:33, 4.94s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2470/2500 [3:14:21<02:27, 4.91s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2471/2500 [3:14:24<02:11, 4.53s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 1.0, 'em': 1.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2472/2500 [3:14:29<02:08, 4.58s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 1.0, 'em': 1.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2473/2500 [3:14:34<02:08, 4.76s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2474/2500 [3:14:39<01:59, 4.61s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2475/2500 [3:14:43<01:56, 4.67s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2476/2500 [3:14:47<01:42, 4.27s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 1.0, 'em': 1.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2477/2500 [3:14:54<01:56, 5.06s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2478/2500 [3:14:57<01:41, 4.63s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2479/2500 [3:15:01<01:34, 4.51s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2480/2500 [3:15:09<01:46, 5.31s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 1.0, 'em': 1.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2481/2500 [3:15:13<01:37, 5.15s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2482/2500 [3:15:17<01:25, 4.76s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 1.0, 'em': 1.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2483/2500 [3:15:21<01:16, 4.48s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2484/2500 [3:15:26<01:11, 4.50s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2485/2500 [3:15:31<01:10, 4.73s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2486/2500 [3:15:36<01:06, 4.74s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 99%|█████████▉| 2487/2500 [3:15:39<00:55, 4.30s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 100%|█████████▉| 2488/2500 [3:15:44<00:52, 4.41s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 100%|█████████▉| 2489/2500 [3:15:49<00:51, 4.68s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 100%|█████████▉| 2490/2500 [3:15:54<00:48, 4.90s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 100%|█████████▉| 2491/2500 [3:16:01<00:49, 5.47s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 100%|█████████▉| 2492/2500 [3:16:06<00:42, 5.34s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 100%|█████████▉| 2493/2500 [3:16:12<00:38, 5.46s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 100%|█████████▉| 2494/2500 [3:16:18<00:32, 5.49s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 1.0, 'em': 1.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 100%|█████████▉| 2495/2500 [3:16:21<00:24, 4.97s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 1.0, 'em': 1.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 100%|█████████▉| 2496/2500 [3:16:25<00:17, 4.50s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 100%|█████████▉| 2497/2500 [3:16:29<00:12, 4.32s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 100%|█████████▉| 2498/2500 [3:16:34<00:09, 4.72s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 100%|█████████▉| 2499/2500 [3:16:38<00:04, 4.46s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Evaluating workflow: 100%|██████████| 2500/2500 [3:16:44<00:00, 4.72s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n",
"Evaluation metrics: {'f1': 0.2408, 'em': 0.2408, 'acc': 0.9112}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
}
],
"source": [
"\n",
"optimizer.evaluator.dataname = 'hotpotqa'\n",
"optimizer.optimize(dataset=benchmark,provided_scorer=True)\n",
"optimizer.restore_best_graph()\n",
"optimizer.save(\"./debug/save_30_noreason.json\")\n",
"\n",
"# evaluate the optimized SEW workflow\n",
"\n",
"optimizer.evaluator.dataname = 'hotpotqa'\n",
"with suppress_logger_info():\n",
" metrics = optimizer.evaluate(dataset=benchmark, eval_mode=\"test\")\n",
"print(\"Evaluation metrics: \", metrics)"
]
},
{
"cell_type": "code",
"execution_count": 18,
"id": "491d1969",
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-01 17:07:57.192\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36mrestore_best_graph\u001b[0m:\u001b[36m1211\u001b[0m - \u001b[1mRestore the best graph from snapshot with metrics {'f1': 0.0, 'em': 0.0, 'acc': 0.98} ...\u001b[0m\n"
]
}
],
"source": [
"optimizer.restore_best_graph()"
]
},
{
"cell_type": "code",
"execution_count": 33,
"id": "31106952",
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'f1': 0.2408, 'em': 0.2408, 'acc': 0.9112}"
]
},
"execution_count": 33,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"metrics"
]
},
{
"cell_type": "code",
"execution_count": 20,
"id": "9e7d33f4",
"metadata": {
"scrolled": true
},
"outputs": [
{
"data": {
"text/plain": [
"SequentialWorkFlowGraph(class_name='SequentialWorkFlowGraph', goal='Provide a concise answer to the question using relevant context. The answer must be straightforward and avoid unnecessary explanations.', nodes=[WorkFlowNode(class_name='WorkFlowNode', name='generate_answer', description='Extract and formulate an answer from the given context.', inputs=[Parameter(class_name='Parameter', name='question', type='str', description='The question that needs to be answered.', required=True)], outputs=[Parameter(class_name='Parameter', name='answer', type='str', description='The direct answer to the question.', required=True)], reason=None, agents=[{'name': 'GenerateAnswerAgent', 'description': 'Extract and formulate an answer from the given context.', 'prompt': '\"\"\"\\nUse the context provided in `{question}` to determine the best answer. Validate the answer for accuracy against relevant criteria before finalization. Present the final answer in a clear and consistent format, such as a single sentence or short phrase. If the answer is ambiguous or unclear, indicate this explicitly. Address any complexities or nuances appropriately while avoiding unnecessary commentary or reasoning.\\n\"\"\"', 'prompt_template': StringTemplate(class_name='StringTemplate', instruction='Use the context to determine the best answer to the question. Provide your final answer in a clear format, without extra commentary or reasoning.', context=None, constraints=None, tools=None, demonstrations=None, history=None), 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'The question that needs to be answered.', 'required': True}], 'outputs': [{'name': 'answer', 'type': 'str', 'description': 'The direct answer to the question.', 'required': True}], 'output_parser': None, 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}], action_graph=None, status=), WorkFlowNode(class_name='WorkFlowNode', name='handle_format_errors5318', description='Task to handle_format_errors5318. Takes validated_answer as input. Produces final_answer as output.', inputs=[Parameter(class_name='Parameter', name='validated_answer', type='str', description='Input parameter validated_answer for handle_format_errors5318', required=False)], outputs=[Parameter(class_name='Parameter', name='final_answer', type='str', description='Output parameter final_answer from handle_format_errors5318', required=True)], reason=None, agents=[{'name': 'HandleFormatErrors5318Agent', 'description': 'Task to handle_format_errors5318. Takes validated_answer as input. Produces final_answer as output.', 'prompt': '```xml\\n\"\"\"\\nThink step by step to answer the question based on the context provided in {question}. Clearly define what constitutes a \"significant change\" in gene expression based on the context. If the perturbation does not lead to a significant change, explicitly state that in your response. Additionally, if there are ambiguous elements or discrepancies between predictions and ground-truth solutions, identify those aspects and adjust the answer accordingly. Ensure that your response is clear and concise. Format your output in xml format, such as {thought} and {answer}.\\n\"\"\"\\n```', 'prompt_template': StringTemplate(class_name='StringTemplate', instruction=\"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\", context=None, constraints=None, tools=None, demonstrations=None, history=None), 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for handle_format_errors5318', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from handle_format_errors5318', 'required': True}], 'output_parser': None, 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}], action_graph=None, status=), WorkFlowNode(class_name='WorkFlowNode', name='validate_answer4773', description='Task to validate_answer4773. Takes answer as input. Produces validated_answer as output.', inputs=[Parameter(class_name='Parameter', name='answer', type='str', description='Input parameter answer for validate_answer4773', required=False)], outputs=[Parameter(class_name='Parameter', name='validated_answer', type='str', description='Output parameter validated_answer from validate_answer4773', required=True)], reason=None, agents=[{'name': 'ValidateAnswer4773Agent', 'description': 'Task to validate_answer4773. Takes answer as input. Produces validated_answer as output.', 'prompt': '``` \\nINSTRUCTION for the 3-th task:\\n\"\"\"\\nAnalyze the provided {question} thoroughly to generate a relevant and accurate answer. Clearly define what constitutes a \"significant change\" based on the context provided. In the \\'thought\\' field, detail your reasoning process, addressing any potential ambiguities, conflicts, or uncertainties that may arise in the answer. If there are conflicting predictions or solutions, clarify how you resolved them and prioritize the evidence used in your reasoning. Validate the accuracy of your answer against known ground-truth solutions before finalizing it. In the \\'answer\\' field, provide the final response, ensuring it adheres to the expected format. If the answer does not conform to the expected format, clearly indicate the issue. Format your output in XML format, such as {thought} and {answer}.\\n\"\"\"\\n```', 'prompt_template': StringTemplate(class_name='StringTemplate', instruction=\"Think step by step to answer the question based on the question context. You should integrate context for answering. You should explain your thinking process in the 'thought' field, and provide the final answer in the 'answer' field.\\nFormat your output in xml format, such as xxx and xxx.\", context=None, constraints=None, tools=None, demonstrations=None, history=None), 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer4773', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer4773', 'required': True}], 'output_parser': None, 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None}], action_graph=None, status=)], edges=[WorkFlowEdge(class_name='WorkFlowEdge', source='generate_answer', target='validate_answer4773', priority=0), WorkFlowEdge(class_name='WorkFlowEdge', source='validate_answer4773', target='handle_format_errors5318', priority=0)], graph=)"
]
},
"execution_count": 20,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"optimizer.graph"
]
},
{
"cell_type": "code",
"execution_count": 21,
"id": "3386cab6",
"metadata": {},
"outputs": [],
"source": [
"# optimizer.save(\"./debug/agent_check_ourloop.json\")"
]
},
{
"cell_type": "code",
"execution_count": 16,
"id": "7088f101",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"\u001b[32m2025-12-28 15:25:07.156\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.benchmark.pertqa\u001b[0m:\u001b[36m_load_data_from_file\u001b[0m:\u001b[36m52\u001b[0m - \u001b[1mloading HotPotQA data from /home/tl688/pitl688/selfevolve/EvoAgentX/examples/pertqa/adamson_train.json ...\u001b[0m\n",
"\u001b[32m2025-12-28 15:25:07.157\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.benchmark.pertqa\u001b[0m:\u001b[36m_load_data_from_file\u001b[0m:\u001b[36m52\u001b[0m - \u001b[1mloading HotPotQA data from /home/tl688/pitl688/selfevolve/EvoAgentX/examples/pertqa/adamson_train.json ...\u001b[0m\n",
"\u001b[32m2025-12-28 15:25:07.158\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.benchmark.pertqa\u001b[0m:\u001b[36m_load_data_from_file\u001b[0m:\u001b[36m52\u001b[0m - \u001b[1mloading HotPotQA data from /home/tl688/pitl688/selfevolve/EvoAgentX/examples/pertqa/adamson_test.json ...\u001b[0m\n",
"\u001b[32m2025-12-28 15:25:07.172\u001b[0m | \u001b[33m\u001b[1mWARNING \u001b[0m | \u001b[36mevoagentx.agents.customize_agent\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m92\u001b[0m - \u001b[33m\u001b[1mBoth `prompt` and `prompt_template` are provided in `CustomizeAgent`. `prompt_template` will be used.\u001b[0m\n",
"\u001b[32m2025-12-28 15:25:07.174\u001b[0m | \u001b[33m\u001b[1mWARNING \u001b[0m | \u001b[36mevoagentx.agents.customize_agent\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m92\u001b[0m - \u001b[33m\u001b[1mBoth `prompt` and `prompt_template` are provided in `CustomizeAgent`. `prompt_template` will be used.\u001b[0m\n",
"\u001b[32m2025-12-28 15:25:07.177\u001b[0m | \u001b[33m\u001b[1mWARNING \u001b[0m | \u001b[36mevoagentx.agents.customize_agent\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m92\u001b[0m - \u001b[33m\u001b[1mBoth `prompt` and `prompt_template` are provided in `CustomizeAgent`. `prompt_template` will be used.\u001b[0m\n",
"\u001b[32m2025-12-28 15:25:07.180\u001b[0m | \u001b[33m\u001b[1mWARNING \u001b[0m | \u001b[36mevoagentx.agents.customize_agent\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m92\u001b[0m - \u001b[33m\u001b[1mBoth `prompt` and `prompt_template` are provided in `CustomizeAgent`. `prompt_template` will be used.\u001b[0m\n",
"\u001b[32m2025-12-28 15:25:07.182\u001b[0m | \u001b[33m\u001b[1mWARNING \u001b[0m | \u001b[36mevoagentx.agents.customize_agent\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m92\u001b[0m - \u001b[33m\u001b[1mBoth `prompt` and `prompt_template` are provided in `CustomizeAgent`. `prompt_template` will be used.\u001b[0m\n",
"\u001b[32m2025-12-28 15:25:07.184\u001b[0m | \u001b[33m\u001b[1mWARNING \u001b[0m | \u001b[36mevoagentx.agents.customize_agent\u001b[0m:\u001b[36m__init__\u001b[0m:\u001b[36m92\u001b[0m - \u001b[33m\u001b[1mBoth `prompt` and `prompt_template` are provided in `CustomizeAgent`. `prompt_template` will be used.\u001b[0m\n"
]
}
],
"source": [
"benchmark = PertQA()\n",
"graphinfo = optimizer.load_module(\"./debug/agent_check_ourloop.json\")\n",
"sew_graph = SequentialWorkFlowGraph.from_dict(graphinfo)\n",
"agent_manager = AgentManager(tools=[search_toolkit,wiki_toolkit,arxiv_toolkit])\n",
"agent_manager.add_agents_from_workflow(sew_graph, llm_config=llm_config)\n",
"evaluator = Evaluator(llm=llm, agent_manager=agent_manager, collate_func=collate_func, num_workers=20, verbose=True)\n",
"from evoagentx.optimizers import QASTRUCTUREOptimizer, TextGradOptimizer\n",
"evaluator = Evaluator(llm=llm, agent_manager=agent_manager, collate_func=collate_func, num_workers=20, verbose=True)\n",
"# obtain SEWOptimizer after having more roles\n",
"optimizer = QASTRUCTUREOptimizer(\n",
" graph=sew_graph, \n",
" evaluator=evaluator, \n",
" llm=llm, \n",
" max_steps=5,\n",
" eval_rounds=1, \n",
" repr_scheme=\"python\", \n",
" optimize_mode=\"all\", \n",
" order=\"zero-order\",\n",
" max_rounds=1\n",
")\n",
"# metrics\n",
"\n"
]
},
{
"cell_type": "code",
"execution_count": 18,
"id": "39fc99bd",
"metadata": {
"scrolled": true
},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"Evaluating workflow: 0%| | 1/2500 [00:12<8:23:59, 12.10s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Task exception was never retrieved\n",
"future: exception=RuntimeError('Event loop is closed')>\n",
"Traceback (most recent call last):\n",
" File \"/gpfs/radev/home/tl688/.conda/envs/evoagentx/lib/python3.11/asyncio/tasks.py\", line 277, in __step\n",
" result = coro.send(None)\n",
" ^^^^^^^^^^^^^^^\n",
" File \"/gpfs/radev/home/tl688/.conda/envs/evoagentx/lib/python3.11/site-packages/litellm/utils.py\", line 873, in _client_async_logging_helper\n",
" GLOBAL_LOGGING_WORKER.ensure_initialized_and_enqueue(\n",
" File \"/gpfs/radev/home/tl688/.conda/envs/evoagentx/lib/python3.11/site-packages/litellm/litellm_core_utils/logging_worker.py\", line 322, in ensure_initialized_and_enqueue\n",
" self.enqueue(async_coroutine)\n",
" File \"/gpfs/radev/home/tl688/.conda/envs/evoagentx/lib/python3.11/site-packages/litellm/litellm_core_utils/logging_worker.py\", line 131, in enqueue\n",
" self._queue.put_nowait(task)\n",
" File \"/gpfs/radev/home/tl688/.conda/envs/evoagentx/lib/python3.11/asyncio/queues.py\", line 147, in put_nowait\n",
" self._wakeup_next(self._getters)\n",
" File \"/gpfs/radev/home/tl688/.conda/envs/evoagentx/lib/python3.11/asyncio/queues.py\", line 63, in _wakeup_next\n",
" waiter.set_result(None)\n",
" File \"/gpfs/radev/home/tl688/.conda/envs/evoagentx/lib/python3.11/asyncio/futures.py\", line 263, in set_result\n",
" self.__schedule_callbacks()\n",
" File \"/gpfs/radev/home/tl688/.conda/envs/evoagentx/lib/python3.11/asyncio/futures.py\", line 173, in __schedule_callbacks\n",
" self._loop.call_soon(callback, self, context=ctx)\n",
" File \"/gpfs/radev/home/tl688/.conda/envs/evoagentx/lib/python3.11/asyncio/base_events.py\", line 762, in call_soon\n",
" self._check_closed()\n",
" File \"/gpfs/radev/home/tl688/.conda/envs/evoagentx/lib/python3.11/asyncio/base_events.py\", line 520, in _check_closed\n",
" raise RuntimeError('Event loop is closed')\n",
"RuntimeError: Event loop is closed\n",
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]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
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]
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]
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"Unclosed client session\n",
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"connector: \n",
"Unclosed client session\n",
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"connector: \n",
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"Unclosed client session\n",
"client_session: \n",
"Unclosed client session\n",
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