{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"id": "15f4833b",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"/gpfs/radev/home/tl688/.conda/envs/evoagentx/lib/python3.11/site-packages/PyPDF2/__init__.py:21: DeprecationWarning: PyPDF2 is deprecated. Please move to the pypdf library instead.\n",
" warnings.warn(\n"
]
}
],
"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": 2,
"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": 3,
"id": "a3bcfc25",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-13 19:45:05.180\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": 4,
"id": "a962ae1e",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-13 19:45:05.189\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_update_train.json ...\u001b[0m\n",
"\u001b[32m2026-01-13 19:45:05.220\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_update_train.json ...\u001b[0m\n",
"\u001b[32m2026-01-13 19:45:05.224\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_update_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(pertdata='reploge')\n",
"dataset_info = 'adamson'\n",
"benchmark = PertQA(pertdata=dataset_info)\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": 5,
"id": "656b3c46",
"metadata": {},
"outputs": [],
"source": [
"from evoagentx.optimizers import QASTRUCTUREOptimizer, TextGradOptimizer"
]
},
{
"cell_type": "code",
"execution_count": 6,
"id": "4318bce0",
"metadata": {
"scrolled": true
},
"outputs": [
{
"data": {
"text/plain": [
"2160"
]
},
"execution_count": 6,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"# graph = QASTRUCTUREOptimizer.load_module(\"./debug/save_10_noreason.json\")\n",
"# SequentialWorkFlowGraph.from_dict(graph['graph'])\n",
"len(benchmark._train_data)"
]
},
{
"cell_type": "code",
"execution_count": 7,
"id": "eaea09d1",
"metadata": {},
"outputs": [],
"source": [
"# graph\n",
"# benchmark._train_data = \n",
"# benchmark._fulldata"
]
},
{
"cell_type": "code",
"execution_count": 8,
"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=10,\n",
" eval_rounds=1, \n",
" repr_scheme=\"python\", \n",
" optimize_mode=\"all\", \n",
" order=\"zero-order\",\n",
" max_rounds=1\n",
")\n",
"optimizer.calltime = 3\n",
"optimizer.collate_func = collate_func\n",
"\n",
"benchmark.error_list = {}\n",
"benchmark.timeout = 900\n",
"benchmark.dataname = 'pubmedxqa'"
]
},
{
"cell_type": "code",
"execution_count": 9,
"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": 12,
"id": "26b9a17d",
"metadata": {},
"outputs": [],
"source": [
"# metrics"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "058a5e87",
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": 13,
"id": "3984171e",
"metadata": {},
"outputs": [],
"source": [
"# metrics\n",
"# # metrics\n",
"import numpy as np\n",
"np.random.seed(2024)\n",
"out = np.random.choice(benchmark._train_data, size=150, replace=False)\n",
"benchmark._fulldata = deepcopy(benchmark._train_data)\n",
"benchmark._train_data = out\n",
"benchmark._dev_data = out"
]
},
{
"cell_type": "code",
"execution_count": 14,
"id": "c0648c81",
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-13 19:49:47.463\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1016\u001b[0m - \u001b[1mOptimizing the SequentialWorkFlowGraph workflow with python representation.\u001b[0m\n",
"\u001b[32m2026-01-13 19:49:47.464\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1020\u001b[0m - \u001b[1mRun initial evaluation on the original workflow ...\u001b[0m\n",
"Evaluating workflow: 1%| | 1/150 [00:01<03:39, 1.47s/it]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\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",
"Evaluating workflow: 1%|▏ | 2/150 [00:02<03:05, 1.26s/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: 2%|▏ | 3/150 [00:03<02:36, 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: 3%|▎ | 4/150 [00:04<02:25, 1.00it/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: 3%|▎ | 5/150 [00:04<02:07, 1.14it/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: 4%|▍ | 6/150 [00:05<01:56, 1.24it/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: 5%|▍ | 7/150 [00:06<01:53, 1.26it/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: 5%|▌ | 8/150 [00:07<01:46, 1.34it/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: 6%|▌ | 9/150 [00:07<01:39, 1.41it/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: 7%|▋ | 10/150 [00:08<01:36, 1.45it/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: 7%|▋ | 11/150 [00:09<01:36, 1.44it/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: 8%|▊ | 12/150 [00:09<01:36, 1.43it/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: 9%|▊ | 13/150 [00:10<01:37, 1.41it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
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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[32m2026-01-13 20:01:34.870\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1024\u001b[0m - \u001b[1mInitial metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.6}\u001b[0m\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-13 20:01:36.552\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.019 | Total tokens: 107004 | Current cost: $0.003 | Current tokens: 14811\u001b[0m\n",
"\u001b[32m2026-01-13 20:01:38.201\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.021 | Total tokens: 121803 | Current cost: $0.003 | Current tokens: 14799\u001b[0m\n",
"\u001b[32m2026-01-13 20:01:39.750\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: $0.024 | Total tokens: 136622 | Current cost: $0.003 | Current tokens: 14819\u001b[0m\n",
"\u001b[32m2026-01-13 20:01:40.921\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: $0.024 | Total tokens: 137231 | Current cost: $0.000 | Current tokens: 609\u001b[0m\n",
"The detected issues across the workflows highlight several critical shortcomings: a lack of validation steps to confirm prediction accuracy, resulting in numerous incorrect solutions; absence of error handling mechanisms to identify and rectify computational issues; and failure to account for ambiguous or context-dependent questions, which can lead to misinterpretation of data. Additionally, the strict requirement for responses in a binary format ('Final Answer: Yes' or 'Final Answer: No') risks oversimplifying complex inquiries, potentially omitting essential nuances. The recurring pattern of incorrect predictions suggests underlying flaws in the model or data processing, indicating a need for reevaluation of the training data and methodology to better align with the tasks.\n",
"\u001b[32m2026-01-13 20:01:41.955\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.024 | Total tokens: 137856 | Current cost: $0.000 | Current tokens: 625\u001b[0m\n",
"```python\n",
"steps = [\n",
" {'name': 'validate_answer', 'args': ['answer'], 'outputs': ['validated_answer']},\n",
" {'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
" {'name': 'handle_errors', 'args': ['validated_answer'], 'outputs': ['final_answer']},\n",
" {'name': 'finalize_response', 'args': ['final_answer'], 'outputs': ['response']}\n",
"]\n",
"```\n",
"Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, OST4 is perturbed and the expression of DOK3 is measured. Does this perturbation cause a significant change in DOK3 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, PDIA6 is perturbed and LBX1 expression is quantified. Does this perturbation result in a significant change in LBX1 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 MRGBP, does the expression profile of LRIF1 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 SLMO2 is perturbed and FAM114A1 expression is observed. Does this perturbation lead to a significant difference in FAM114A1 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: 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 GNPNAT1 and then measure expression of RP11-212I21.4. Does this perturbation cause a significant change in RP11-212I21.4 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, SRP72 is perturbed and NOX5 expression is quantified. Does this perturbation result in a significant change in NOX5 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 functional genomics specialist. In K562 cells, we perturb COPZ1 and monitor STARD9 expression. Decide whether this perturbation leads to a significant alteration in STARD9 expression. Answer only in the format '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 NBEAL2 expression is measured. Determine whether NBEAL2 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, DERL2 is perturbed and the expression of CENPC is measured. Does this perturbation cause a significant change in CENPC 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 CCND3 and then measure expression of CENPF. Does this perturbation cause a significant change in CENPF 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 MTHFD1 and then measure expression of C12orf23. Does this perturbation cause a significant change in C12orf23 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 EPB42. Does this perturbation cause a significant change in EPB42 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, CHERP is perturbed and the expression of IFT27 is measured. Does this perturbation cause a significant change in IFT27 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, PPWD1 is perturbed and CTBS expression is quantified. Does this perturbation result in a significant change in CTBS 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 SEL1L is perturbed and C12orf44 expression is observed. Does this perturbation lead to a significant difference in C12orf44 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: 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 PPWD1, does the expression profile of NAV1 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 SCYL1 and examine the expression of PTGS1. Does perturbing SCYL1 lead to a significant change in PTGS1 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, YIPF5 is perturbed and the expression of CTD-2001C12.1 is measured. Does this perturbation cause a significant change in CTD-2001C12.1 expression? Answer strictly in the format '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 TTI1 and monitor TTC32 expression. Decide whether this perturbation leads to a significant alteration in TTC32 expression. Answer only in the format '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, TTI2 is perturbed and the expression of EP300 is measured. Determine whether EP300 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, COPB1 is perturbed and the expression of RILPL2 is measured. Determine whether RILPL2 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, CCND3 is perturbed and the expression of RP1-274L7.1 is measured. Determine whether RP1-274L7.1 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: No\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 P4HB, does the expression profile of CELF6 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: 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 DDIT3 is associated with a significant change in PDE9A 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 TMEM167A and monitor CRNDE expression. Decide whether this perturbation leads to a significant alteration in CRNDE expression. Answer only in the format '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 SAMM50 is perturbed and GUSB expression is observed. Does this perturbation lead to a significant difference in GUSB 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, STT3A is perturbed and RCBTB2 expression is quantified. Does this perturbation result in a significant change in RCBTB2 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 XRN1 is perturbed and MBNL1 expression is observed. Does this perturbation lead to a significant difference in MBNL1 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, DERL2 is perturbed and ACSM3 expression is quantified. Does this perturbation result in a significant change in ACSM3 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, SCYL1 is perturbed and the expression of TMEM60 is measured. Determine whether TMEM60 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: 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 DDOST is perturbed and TRPM4 expression is observed. Does this perturbation lead to a significant difference in TRPM4 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, CREB1 is perturbed and ZNF429 expression is quantified. Does this perturbation result in a significant change in ZNF429 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 DARS, does the expression profile of SPAST 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, DDRGK1 is perturbed and the expression of UBE3A is measured. Does this perturbation cause a significant change in UBE3A 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 TARS and monitor AC007038.7 expression. Decide whether this perturbation leads to a significant alteration in AC007038.7 expression. Answer only in the format '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, SEC61G is perturbed and LTB expression is quantified. Does this perturbation result in a significant change in LTB 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, SYVN1 is perturbed and LST1 expression is measured. Determine whether LST1 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 KCTD16 is associated with a significant change in ARHGAP6 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 DNAJC19 is associated with a significant change in PDE3B 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: 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 EIF2B4 and then measure expression of DOCK11. Does this perturbation cause a significant change in DOCK11 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, SPCS3 is perturbed and the expression of PCF11 is measured. Determine whether PCF11 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, EIF2B2 is perturbed and the expression of C10orf32 is measured. Determine whether C10orf32 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: 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, ARHGAP22 is perturbed and DYNC1H1 expression is measured. Determine whether DYNC1H1 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 ATP5B and monitor SERPINH1 expression. Decide whether this perturbation leads to a significant alteration in SERPINH1 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 UFL1 is perturbed and KDM1B expression is observed. Does this perturbation lead to a significant difference in KDM1B 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 DDX3X expression is measured. Determine whether DDX3X 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 SLC35B1 is associated with a significant change in ZXDA 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: 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, SRPRB is perturbed and the expression of RP11-181G12.2 is measured. Does this perturbation cause a significant change in RP11-181G12.2 expression? Answer strictly in the format '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 MRPL39, does the expression profile of RP13-216E22.4 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: 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 SEC61A1, does the expression profile of LTB 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 ARHGAP5 is measured. Does this perturbation cause a significant change in ARHGAP5 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 ARHGAP22 and monitor RGS20 expression. Decide whether this perturbation leads to a significant alteration in RGS20 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 SAMM50 is associated with a significant change in RP11-61E11.1 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: No\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 SLC37A1. Does this perturbation cause a significant change in SLC37A1 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, EIF2B4 is perturbed and the expression of HMGCS1 is measured. Determine whether HMGCS1 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 ZNF326 is perturbed and RP11-141B14.1 expression is observed. Does this perturbation lead to a significant difference in RP11-141B14.1 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: 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, TMED10 is perturbed and PELO expression is measured. Determine whether PELO 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 TMED10 and examine the expression of IL2RB. Does perturbing TMED10 lead to a significant change in IL2RB 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 SARS and then measure expression of PHF19. Does this perturbation cause a significant change in PHF19 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 SARS and examine the expression of PHF19. Does perturbing SARS lead to a significant change in PHF19 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, MANF is perturbed and the expression of IDH3A is measured. Determine whether IDH3A 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 RP3-465N24.6. Does this perturbation cause a significant change in RP3-465N24.6 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 SRP68, does the expression profile of RP3-465N24.6 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: 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 TIMM23, does the expression profile of REST 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 ARHGAP22 is perturbed and RGS20 expression is observed. Does this perturbation lead to a significant difference in RGS20 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 GBF1 is perturbed and NUFIP2 expression is observed. Does this perturbation lead to a significant difference in NUFIP2 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 ARHGAP22 and then measure expression of SLC25A35. Does this perturbation cause a significant change in SLC25A35 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 SEC61A1 is associated with a significant change in PCK2 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: No\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 TIMM44 is associated with a significant change in SLC27A2 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 EIF2B4 and examine the expression of DOCK11. Does perturbing EIF2B4 lead to a significant change in DOCK11 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 SEC61B is perturbed and RGS3 expression is observed. Does this perturbation lead to a significant difference in RGS3 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: 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 STT3A, does the expression profile of NPDC1 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, SCYL1 is perturbed and the expression of DST is measured. Determine whether DST 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 CAD and monitor AC008074.3 expression. Decide whether this perturbation leads to a significant alteration in AC008074.3 expression. Answer only in the format '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, SARS is perturbed and the expression of NXF1 is measured. Determine whether NXF1 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: 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, PTDSS1 is perturbed and KIAA1432 expression is quantified. Does this perturbation result in a significant change in KIAA1432 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 DERL2 and examine the expression of CENPC. Does perturbing DERL2 lead to a significant change in CENPC 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, HSPA5 is perturbed and the expression of TSC22D4 is measured. Does this perturbation cause a significant change in TSC22D4 expression? Answer strictly in the format '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 DHDDS and monitor ATF7IP2 expression. Decide whether this perturbation leads to a significant alteration in ATF7IP2 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 SEC61B is perturbed and OXLD1 expression is observed. Does this perturbation lead to a significant difference in OXLD1 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: 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, FECH is perturbed and ATAD2B expression is measured. Determine whether ATAD2B 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 HARS and examine the expression of PBDC1. Does perturbing HARS lead to a significant change in PBDC1 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, DERL2 is perturbed and CENPC expression is measured. Determine whether CENPC 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, EIF2B4 is perturbed and the expression of GDF11 is measured. Determine whether GDF11 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: 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, SLC35B1 is perturbed and the expression of TFPI is measured. Determine whether TFPI 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 MRPL39 and then measure expression of RP11-119J18.1. Does this perturbation cause a significant change in RP11-119J18.1 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 NEDD8 and then measure expression of GPRC5C. Does this perturbation cause a significant change in GPRC5C 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, SPCS3 is perturbed and LAMP2 expression is quantified. Does this perturbation result in a significant change in LAMP2 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 IARS2 and monitor KHDC1L expression. Decide whether this perturbation leads to a significant alteration in KHDC1L expression. Answer only in the format '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, DDIT3 is perturbed and the expression of PTPRC is measured. Determine whether PTPRC 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: 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, GMPPB is perturbed and TRAPPC10 expression is quantified. Does this perturbation result in a significant change in TRAPPC10 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 TMEM167A and examine the expression of CRNDE. Does perturbing TMEM167A lead to a significant change in CRNDE 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 GMPPB, does the expression profile of NFAT5 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 CCND3, does the expression profile of SNHG7 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, CAD is perturbed and the expression of RP11-434H6.6 is measured. Determine whether RP11-434H6.6 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: 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 SAMM50 is perturbed and ZEB1 expression is observed. Does this perturbation lead to a significant difference in ZEB1 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 MTHFD1 is perturbed and C12orf23 expression is observed. Does this perturbation lead to a significant difference in C12orf23 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 FOXO6 is measured. Does this perturbation cause a significant change in FOXO6 expression? Answer strictly in the format '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, KCTD16 is perturbed and CCDC69 expression is measured. Determine whether CCDC69 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, PPWD1 is perturbed and the expression of SMCO1 is measured. Determine whether SMCO1 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: 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 SEL1L and monitor RP11-381O7.3 expression. Decide whether this perturbation leads to a significant alteration in RP11-381O7.3 expression. Answer only in the format '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 DNAJC19 and monitor PAXBP1 expression. Decide whether this perturbation leads to a significant alteration in PAXBP1 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 SCYL1 is associated with a significant change in TSPAN33 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: No\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 PPWD1 and then measure expression of CTBS. Does this perturbation cause a significant change in CTBS 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 DAD1 and then measure expression of ANXA4. Does this perturbation cause a significant change in ANXA4 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 COPB1 expression is observed. Does this perturbation lead to a significant difference in COPB1 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 DARS is associated with a significant change in SPAST 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 domain expert in functional genomics. For experiments carried out in K562 cells, we perturb CHERP and examine the expression of IFT27. Does perturbing CHERP lead to a significant change in IFT27 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, TELO2 is perturbed and KLF6 expression is quantified. Does this perturbation result in a significant change in KLF6 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, UFL1 is perturbed and the expression of SLC37A1 is measured. Does this perturbation cause a significant change in SLC37A1 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 UFL1 and monitor RP11-435O5.4 expression. Decide whether this perturbation leads to a significant alteration in RP11-435O5.4 expression. Answer only in the format '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 AMIGO3 is associated with a significant change in ATF6 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, TELO2 is perturbed and the expression of ANKLE2 is measured. Does this perturbation cause a significant change in ANKLE2 expression? Answer strictly in the format '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 NEDD8 and monitor GPRC5C expression. Decide whether this perturbation leads to a significant alteration in GPRC5C 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, IARS2 is perturbed and ADAMTS10 expression is quantified. Does this perturbation result in a significant change in ADAMTS10 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 AMIGO3, does the expression profile of ESCO1 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 MTHFD1 is perturbed and ARHGAP6 expression is observed. Does this perturbation lead to a significant difference in ARHGAP6 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 LAMP2 expression is measured. Determine whether LAMP2 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, BHLHE40 is perturbed and the expression of CTSF is measured. Determine whether CTSF 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: 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 DNAJC19 and examine the expression of ANPEP. Does perturbing DNAJC19 lead to a significant change in ANPEP 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, EIF2S1 is perturbed and RP11-3D4.3 expression is measured. Determine whether RP11-3D4.3 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 PTDSS1 is perturbed and KIAA1432 expression is observed. Does this perturbation lead to a significant difference in KIAA1432 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: 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, SEC63 is perturbed and the expression of CTCFL is measured. Does this perturbation cause a significant change in CTCFL 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 SEC61B and examine the expression of PIK3IP1. Does perturbing SEC61B lead to a significant change in PIK3IP1 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, GBF1 is perturbed and the expression of UFD1L is measured. Determine whether UFD1L 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: 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 SLC39A7 and then measure expression of TXNIP. Does this perturbation cause a significant change in TXNIP 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 MANF, does the expression profile of CD83 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: 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, SAMM50 is perturbed and the expression of NUF2 is measured. Does this perturbation cause a significant change in NUF2 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, TIMM44 is perturbed and the expression of C17orf64 is measured. Does this perturbation cause a significant change in C17orf64 expression? Answer strictly in the format '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 SPCS3 is perturbed and GPR146 expression is observed. Does this perturbation lead to a significant difference in GPR146 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: 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, SEC61A1 is perturbed and the expression of LTB is measured. Does this perturbation cause a significant change in LTB 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, SLC39A7 is perturbed and PTAR1 expression is quantified. Does this perturbation result in a significant change in PTAR1 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 ZNF326 is perturbed and RP11-65L19.4 expression is observed. Does this perturbation lead to a significant difference in RP11-65L19.4 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: 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 P4HB is associated with a significant change in THBS1 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: 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 TMED10 is perturbed and SEC23IP expression is observed. Does this perturbation lead to a significant difference in SEC23IP 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 OST4 and examine the expression of DUT. Does perturbing OST4 lead to a significant change in DUT 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, GBF1 is perturbed and the expression of NUFIP2 is measured. Does this perturbation cause a significant change in NUFIP2 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, TIMM44 is perturbed and the expression of SLC27A2 is measured. Determine whether SLC27A2 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, SARS is perturbed and the expression of PHF19 is measured. Does this perturbation cause a significant change in PHF19 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 PTPN11 expression. Decide whether this perturbation leads to a significant alteration in PTPN11 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, FECH is perturbed and the expression of RP11-157D23.2 is measured. Determine whether RP11-157D23.2 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: 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 LRRC4B. Does this perturbation cause a significant change in LRRC4B 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, IARS2 is perturbed and the expression of HIST1H1E is measured. Does this perturbation cause a significant change in HIST1H1E expression? Answer strictly in the format '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 DDIT3 is perturbed and PDE9A expression is observed. Does this perturbation lead to a significant difference in PDE9A 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, SLMO2 is perturbed and the expression of PTBP3 is measured. Determine whether PTBP3 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 MTHFD1 is associated with a significant change in RPL39 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 SOCS1 and monitor DDX3X expression. Decide whether this perturbation leads to a significant alteration in DDX3X 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 TTI1 and then measure expression of GSN. Does this perturbation cause a significant change in GSN 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, SEC63 is perturbed and the expression of RP11-471M2.3 is measured. Does this perturbation cause a significant change in RP11-471M2.3 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, BHLHE40 is perturbed and the expression of NRIP1 is measured. Determine whether NRIP1 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': 'validate_answer8853', 'description': 'Task to validate_answer8853. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer8853', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer8853', 'required': True}], 'prompt': 'Your are a task solver.', 'prompt_template': None, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None, 'tools': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-13 20:01:44.463\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.027 | Total tokens: 152819 | Current cost: $0.003 | Current tokens: 14963\u001b[0m\n",
"\u001b[32m2026-01-13 20:01:44.937\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: $0.027 | Total tokens: 152915 | Current cost: $0.000 | Current tokens: 96\u001b[0m\n",
"\u001b[32m2026-01-13 20:01:45.800\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: $0.027 | Total tokens: 153472 | Current cost: $0.000 | Current tokens: 557\u001b[0m\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, 'tools': None}\n",
"\u001b[32m2026-01-13 20:01:47.395\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.030 | Total tokens: 168406 | Current cost: $0.003 | Current tokens: 14934\u001b[0m\n",
"\u001b[32m2026-01-13 20:01:47.976\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.030 | Total tokens: 168516 | Current cost: $0.000 | Current tokens: 110\u001b[0m\n",
"\u001b[32m2026-01-13 20:01:48.671\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.030 | Total tokens: 169043 | Current cost: $0.000 | Current tokens: 527\u001b[0m\n",
"{'name': 'handle_errors9808', 'description': 'Task to handle_errors9808. Takes validated_answer as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for handle_errors9808', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from handle_errors9808', 'required': True}], 'prompt': 'Your are a task solver.', 'prompt_template': None, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None, 'tools': None}\n",
"\u001b[32m2026-01-13 20:01:50.514\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.032 | Total tokens: 183981 | Current cost: $0.003 | Current tokens: 14938\u001b[0m\n",
"\u001b[32m2026-01-13 20:01:51.114\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: $0.032 | Total tokens: 184076 | Current cost: $0.000 | Current tokens: 95\u001b[0m\n",
"\u001b[32m2026-01-13 20:01:51.893\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.032 | Total tokens: 184616 | Current cost: $0.000 | Current tokens: 540\u001b[0m\n",
"{'name': 'finalize_response7276', 'description': 'Task to finalize_response7276. Takes final_answer as input. Produces response as output.', 'inputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Input parameter final_answer for finalize_response7276', 'required': False}], 'outputs': [{'name': 'response', 'type': 'str', 'description': 'Output parameter response from finalize_response7276', 'required': True}], 'prompt': 'Your are a task solver.', 'prompt_template': None, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None, 'tools': None}\n",
"\u001b[32m2026-01-13 20:01:54.097\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.035 | Total tokens: 199533 | Current cost: $0.003 | Current tokens: 14917\u001b[0m\n",
"\u001b[32m2026-01-13 20:01:54.611\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.035 | Total tokens: 199629 | Current cost: $0.000 | Current tokens: 96\u001b[0m\n",
"\u001b[32m2026-01-13 20:01:55.680\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.035 | Total tokens: 200155 | Current cost: $0.000 | Current tokens: 526\u001b[0m\n",
"\u001b[32m2026-01-13 20:01:55.682\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1054\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[32m2026-01-13 20:03:41.993\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1057\u001b[0m - \u001b[1mStep 1 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.58}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-13 20:03:43.474\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: $0.054 | Total tokens: 307148 | Current cost: $0.003 | Current tokens: 14800\u001b[0m\n",
"\u001b[32m2026-01-13 20:03:44.582\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.057 | Total tokens: 321926 | Current cost: $0.002 | Current tokens: 14778\u001b[0m\n",
"\u001b[32m2026-01-13 20:03:46.473\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.059 | Total tokens: 336713 | Current cost: $0.002 | Current tokens: 14787\u001b[0m\n",
"\u001b[32m2026-01-13 20:03:48.118\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.059 | Total tokens: 337243 | Current cost: $0.000 | Current tokens: 530\u001b[0m\n",
"The detected issues across the workflows highlight several critical problems: a lack of validation steps to ensure the accuracy of predictions before finalizing answers, resulting in a high rate of incorrect solutions; a consistent pattern of erroneous predictions suggesting flaws in the model or data processing; overly rigid response instructions that may hinder nuanced interpretations of complex questions; insufficient handling of ambiguous queries, which can lead to misleading outputs; and a lack of feedback mechanisms to learn from past errors, preventing improvements in future predictions. These factors collectively indicate a need for enhanced monitoring, flexibility in response generation, and mechanisms for learning from mistakes.\n",
"\u001b[32m2026-01-13 20:03:49.228\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.059 | Total tokens: 337853 | Current cost: $0.000 | Current tokens: 610\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': 'handle_ambiguity', 'args': ['question'], 'outputs': ['clarified_question']},\n",
" {'name': 'feedback_loop', 'args': ['validated_answer'], 'outputs': []}\n",
"]\n",
"```\n",
"\u001b[32m2026-01-13 20:03:49.231\u001b[0m | \u001b[33m\u001b[1mWARNING \u001b[0m | \u001b[36mevoagentx.workflow.workflow_graph\u001b[0m:\u001b[36m_validate_workflow_structure\u001b[0m:\u001b[36m363\u001b[0m - \u001b[33m\u001b[1mThe workflow contains isolated nodes: ['handle_ambiguity8331']\u001b[0m\n",
"Questions: Question: You are an expert in single-cell biology and functional genomics. In K562 cells, OST4 is perturbed and the expression of DOK3 is measured. Does this perturbation cause a significant change in DOK3 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, PDIA6 is perturbed and LBX1 expression is quantified. Does this perturbation result in a significant change in LBX1 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 MRGBP, does the expression profile of LRIF1 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 SLMO2 is perturbed and FAM114A1 expression is observed. Does this perturbation lead to a significant difference in FAM114A1 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: 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 GNPNAT1 and then measure expression of RP11-212I21.4. Does this perturbation cause a significant change in RP11-212I21.4 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, SRP72 is perturbed and NOX5 expression is quantified. Does this perturbation result in a significant change in NOX5 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 functional genomics specialist. In K562 cells, we perturb COPZ1 and monitor STARD9 expression. Decide whether this perturbation leads to a significant alteration in STARD9 expression. Answer only in the format '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 NBEAL2 expression is measured. Determine whether NBEAL2 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, DERL2 is perturbed and the expression of CENPC is measured. Does this perturbation cause a significant change in CENPC 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 CCND3 and then measure expression of CENPF. Does this perturbation cause a significant change in CENPF 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 MTHFD1 and then measure expression of C12orf23. Does this perturbation cause a significant change in C12orf23 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 EPB42. Does this perturbation cause a significant change in EPB42 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, CHERP is perturbed and the expression of IFT27 is measured. Does this perturbation cause a significant change in IFT27 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, PPWD1 is perturbed and CTBS expression is quantified. Does this perturbation result in a significant change in CTBS 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 SEL1L is perturbed and C12orf44 expression is observed. Does this perturbation lead to a significant difference in C12orf44 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: 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 PPWD1, does the expression profile of NAV1 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 SCYL1 and examine the expression of PTGS1. Does perturbing SCYL1 lead to a significant change in PTGS1 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, YIPF5 is perturbed and the expression of CTD-2001C12.1 is measured. Does this perturbation cause a significant change in CTD-2001C12.1 expression? Answer strictly in the format '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 TTI1 and monitor TTC32 expression. Decide whether this perturbation leads to a significant alteration in TTC32 expression. Answer only in the format '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, TTI2 is perturbed and the expression of EP300 is measured. Determine whether EP300 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, COPB1 is perturbed and the expression of RILPL2 is measured. Determine whether RILPL2 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, CCND3 is perturbed and the expression of RP1-274L7.1 is measured. Determine whether RP1-274L7.1 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: 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 P4HB, does the expression profile of CELF6 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: 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 DDIT3 is associated with a significant change in PDE9A 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 TMEM167A and monitor CRNDE expression. Decide whether this perturbation leads to a significant alteration in CRNDE expression. Answer only in the format '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 SAMM50 is perturbed and GUSB expression is observed. Does this perturbation lead to a significant difference in GUSB 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, STT3A is perturbed and RCBTB2 expression is quantified. Does this perturbation result in a significant change in RCBTB2 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 XRN1 is perturbed and MBNL1 expression is observed. Does this perturbation lead to a significant difference in MBNL1 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, DERL2 is perturbed and ACSM3 expression is quantified. Does this perturbation result in a significant change in ACSM3 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, SCYL1 is perturbed and the expression of TMEM60 is measured. Determine whether TMEM60 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: 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 DDOST is perturbed and TRPM4 expression is observed. Does this perturbation lead to a significant difference in TRPM4 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, CREB1 is perturbed and ZNF429 expression is quantified. Does this perturbation result in a significant change in ZNF429 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 DARS, does the expression profile of SPAST 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, DDRGK1 is perturbed and the expression of UBE3A is measured. Does this perturbation cause a significant change in UBE3A 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 TARS and monitor AC007038.7 expression. Decide whether this perturbation leads to a significant alteration in AC007038.7 expression. Answer only in the format '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, SEC61G is perturbed and LTB expression is quantified. Does this perturbation result in a significant change in LTB 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, SYVN1 is perturbed and LST1 expression is measured. Determine whether LST1 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 KCTD16 is associated with a significant change in ARHGAP6 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 DNAJC19 is associated with a significant change in PDE3B 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: 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 EIF2B4 and then measure expression of DOCK11. Does this perturbation cause a significant change in DOCK11 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, SPCS3 is perturbed and the expression of PCF11 is measured. Determine whether PCF11 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, EIF2B2 is perturbed and the expression of C10orf32 is measured. Determine whether C10orf32 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: 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, ARHGAP22 is perturbed and DYNC1H1 expression is measured. Determine whether DYNC1H1 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 ATP5B and monitor SERPINH1 expression. Decide whether this perturbation leads to a significant alteration in SERPINH1 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 UFL1 is perturbed and KDM1B expression is observed. Does this perturbation lead to a significant difference in KDM1B 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 DDX3X expression is measured. Determine whether DDX3X 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 SLC35B1 is associated with a significant change in ZXDA 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: 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, SRPRB is perturbed and the expression of RP11-181G12.2 is measured. Does this perturbation cause a significant change in RP11-181G12.2 expression? Answer strictly in the format '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 MRPL39, does the expression profile of RP13-216E22.4 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: 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 SEC61A1, does the expression profile of LTB 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 ARHGAP5 is measured. Does this perturbation cause a significant change in ARHGAP5 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 ARHGAP22 and monitor RGS20 expression. Decide whether this perturbation leads to a significant alteration in RGS20 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 SAMM50 is associated with a significant change in RP11-61E11.1 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: 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 UFL1 and then measure expression of SLC37A1. Does this perturbation cause a significant change in SLC37A1 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, EIF2B4 is perturbed and the expression of HMGCS1 is measured. Determine whether HMGCS1 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 ZNF326 is perturbed and RP11-141B14.1 expression is observed. Does this perturbation lead to a significant difference in RP11-141B14.1 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: 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, TMED10 is perturbed and PELO expression is measured. Determine whether PELO 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 TMED10 and examine the expression of IL2RB. Does perturbing TMED10 lead to a significant change in IL2RB 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 SARS and then measure expression of PHF19. Does this perturbation cause a significant change in PHF19 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 SARS and examine the expression of PHF19. Does perturbing SARS lead to a significant change in PHF19 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, MANF is perturbed and the expression of IDH3A is measured. Determine whether IDH3A 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 RP3-465N24.6. Does this perturbation cause a significant change in RP3-465N24.6 expression? Reply only in the form 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: No\n",
"Solutions: No\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 SRP68, does the expression profile of RP3-465N24.6 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: 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 TIMM23, does the expression profile of REST 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 ARHGAP22 is perturbed and RGS20 expression is observed. Does this perturbation lead to a significant difference in RGS20 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 GBF1 is perturbed and NUFIP2 expression is observed. Does this perturbation lead to a significant difference in NUFIP2 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 ARHGAP22 and then measure expression of SLC25A35. Does this perturbation cause a significant change in SLC25A35 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 SEC61A1 is associated with a significant change in PCK2 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: No\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 TIMM44 is associated with a significant change in SLC27A2 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 domain expert in functional genomics. For experiments carried out in K562 cells, we perturb EIF2B4 and examine the expression of DOCK11. Does perturbing EIF2B4 lead to a significant change in DOCK11 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 SEC61B is perturbed and RGS3 expression is observed. Does this perturbation lead to a significant difference in RGS3 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: 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 STT3A, does the expression profile of NPDC1 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, SCYL1 is perturbed and the expression of DST is measured. Determine whether DST 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 CAD and monitor AC008074.3 expression. Decide whether this perturbation leads to a significant alteration in AC008074.3 expression. Answer only in the format '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, SARS is perturbed and the expression of NXF1 is measured. Determine whether NXF1 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: 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, PTDSS1 is perturbed and KIAA1432 expression is quantified. Does this perturbation result in a significant change in KIAA1432 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 DERL2 and examine the expression of CENPC. Does perturbing DERL2 lead to a significant change in CENPC 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, HSPA5 is perturbed and the expression of TSC22D4 is measured. Does this perturbation cause a significant change in TSC22D4 expression? Answer strictly in the format '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 DHDDS and monitor ATF7IP2 expression. Decide whether this perturbation leads to a significant alteration in ATF7IP2 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 SEC61B is perturbed and OXLD1 expression is observed. Does this perturbation lead to a significant difference in OXLD1 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: 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, FECH is perturbed and ATAD2B expression is measured. Determine whether ATAD2B 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 HARS and examine the expression of PBDC1. Does perturbing HARS lead to a significant change in PBDC1 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, DERL2 is perturbed and CENPC expression is measured. Determine whether CENPC 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, EIF2B4 is perturbed and the expression of GDF11 is measured. Determine whether GDF11 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: 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, SLC35B1 is perturbed and the expression of TFPI is measured. Determine whether TFPI 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 MRPL39 and then measure expression of RP11-119J18.1. Does this perturbation cause a significant change in RP11-119J18.1 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 NEDD8 and then measure expression of GPRC5C. Does this perturbation cause a significant change in GPRC5C 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, SPCS3 is perturbed and LAMP2 expression is quantified. Does this perturbation result in a significant change in LAMP2 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 a functional genomics specialist. In K562 cells, we perturb IARS2 and monitor KHDC1L expression. Decide whether this perturbation leads to a significant alteration in KHDC1L expression. Answer only in the format '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, DDIT3 is perturbed and the expression of PTPRC is measured. Determine whether PTPRC 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: 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, GMPPB is perturbed and TRAPPC10 expression is quantified. Does this perturbation result in a significant change in TRAPPC10 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 TMEM167A and examine the expression of CRNDE. Does perturbing TMEM167A lead to a significant change in CRNDE 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 GMPPB, does the expression profile of NFAT5 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 CCND3, does the expression profile of SNHG7 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, CAD is perturbed and the expression of RP11-434H6.6 is measured. Determine whether RP11-434H6.6 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: 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 SAMM50 is perturbed and ZEB1 expression is observed. Does this perturbation lead to a significant difference in ZEB1 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 MTHFD1 is perturbed and C12orf23 expression is observed. Does this perturbation lead to a significant difference in C12orf23 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 FOXO6 is measured. Does this perturbation cause a significant change in FOXO6 expression? Answer strictly in the format '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, KCTD16 is perturbed and CCDC69 expression is measured. Determine whether CCDC69 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, PPWD1 is perturbed and the expression of SMCO1 is measured. Determine whether SMCO1 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: 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 SEL1L and monitor RP11-381O7.3 expression. Decide whether this perturbation leads to a significant alteration in RP11-381O7.3 expression. Answer only in the format '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 DNAJC19 and monitor PAXBP1 expression. Decide whether this perturbation leads to a significant alteration in PAXBP1 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 SCYL1 is associated with a significant change in TSPAN33 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: No\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 PPWD1 and then measure expression of CTBS. Does this perturbation cause a significant change in CTBS 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 DAD1 and then measure expression of ANXA4. Does this perturbation cause a significant change in ANXA4 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 COPB1 expression is observed. Does this perturbation lead to a significant difference in COPB1 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 DARS is associated with a significant change in SPAST 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 domain expert in functional genomics. For experiments carried out in K562 cells, we perturb CHERP and examine the expression of IFT27. Does perturbing CHERP lead to a significant change in IFT27 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, TELO2 is perturbed and KLF6 expression is quantified. Does this perturbation result in a significant change in KLF6 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, UFL1 is perturbed and the expression of SLC37A1 is measured. Does this perturbation cause a significant change in SLC37A1 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 UFL1 and monitor RP11-435O5.4 expression. Decide whether this perturbation leads to a significant alteration in RP11-435O5.4 expression. Answer only in the format '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 AMIGO3 is associated with a significant change in ATF6 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, TELO2 is perturbed and the expression of ANKLE2 is measured. Does this perturbation cause a significant change in ANKLE2 expression? Answer strictly in the format '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 NEDD8 and monitor GPRC5C expression. Decide whether this perturbation leads to a significant alteration in GPRC5C 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, IARS2 is perturbed and ADAMTS10 expression is quantified. Does this perturbation result in a significant change in ADAMTS10 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 AMIGO3, does the expression profile of ESCO1 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 MTHFD1 is perturbed and ARHGAP6 expression is observed. Does this perturbation lead to a significant difference in ARHGAP6 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 LAMP2 expression is measured. Determine whether LAMP2 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, BHLHE40 is perturbed and the expression of CTSF is measured. Determine whether CTSF 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: 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 DNAJC19 and examine the expression of ANPEP. Does perturbing DNAJC19 lead to a significant change in ANPEP 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, EIF2S1 is perturbed and RP11-3D4.3 expression is measured. Determine whether RP11-3D4.3 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 PTDSS1 is perturbed and KIAA1432 expression is observed. Does this perturbation lead to a significant difference in KIAA1432 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: 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, SEC63 is perturbed and the expression of CTCFL is measured. Does this perturbation cause a significant change in CTCFL 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 SEC61B and examine the expression of PIK3IP1. Does perturbing SEC61B lead to a significant change in PIK3IP1 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, GBF1 is perturbed and the expression of UFD1L is measured. Determine whether UFD1L 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: 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 SLC39A7 and then measure expression of TXNIP. Does this perturbation cause a significant change in TXNIP 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 MANF, does the expression profile of CD83 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: 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, SAMM50 is perturbed and the expression of NUF2 is measured. Does this perturbation cause a significant change in NUF2 expression? Answer strictly in the format '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 single-cell biology and functional genomics. In K562 cells, TIMM44 is perturbed and the expression of C17orf64 is measured. Does this perturbation cause a significant change in C17orf64 expression? Answer strictly in the format 'Final Answer: Yes' or 'Final Answer: No'.\n",
"\n",
"Answer:\n",
"Predictions: Final Answer: No\n",
"Solutions: No\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 SPCS3 is perturbed and GPR146 expression is observed. Does this perturbation lead to a significant difference in GPR146 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: 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, SEC61A1 is perturbed and the expression of LTB is measured. Does this perturbation cause a significant change in LTB 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, SLC39A7 is perturbed and PTAR1 expression is quantified. Does this perturbation result in a significant change in PTAR1 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 ZNF326 is perturbed and RP11-65L19.4 expression is observed. Does this perturbation lead to a significant difference in RP11-65L19.4 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: 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 P4HB is associated with a significant change in THBS1 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: 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 TMED10 is perturbed and SEC23IP expression is observed. Does this perturbation lead to a significant difference in SEC23IP 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 OST4 and examine the expression of DUT. Does perturbing OST4 lead to a significant change in DUT 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, GBF1 is perturbed and the expression of NUFIP2 is measured. Does this perturbation cause a significant change in NUFIP2 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, TIMM44 is perturbed and the expression of SLC27A2 is measured. Determine whether SLC27A2 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 single-cell biology and functional genomics. In K562 cells, SARS is perturbed and the expression of PHF19 is measured. Does this perturbation cause a significant change in PHF19 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 PTPN11 expression. Decide whether this perturbation leads to a significant alteration in PTPN11 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, FECH is perturbed and the expression of RP11-157D23.2 is measured. Determine whether RP11-157D23.2 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: 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 LRRC4B. Does this perturbation cause a significant change in LRRC4B 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, IARS2 is perturbed and the expression of HIST1H1E is measured. Does this perturbation cause a significant change in HIST1H1E 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 DDIT3 is perturbed and PDE9A expression is observed. Does this perturbation lead to a significant difference in PDE9A 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, SLMO2 is perturbed and the expression of PTBP3 is measured. Determine whether PTBP3 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 MTHFD1 is associated with a significant change in RPL39 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 SOCS1 and monitor DDX3X expression. Decide whether this perturbation leads to a significant alteration in DDX3X 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 TTI1 and then measure expression of GSN. Does this perturbation cause a significant change in GSN 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, SEC63 is perturbed and the expression of RP11-471M2.3 is measured. Does this perturbation cause a significant change in RP11-471M2.3 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, BHLHE40 is perturbed and the expression of NRIP1 is measured. Determine whether NRIP1 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, 'tools': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-13 20:03:51.548\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.062 | Total tokens: 352812 | Current cost: $0.003 | Current tokens: 14959\u001b[0m\n",
"\u001b[32m2026-01-13 20:03:52.074\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.062 | Total tokens: 352916 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-13 20:03:52.900\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.062 | Total tokens: 353542 | Current cost: $0.000 | Current tokens: 626\u001b[0m\n",
"{'name': 'validate_answer6014', 'description': 'Task to validate_answer6014. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer6014', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer6014', 'required': True}], 'prompt': 'Your are a task solver.', 'prompt_template': None, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None, 'tools': None}\n",
"\u001b[32m2026-01-13 20:03:54.536\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: $0.065 | Total tokens: 368488 | Current cost: $0.003 | Current tokens: 14946\u001b[0m\n",
"\u001b[32m2026-01-13 20:03:55.148\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.065 | Total tokens: 368594 | Current cost: $0.000 | Current tokens: 106\u001b[0m\n",
"\u001b[32m2026-01-13 20:03:56.108\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.065 | Total tokens: 369140 | Current cost: $0.000 | Current tokens: 546\u001b[0m\n",
"{'name': 'handle_ambiguity8331', 'description': 'Task to handle_ambiguity8331. Takes question as input. Produces clarified_question as output.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'Input parameter question for handle_ambiguity8331', 'required': False}], 'outputs': [{'name': 'clarified_question', 'type': 'str', 'description': 'Output parameter clarified_question from handle_ambiguity8331', 'required': True}], 'prompt': 'Your are a task solver.', 'prompt_template': None, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None, 'tools': None}\n",
"\u001b[32m2026-01-13 20:03:57.762\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: $0.067 | Total tokens: 384076 | Current cost: $0.003 | Current tokens: 14936\u001b[0m\n",
"\u001b[32m2026-01-13 20:03:58.319\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.067 | Total tokens: 384181 | Current cost: $0.000 | Current tokens: 105\u001b[0m\n",
"\u001b[32m2026-01-13 20:03:59.207\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.068 | Total tokens: 384729 | Current cost: $0.000 | Current tokens: 548\u001b[0m\n",
"{'name': 'feedback_loop4264', 'description': 'Task to feedback_loop4264. Takes validated_answer as input. ', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for feedback_loop4264', 'required': False}], 'outputs': [], 'prompt': 'Your are a task solver.', 'prompt_template': None, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None, 'tools': None}\n",
"\u001b[32m2026-01-13 20:04:01.124\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.070 | Total tokens: 399688 | Current cost: $0.003 | Current tokens: 14959\u001b[0m\n",
"\u001b[32m2026-01-13 20:04:01.830\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.070 | Total tokens: 399815 | Current cost: $0.000 | Current tokens: 127\u001b[0m\n",
"\u001b[32m2026-01-13 20:04:02.973\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: $0.070 | Total tokens: 400441 | Current cost: $0.000 | Current tokens: 626\u001b[0m\n",
"\u001b[32m2026-01-13 20:04:02.976\u001b[0m | \u001b[33m\u001b[1mWARNING \u001b[0m | \u001b[36mevoagentx.workflow.workflow_graph\u001b[0m:\u001b[36m_validate_workflow_structure\u001b[0m:\u001b[36m363\u001b[0m - \u001b[33m\u001b[1mThe workflow contains isolated nodes: ['handle_ambiguity8331']\u001b[0m\n",
"\u001b[32m2026-01-13 20:04:02.976\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1054\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"
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"output_type": "stream",
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"\r",
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]
},
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"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
},
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"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 92%|█████████▏| 46/50 [00:32<00:02, 1.39it/s]"
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"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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"\r",
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
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"\r",
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"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
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"output_type": "stream",
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n",
"\u001b[32m2026-01-13 20:04:38.335\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1057\u001b[0m - \u001b[1mStep 2 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.46}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-13 20:04:40.003\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.078 | Total tokens: 445981 | Current cost: $0.003 | Current tokens: 14811\u001b[0m\n",
"\u001b[32m2026-01-13 20:04:41.082\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.081 | Total tokens: 460757 | Current cost: $0.002 | Current tokens: 14776\u001b[0m\n",
"\u001b[32m2026-01-13 20:04:42.519\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.083 | Total tokens: 475557 | Current cost: $0.003 | Current tokens: 14800\u001b[0m\n",
"\u001b[32m2026-01-13 20:04:43.924\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.083 | Total tokens: 476122 | Current cost: $0.000 | Current tokens: 565\u001b[0m\n",
"The identified issues across the workflows highlight several critical shortcomings: a lack of validation steps to confirm prediction accuracy, resulting in multiple incorrect solutions; a simplistic control flow that fails to accommodate the complexity of biological data interpretation; and rigid output formats that restrict nuanced responses. Additionally, there is no mechanism for error reporting or handling, which could aid in identifying computational issues. The workflows also exhibit a tendency for cascading errors due to flawed control logic and an over-reliance on a single answer generation step without intermediate checks. Lastly, the ambiguity in prompts and the absence of feedback mechanisms hinder the ability to learn from past mistakes, further complicating the accuracy of predictions.\n",
"\u001b[32m2026-01-13 20:04:45.329\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.084 | Total tokens: 476753 | Current cost: $0.000 | Current tokens: 631\u001b[0m\n",
"```python\n",
"steps = [\n",
" {'name': 'generate_answer', 'args': ['question'], 'outputs': ['answer']},\n",
" {'name': 'validate_answer', 'args': ['answer'], 'outputs': ['is_valid']},\n",
" {'name': 'error_handling', 'args': ['is_valid'], 'outputs': ['error_report']},\n",
" {'name': 'feedback_mechanism', 'args': ['question', 'answer', 'error_report'], 'outputs': ['feedback']}\n",
"]\n",
"```\n",
"Questions: Question: You are a specialist in gene perturbation experiments. In K562 cells, we introduce a perturbation to EIF2B3 and then measure expression of BOLA3. Does this perturbation cause a significant change in BOLA3 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, SRPR is perturbed and ERV3-1 expression is quantified. Does this perturbation result in a significant change in ERV3-1 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 DARS and examine the expression of RP11-863K10.7. Does perturbing DARS lead to a significant change in RP11-863K10.7 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, SRP68 is perturbed and the expression of CCRL2 is measured. Does this perturbation cause a significant change in CCRL2 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 ANKLE2 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: 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 RP11-685N10.1 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: 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 ZNF326 and examine the expression of NBEAL2. Does perturbing ZNF326 lead to a significant change in NBEAL2 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 FECH, does the expression profile of AC005540.3 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: 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 SEC61B and monitor PIK3IP1 expression. Decide whether this perturbation leads to a significant alteration in PIK3IP1 expression. Answer only in the format '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 SRPRB and examine the expression of NOSTRIN. Does perturbing SRPRB lead to a significant change in NOSTRIN 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 SRP72 and examine the expression of LIMS1. Does perturbing SRP72 lead to a significant change in LIMS1 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 SEC63, does the expression profile of KIF4A 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 CHERP and monitor IFT27 expression. Decide whether this perturbation leads to a significant alteration in IFT27 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 S100A10 expression is measured. Determine whether S100A10 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, CREB1 is perturbed and the expression of P4HA2 is measured. Determine whether P4HA2 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 TARS is perturbed and AC007038.7 expression is observed. Does this perturbation lead to a significant difference in AC007038.7 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: 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 FECH is associated with a significant change in RP11-157D23.2 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: 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 SPCS3 is perturbed and ERP29 expression is observed. Does this perturbation lead to a significant difference in ERP29 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: 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, PSMD4 is perturbed and the expression of AP000688.8 is measured. Does this perturbation cause a significant change in AP000688.8 expression? Answer strictly in the format '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 COPB1 is perturbed and CTD-2020K17.1 expression is observed. Does this perturbation lead to a significant difference in CTD-2020K17.1 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: 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, HYOU1 is perturbed and the expression of PLA2G15 is measured. Does this perturbation cause a significant change in PLA2G15 expression? Answer strictly in the format '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 XRN1 is perturbed and MBNL1 expression is observed. Does this perturbation lead to a significant difference in MBNL1 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, SEL1L is perturbed and the expression of CTD-2267D19.3 is measured. Does this perturbation cause a significant change in CTD-2267D19.3 expression? Answer strictly in the format '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 ATP5B, does the expression profile of RP11-247A12.2 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: 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 SARS and then measure expression of GNPTG. Does this perturbation cause a significant change in GNPTG 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 EIF2S1, does the expression profile of TIPARP 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 SRP72 and monitor LIMS1 expression. Decide whether this perturbation leads to a significant alteration in LIMS1 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 GPR146 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: 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, DAD1 is perturbed and the expression of HLA-AS1 is measured. Determine whether HLA-AS1 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: 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, BHLHE40 is perturbed and the expression of CTSF is measured. Does this perturbation cause a significant change in CTSF expression? Answer strictly in the format '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 SEC61A1, does the expression profile of LTB 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 TIMM44, does the expression profile of ZC3H7A 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, TTI2 is perturbed and the expression of RTN2 is measured. Determine whether RTN2 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, EIF2S1 is perturbed and SOBP expression is measured. Determine whether SOBP 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 TTI2 is perturbed and PGM3 expression is observed. Does this perturbation lead to a significant difference in PGM3 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: 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 ATP5B and examine the expression of RP11-247A12.2. Does perturbing ATP5B lead to a significant change in RP11-247A12.2 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, SRP72 is perturbed and the expression of LIMS1 is measured. Determine whether LIMS1 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, MRPL39 is perturbed and the expression of RP13-216E22.4 is measured. Does this perturbation cause a significant change in RP13-216E22.4 expression? Answer strictly in the format '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, DDOST is perturbed and the expression of PHF21A is measured. Determine whether PHF21A 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 GBF1, does the expression profile of SETX 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 MRPL39 is associated with a significant change in MANF 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, HSPA5 is perturbed and GS1-166A23.1 expression is quantified. Does this perturbation result in a significant change in GS1-166A23.1 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: No\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, UFL1 is perturbed and the expression of SLC37A1 is measured. Does this perturbation cause a significant change in SLC37A1 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, SLMO2 is perturbed and FAM114A1 expression is measured. Determine whether FAM114A1 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, GMPPB is perturbed and the expression of TRAPPC10 is measured. Does this perturbation cause a significant change in TRAPPC10 expression? Answer strictly in the format '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 TFPI. Does perturbing SLC35B1 lead to a significant change in TFPI 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, YIPF5 is perturbed and the expression of PCF11 is measured. Determine whether PCF11 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 MANF, does the expression profile of ASPM 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 STT3A and examine the expression of TAGLN. Does perturbing STT3A lead to a significant change in TAGLN 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 EPB42. Does this perturbation cause a significant change in EPB42 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.\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, 'tools': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-13 20:04:47.214\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: $0.085 | Total tokens: 482104 | Current cost: $0.001 | Current tokens: 5351\u001b[0m\n",
"\u001b[32m2026-01-13 20:04:47.766\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.085 | Total tokens: 482208 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-13 20:04:48.591\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: $0.085 | Total tokens: 482894 | Current cost: $0.000 | Current tokens: 686\u001b[0m\n",
"{'name': 'validate_answer9860', 'description': 'Task to validate_answer9860. Takes answer as input. Produces is_valid as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer9860', 'required': False}], 'outputs': [{'name': 'is_valid', 'type': 'str', 'description': 'Output parameter is_valid from validate_answer9860', 'required': True}], 'prompt': 'Your are a task solver.', 'prompt_template': None, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None, 'tools': None}\n",
"\u001b[32m2026-01-13 20:04:50.008\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: $0.086 | Total tokens: 488231 | Current cost: $0.001 | Current tokens: 5337\u001b[0m\n",
"\u001b[32m2026-01-13 20:04:50.559\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.086 | Total tokens: 488331 | Current cost: $0.000 | Current tokens: 100\u001b[0m\n",
"\u001b[32m2026-01-13 20:04:52.390\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.086 | Total tokens: 488948 | Current cost: $0.000 | Current tokens: 617\u001b[0m\n",
"{'name': 'error_handling5681', 'description': 'Task to error_handling5681. Takes is_valid as input. Produces error_report as output.', 'inputs': [{'name': 'is_valid', 'type': 'str', 'description': 'Input parameter is_valid for error_handling5681', 'required': False}], 'outputs': [{'name': 'error_report', 'type': 'str', 'description': 'Output parameter error_report from error_handling5681', 'required': True}], 'prompt': 'Your are a task solver.', 'prompt_template': None, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None, 'tools': None}\n",
"\u001b[32m2026-01-13 20:04:53.854\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.087 | Total tokens: 494282 | Current cost: $0.001 | Current tokens: 5334\u001b[0m\n",
"\u001b[32m2026-01-13 20:04:54.281\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: $0.087 | Total tokens: 494375 | Current cost: $0.000 | Current tokens: 93\u001b[0m\n",
"\u001b[32m2026-01-13 20:04:56.816\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.087 | Total tokens: 494954 | Current cost: $0.000 | Current tokens: 579\u001b[0m\n",
"{'name': 'feedback_mechanism7380', 'description': 'Task to feedback_mechanism7380. Takes question, answer, error_report as input. Produces feedback as output.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'Input parameter question for feedback_mechanism7380', 'required': False}, {'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for feedback_mechanism7380', 'required': False}, {'name': 'error_report', 'type': 'str', 'description': 'Input parameter error_report for feedback_mechanism7380', 'required': False}], 'outputs': [{'name': 'feedback', 'type': 'str', 'description': 'Output parameter feedback from feedback_mechanism7380', 'required': True}], 'prompt': 'Your are a task solver.', 'prompt_template': None, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None, 'tools': None}\n",
"\u001b[32m2026-01-13 20:04:58.470\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: $0.088 | Total tokens: 500281 | Current cost: $0.001 | Current tokens: 5327\u001b[0m\n",
"\u001b[32m2026-01-13 20:04:59.270\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.088 | Total tokens: 500386 | Current cost: $0.000 | Current tokens: 105\u001b[0m\n",
"\u001b[32m2026-01-13 20:05:00.128\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.088 | Total tokens: 500935 | Current cost: $0.000 | Current tokens: 549\u001b[0m\n",
"\u001b[32m2026-01-13 20:05:00.130\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1054\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"
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]
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"text": [
"\r",
"Evaluating workflow: 82%|████████▏ | 41/50 [00:30<00:06, 1.40it/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: 84%|████████▍ | 42/50 [00:31<00:05, 1.45it/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: 86%|████████▌ | 43/50 [00:31<00:04, 1.42it/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: 88%|████████▊ | 44/50 [00:32<00:04, 1.44it/s]"
]
},
{
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"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
},
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"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 90%|█████████ | 45/50 [00:33<00:03, 1.37it/s]"
]
},
{
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"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 92%|█████████▏| 46/50 [00:33<00:02, 1.37it/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 [00:34<00:02, 1.40it/s]"
]
},
{
"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": [
"\r",
"Evaluating workflow: 96%|█████████▌| 48/50 [00:35<00:01, 1.42it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
},
{
"name": "stderr",
"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"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Evaluating workflow: 100%|██████████| 50/50 [00:36<00:00, 1.36it/s]"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n",
"\u001b[32m2026-01-13 20:05:36.869\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1057\u001b[0m - \u001b[1mStep 3 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.56}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-13 20:05:38.316\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: $0.096 | Total tokens: 546434 | Current cost: $0.003 | Current tokens: 14792\u001b[0m\n",
"\u001b[32m2026-01-13 20:05:40.224\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.099 | Total tokens: 561241 | Current cost: $0.003 | Current tokens: 14807\u001b[0m\n",
"\u001b[32m2026-01-13 20:05:41.824\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.101 | Total tokens: 576062 | Current cost: $0.003 | Current tokens: 14821\u001b[0m\n",
"\u001b[32m2026-01-13 20:05:43.405\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.101 | Total tokens: 576664 | Current cost: $0.000 | Current tokens: 602\u001b[0m\n",
"The detected issues across the workflows highlight several critical shortcomings: a lack of validation steps to confirm prediction accuracy, leading to multiple incorrect outcomes; a flawed control flow that fails to cross-verify predictions against known results or significance thresholds; and overly rigid or ambiguous prompt instructions that restrict nuanced responses and may result in misinterpretations. Additionally, there is a repetitive pattern of incorrect predictions suggesting systemic issues with the underlying model or data processing, as well as a failure to incorporate feedback mechanisms for learning from past errors. Furthermore, the absence of error reporting and inadequate handling of ambiguous queries contribute to misleading conclusions, while strict adherence to a simplistic answer format risks oversimplifying complex biological contexts.\n",
"\u001b[32m2026-01-13 20:05:44.441\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.101 | Total tokens: 577268 | Current cost: $0.000 | Current tokens: 604\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': 'cross_verify', 'args': ['validated_answer'], 'outputs': ['final_answer']}\n",
"]\n",
"```\n",
"Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb SOCS1 and monitor ZNF280B expression. Decide whether this perturbation leads to a significant alteration in ZNF280B 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 MTHFD1 is associated with a significant change in SDF4 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: 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, PSMD4 is perturbed and EXOC3L2 expression is quantified. Does this perturbation result in a significant change in EXOC3L2 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, GNPNAT1 is perturbed and the expression of KLF3 is measured. Determine whether KLF3 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, EIF2B2 is perturbed and the expression of RP11-363D14.1 is measured. Does this perturbation cause a significant change in RP11-363D14.1 expression? Answer strictly in the format '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, EIF2S1 is perturbed and the expression of KCNJ13 is measured. Does this perturbation cause a significant change in KCNJ13 expression? Answer strictly in the format '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, IARS2 is perturbed and the expression of KHDC1L is measured. Determine whether KHDC1L 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: No\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 CLDN11. Does this perturbation cause a significant change in CLDN11 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 AMIGO3 and monitor GATA3 expression. Decide whether this perturbation leads to a significant alteration in GATA3 expression. Answer only in the format '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 FARSB and examine the expression of RNF139-AS1. Does perturbing FARSB lead to a significant change in RNF139-AS1 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, SRP72 is perturbed and SETX expression is quantified. Does this perturbation result in a significant change in SETX 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 IER3IP1 is associated with a significant change in VIM-AS1 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 HSPA9 is perturbed and FYTTD1 expression is observed. Does this perturbation lead to a significant difference in FYTTD1 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, CREB1 is perturbed and the expression of LPAR5 is measured. Determine whether LPAR5 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: 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 STT3A, does the expression profile of ZNF678 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: 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 ZNF326 is associated with a significant change in RP11-65L19.4 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: 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 HSPA9 is associated with a significant change in PPP4R2 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: No\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 PDIA6, does the expression profile of NFE2L3 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 MANF and examine the expression of ASPM. Does perturbing MANF lead to a significant change in ASPM 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, HYOU1 is perturbed and the expression of POLR2J3 is measured. Determine whether POLR2J3 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 CREB1 is perturbed and P4HA2 expression is observed. Does this perturbation lead to a significant difference in P4HA2 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 EIF2B3 and monitor KIAA1586 expression. Decide whether this perturbation leads to a significant alteration in KIAA1586 expression. Answer only in the format '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, TARS is perturbed and RP11-499F3.2 expression is measured. Determine whether RP11-499F3.2 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, TMED10 is perturbed and PELO expression is measured. Determine whether PELO 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 SPCS2, does the expression profile of GATA2 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 FARSB, does the expression profile of RNF139-AS1 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, PSMD4 is perturbed and EXOC3L2 expression is measured. Determine whether EXOC3L2 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, HSPA9 is perturbed and IL13RA1 expression is measured. Determine whether IL13RA1 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 QARS and then measure expression of RP11-573D15.9. Does this perturbation cause a significant change in RP11-573D15.9 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 SOCS1, does the expression profile of ZNF280B 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, SCYL1 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 expression analysis. For K562 cells, assess whether perturbation of HSD17B12 is associated with a significant change in RILPL2 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: 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 CARS and examine the expression of WARS. Does perturbing CARS lead to a significant change in WARS 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 IER3IP1 and examine the expression of PTPN11. Does perturbing IER3IP1 lead to a significant change in PTPN11 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 OST4 and then measure expression of LINC00657. Does this perturbation cause a significant change in LINC00657 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 DDOST is perturbed and TRPM4 expression is observed. Does this perturbation lead to a significant difference in TRPM4 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 TIMM23 is associated with a significant change in REST 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, GMPPB is perturbed and LTBP1 expression is quantified. Does this perturbation result in a significant change in LTBP1 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 FARSB and monitor ZP3 expression. Decide whether this perturbation leads to a significant alteration in ZP3 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 YIPF5 and then measure expression of OPTN. Does this perturbation cause a significant change in OPTN 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, SEL1L is perturbed and the expression of CTD-2267D19.3 is measured. Determine whether CTD-2267D19.3 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: 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, DAD1 is perturbed and JUND expression is quantified. Does this perturbation result in a significant change in JUND 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, CARS is perturbed and CHD3 expression is quantified. Does this perturbation result in a significant change in CHD3 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 functional genomics specialist. In K562 cells, we perturb DARS and monitor RP11-863K10.7 expression. Decide whether this perturbation leads to a significant alteration in RP11-863K10.7 expression. Answer only in the format '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, TMED2 is perturbed and the expression of TMEM60 is measured. Does this perturbation cause a significant change in TMEM60 expression? Answer strictly in the format '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 PTPN11 expression. Decide whether this perturbation leads to a significant alteration in PTPN11 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 HSPA5 and monitor TSC22D4 expression. Decide whether this perturbation leads to a significant alteration in TSC22D4 expression. Answer only in the format '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 FECH is associated with a significant change in HERPUD1 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: 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 HYOU1 and then measure expression of RP11-445H22.3. Does this perturbation cause a significant change in RP11-445H22.3 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, AMIGO3 is perturbed and the expression of RSL24D1 is measured. Does this perturbation cause a significant change in RSL24D1 expression? Answer strictly in the format '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': 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, 'tools': None}\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-13 20:05:45.966\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.102 | Total tokens: 582545 | Current cost: $0.001 | Current tokens: 5277\u001b[0m\n",
"\u001b[32m2026-01-13 20:05:46.515\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.102 | Total tokens: 582642 | Current cost: $0.000 | Current tokens: 97\u001b[0m\n",
"\u001b[32m2026-01-13 20:05:47.421\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.103 | Total tokens: 583355 | Current cost: $0.000 | Current tokens: 713\u001b[0m\n",
"{'name': 'validate_answer8904', 'description': 'Task to validate_answer8904. Takes answer as input. Produces validated_answer as output.', 'inputs': [{'name': 'answer', 'type': 'str', 'description': 'Input parameter answer for validate_answer8904', 'required': False}], 'outputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Output parameter validated_answer from validate_answer8904', 'required': True}], 'prompt': 'Your are a task solver.', 'prompt_template': None, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None, 'tools': None}\n",
"\u001b[32m2026-01-13 20:05:48.813\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.104 | Total tokens: 588624 | Current cost: $0.001 | Current tokens: 5269\u001b[0m\n",
"\u001b[32m2026-01-13 20:05:49.411\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.104 | Total tokens: 588725 | Current cost: $0.000 | Current tokens: 101\u001b[0m\n",
"\u001b[32m2026-01-13 20:05:51.799\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.104 | Total tokens: 589278 | Current cost: $0.000 | Current tokens: 553\u001b[0m\n",
"{'name': 'cross_verify5091', 'description': 'Task to cross_verify5091. Takes validated_answer as input. Produces final_answer as output.', 'inputs': [{'name': 'validated_answer', 'type': 'str', 'description': 'Input parameter validated_answer for cross_verify5091', 'required': False}], 'outputs': [{'name': 'final_answer', 'type': 'str', 'description': 'Output parameter final_answer from cross_verify5091', 'required': True}], 'prompt': 'Your are a task solver.', 'prompt_template': None, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None, 'tools': None}\n",
"\u001b[32m2026-01-13 20:05:53.389\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.105 | Total tokens: 594539 | Current cost: $0.001 | Current tokens: 5261\u001b[0m\n",
"\u001b[32m2026-01-13 20:05:53.952\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.105 | Total tokens: 594643 | Current cost: $0.000 | Current tokens: 104\u001b[0m\n",
"\u001b[32m2026-01-13 20:05:55.145\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: $0.105 | Total tokens: 595163 | Current cost: $0.000 | Current tokens: 520\u001b[0m\n",
"\u001b[32m2026-01-13 20:05:55.146\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1054\u001b[0m - \u001b[1mEvaluate the workflow at step 4 ...\u001b[0m\n"
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]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
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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"
]
},
{
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"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 86%|████████▌ | 43/50 [00:32<00:05, 1.31it/s]"
]
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"output_type": "stream",
"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
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"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
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"text": [
"\r",
"Evaluating workflow: 92%|█████████▏| 46/50 [00:35<00:03, 1.16it/s]"
]
},
{
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"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': 0.0}\n"
]
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
]
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"text": [
"\r",
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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",
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n",
"\u001b[32m2026-01-13 20:06:33.489\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1057\u001b[0m - \u001b[1mStep 4 metrics: {'f1': 0.0, 'em': 0.0, 'acc': 0.56}\u001b[0m\n",
"randomly update dataset\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-13 20:06:34.912\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.113 | Total tokens: 640629 | Current cost: $0.002 | Current tokens: 14776\u001b[0m\n",
"\u001b[32m2026-01-13 20:06:36.468\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.115 | Total tokens: 655429 | Current cost: $0.003 | Current tokens: 14800\u001b[0m\n",
"\u001b[32m2026-01-13 20:06:38.018\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.118 | Total tokens: 670220 | Current cost: $0.003 | Current tokens: 14791\u001b[0m\n",
"\u001b[32m2026-01-13 20:06:39.161\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: $0.118 | Total tokens: 670745 | Current cost: $0.000 | Current tokens: 525\u001b[0m\n",
"The detected issues across the workflows highlight several critical shortcomings: a lack of validation steps to ensure prediction accuracy, resulting in numerous incorrect solutions; a recurring pattern of errors suggesting flaws in the underlying model or data processing; and insufficient handling of ambiguous or misleading question phrasing, which can lead to misinterpretation. Additionally, the rigid prompt instructions may cause confusion, and the linear control flow fails to incorporate feedback mechanisms for continuous improvement. Overall, these systemic issues indicate a need for enhanced robustness, flexibility, and validation within the workflows to improve accuracy and reliability.\n",
"\u001b[32m2026-01-13 20:06:40.144\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.118 | Total tokens: 671303 | Current cost: $0.000 | Current tokens: 558\u001b[0m\n",
"```python\n",
"steps = [\n",
" {'name': 'validate_question', 'args': ['question'], 'outputs': ['validated_question']},\n",
" {'name': 'generate_answer', 'args': ['validated_question'], 'outputs': ['answer']}\n",
"]\n",
"```\n",
"\u001b[32m2026-01-13 20:06:40.146\u001b[0m | \u001b[33m\u001b[1mWARNING \u001b[0m | \u001b[36mevoagentx.workflow.workflow_graph\u001b[0m:\u001b[36m_validate_workflow_structure\u001b[0m:\u001b[36m363\u001b[0m - \u001b[33m\u001b[1mThe workflow contains isolated nodes: ['validate_question4633', 'generate_answer']\u001b[0m\n",
"Questions: Question: You are an expert analyst of perturbation datasets. For K562 cells subjected to perturbation of SOCS1, does the expression profile of ZFHX3 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: 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, SRPR is perturbed and the expression of CLINT1 is measured. Does this perturbation cause a significant change in CLINT1 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 SLC35B1 and examine the expression of PPM1N. Does perturbing SLC35B1 lead to a significant change in PPM1N 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, SAMM50 is perturbed and the expression of ZEB1 is measured. Determine whether ZEB1 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, ASCC3 is perturbed and SKIL expression is measured. Determine whether SKIL 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 SEC61G and then measure expression of TAP1. Does this perturbation cause a significant change in TAP1 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 FECH, does the expression profile of ATAD2B 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 HARS is perturbed and SAMM50 expression is observed. Does this perturbation lead to a significant difference in SAMM50 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, BHLHE40 is perturbed and the expression of NRIP1 is measured. Determine whether NRIP1 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 TIMM44, does the expression profile of ZC3H7A 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 SARS and monitor PIF1 expression. Decide whether this perturbation leads to a significant alteration in PIF1 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, TMEM167A is perturbed and PRSS57 expression is quantified. Does this perturbation result in a significant change in PRSS57 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: No\n",
"Score: 1.0\n",
"The solution is correct.Questions: Question: You are a functional genomics specialist. In K562 cells, we perturb DDOST and monitor PHF21A expression. Decide whether this perturbation leads to a significant alteration in PHF21A 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, HSPA5 is perturbed and SERPING1 expression is quantified. Does this perturbation result in a significant change in SERPING1 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, MRPL39 is perturbed and CTNNB1 expression is measured. Determine whether CTNNB1 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, DERL2 is perturbed and the expression of ACSM3 is measured. Determine whether ACSM3 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: 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, DDIT3 is perturbed and the expression of NFE2 is measured. Does this perturbation cause a significant change in NFE2 expression? Answer strictly in the format '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, SLMO2 is perturbed and UQCRB expression is measured. Determine whether UQCRB 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 RP11-138C9.1. Does this perturbation cause a significant change in RP11-138C9.1 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, DDIT3 is perturbed and STC2 expression is measured. Determine whether STC2 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, DDOST is perturbed and the expression of C9orf64 is measured. Determine whether C9orf64 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: 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 COPZ1 and monitor WDR3 expression. Decide whether this perturbation leads to a significant alteration in WDR3 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 P4HB and then measure expression of ZCCHC11. Does this perturbation cause a significant change in ZCCHC11 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 MRPL39, does the expression profile of RP13-216E22.4 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: 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, SYVN1 is perturbed and the expression of EPB42 is measured. Does this perturbation cause a significant change in EPB42 expression? Answer strictly in the format '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, TMEM167A is perturbed and the expression of AKAP11 is measured. Determine whether AKAP11 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 PTDSS1 is associated with a significant change in PITPNB 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 COPB1 is perturbed and SSBP2 expression is observed. Does this perturbation lead to a significant difference in SSBP2 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 TTI2 and examine the expression of EP300. Does perturbing TTI2 lead to a significant change in EP300 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 CAD, does the expression profile of AC008074.3 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: 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 ZNF789 is measured. Determine whether ZNF789 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: 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 SEC61A1 and monitor PCK2 expression. Decide whether this perturbation leads to a significant alteration in PCK2 expression. Answer only in the format '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 MRPL39 is associated with a significant change in RP11-119J18.1 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: 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 SLC39A7, does the expression profile of PTAR1 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 COPB1 and examine the expression of CTD-2020K17.1. Does perturbing COPB1 lead to a significant change in CTD-2020K17.1 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 SLMO2 and monitor FAM114A1 expression. Decide whether this perturbation leads to a significant alteration in FAM114A1 expression. Answer only in the format '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 SLC39A7 and examine the expression of SLBP. Does perturbing SLC39A7 lead to a significant change in SLBP 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, IDH3A is perturbed and SHOX2 expression is quantified. Does this perturbation result in a significant change in SHOX2 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, FECH is perturbed and ATAD2B expression is measured. Determine whether ATAD2B 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, SARS is perturbed and the expression of PHF19 is measured. Determine whether PHF19 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 WHSC1. Does perturbing MRGBP lead to a significant change in WHSC1 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, UFM1 is perturbed and DSC2 expression is measured. Determine whether DSC2 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 SLC39A7 and then measure expression of NINJ2. Does this perturbation cause a significant change in NINJ2 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, DHDDS is perturbed and the expression of HM13 is measured. Determine whether HM13 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, EIF2B3 is perturbed and the expression of S100A11 is measured. Does this perturbation cause a significant change in S100A11 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 SRPR is associated with a significant change in CD9 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, IDH3A is perturbed and the expression of SHOX2 is measured. Does this perturbation cause a significant change in SHOX2 expression? Answer strictly in the format '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, ATP5B is perturbed and ATP6AP2 expression is quantified. Does this perturbation result in a significant change in ATP6AP2 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 DERL2 and examine the expression of LRRC4B. Does perturbing DERL2 lead to a significant change in LRRC4B 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, ARHGAP22 is perturbed and the expression of MT2A is measured. Determine whether MT2A 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: No\n",
"Score: 0.0\n",
"Error reason: Computation result is incorrect.\n",
"{'name': 'validate_question4633', 'description': 'Task to validate_question4633. Takes question as input. Produces validated_question as output.', 'inputs': [{'name': 'question', 'type': 'str', 'description': 'Input parameter question for validate_question4633', 'required': False}], 'outputs': [{'name': 'validated_question', 'type': 'str', 'description': 'Output parameter validated_question from validate_question4633', 'required': True}], 'prompt': 'Your are a task solver.', 'prompt_template': None, 'system_prompt': 'You are a helpful and highly intelligent assistant.', 'parse_mode': 'xml', 'parse_func': None, 'parse_title': None, 'tool_names': None, 'tools': None}\n"
]
},
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"name": "stdout",
"output_type": "stream",
"text": [
"\u001b[32m2026-01-13 20:06:42.459\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.119 | Total tokens: 676532 | Current cost: $0.001 | Current tokens: 5229\u001b[0m\n",
"\u001b[32m2026-01-13 20:06:42.991\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: $0.119 | Total tokens: 676635 | Current cost: $0.000 | Current tokens: 103\u001b[0m\n",
"\u001b[32m2026-01-13 20:06:44.383\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: $0.119 | Total tokens: 677147 | Current cost: $0.000 | Current tokens: 512\u001b[0m\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, 'tools': None}\n",
"\u001b[32m2026-01-13 20:06:46.437\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.120 | Total tokens: 682405 | Current cost: $0.001 | Current tokens: 5258\u001b[0m\n",
"\u001b[32m2026-01-13 20:06:46.875\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.120 | Total tokens: 682501 | Current cost: $0.000 | Current tokens: 96\u001b[0m\n",
"\u001b[32m2026-01-13 20:06:48.087\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.models.model_utils\u001b[0m:\u001b[36mupdate_cost\u001b[0m:\u001b[36m87\u001b[0m - \u001b[1mTotal cost: $0.120 | Total tokens: 683305 | Current cost: $0.000 | Current tokens: 804\u001b[0m\n",
"\u001b[32m2026-01-13 20:06:48.089\u001b[0m | \u001b[33m\u001b[1mWARNING \u001b[0m | \u001b[36mevoagentx.workflow.workflow_graph\u001b[0m:\u001b[36m_validate_workflow_structure\u001b[0m:\u001b[36m363\u001b[0m - \u001b[33m\u001b[1mThe workflow contains isolated nodes: ['validate_question4633', 'generate_answer']\u001b[0m\n",
"\u001b[32m2026-01-13 20:06:48.089\u001b[0m | \u001b[1mINFO \u001b[0m | \u001b[36mevoagentx.optimizers.qastructure_optimizer\u001b[0m:\u001b[36moptimize\u001b[0m:\u001b[36m1054\u001b[0m - \u001b[1mEvaluate the workflow at step 5 ...\u001b[0m\n"
]
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"text": [
"Evaluating workflow: 2%|▏ | 1/50 [00:00<00:33, 1.45it/s]"
]
},
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
},
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"output_type": "stream",
"text": [
"\r",
"Evaluating workflow: 4%|▍ | 2/50 [00:01<00:33, 1.42it/s]"
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]
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]
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"\r",
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
},
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"text": [
"\r",
"Evaluating workflow: 10%|█ | 5/50 [00:03<00:35, 1.28it/s]"
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"text": [
"\r",
"Evaluating workflow: 12%|█▏ | 6/50 [00:04<00:33, 1.33it/s]"
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 0.0}\n"
]
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"text": [
"\r",
"Evaluating workflow: 14%|█▍ | 7/50 [00:05<00:31, 1.36it/s]"
]
},
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"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: 16%|█▌ | 8/50 [00:05<00:29, 1.42it/s]"
]
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]
},
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"\r",
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]
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"text": [
"metrics {'f1': 0, 'em': 0.0, 'acc': 1.0}\n"
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"text": [
"\r",
"Evaluating workflow: 20%|██ | 10/50 [00:07<00:27, 1.45it/s]"
]
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]
},
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"text": [
"\r",
"Evaluating workflow: 22%|██▏ | 11/50 [00:07<00:26, 1.45it/s]"
]
},
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"text": [
"\r",
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"\r",
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]
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"client_session: \n",
"Unclosed connector\n",
"connections: ['deque([(, 2365802.11245762)])']\n",
"connector: \n",
"Unclosed client session\n",
"client_session: \n",
"Unclosed connector\n",
"connections: ['deque([(, 2365802.800796115)])']\n",
"connector: \n",
"Unclosed client session\n",
"client_session: \n",
"Unclosed connector\n",
"connections: ['deque([(, 2365803.736241534)])']\n",
"connector: \n",
"Unclosed client session\n",
"client_session: \n",
"Unclosed client session\n",
"client_session: \n",
"Unclosed client session\n",
"client_session: \n",
"Unclosed client session\n",
"client_session: \n",
"Unclosed connector\n",
"connections: ['deque([(, 2365794.476719168)])']\n",
"connector: \n",
"Unclosed connector\n",
"connections: ['deque([(, 2365795.113578844)])']\n",
"connector: \n",
"Unclosed connector\n",
"connections: ['deque([(, 2365797.188739658)])']\n",
"connector: \n",
"Unclosed connector\n",
"connections: ['deque([(, 2365804.440935148)])']\n",
"connector: \n",
"Unclosed client session\n",
"client_session: \n",
"Unclosed connector\n",
"connections: ['deque([(, 2365805.150471751)])']\n",
"connector: \n",
"Unclosed client session\n",
"client_session: \n",
"Unclosed connector\n",
"connections: ['deque([(, 2365805.8043437)])']\n",
"connector: \n",
"Unclosed client session\n",
"client_session: \n",
"Unclosed connector\n",
"connections: ['deque([(, 2365807.359817784)])']\n",
"connector: \n",
"Unclosed client session\n",
"client_session: \n",
"Unclosed connector\n",
"connections: ['deque([(, 2365808.234249733)])']\n",
"connector: \n",
"Unclosed client session\n",
"client_session: \n",
"Unclosed connector\n",
"connections: ['deque([(, 2365808.864292936)])']\n",
"connector: \n",
"Unclosed client session\n",
"client_session: \n",
"Unclosed connector\n",
"connections: ['deque([(, 2365809.471929794)])']\n",
"connector: \n",
"Unclosed client session\n",
"client_session: \n",
"Unclosed connector\n",
"connections: ['deque([(, 2365810.111662392)])']\n",
"connector: \n",
"Unclosed client session\n",
"client_session: \n",
"Unclosed connector\n",
"connections: ['deque([(, 2365810.693529699)])']\n",
"connector: \n",
"Unclosed client session\n",
"client_session: \n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"Unclosed connector\n",
"connections: ['deque([(