Text Generation
Transformers
TensorBoard
Safetensors
biology
genomics
rna
sequence-generation
regression
reinforcement-learning
git-lfs
Instructions to use JoyXiangLab/rnaseek-full with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use JoyXiangLab/rnaseek-full with Transformers:
# Use a pipeline as a high-level helper from transformers import pipeline pipe = pipeline("text-generation", model="JoyXiangLab/rnaseek-full")# Load model directly from transformers import AutoModel model = AutoModel.from_pretrained("JoyXiangLab/rnaseek-full", device_map="auto") - Notebooks
- Google Colab
- Kaggle
- Local Apps Settings
- vLLM
How to use JoyXiangLab/rnaseek-full with vLLM:
Install from pip and serve model
# Install vLLM from pip: pip install vllm # Start the vLLM server: vllm serve "JoyXiangLab/rnaseek-full" # Call the server using curl (OpenAI-compatible API): curl -X POST "http://localhost:8000/v1/completions" \ -H "Content-Type: application/json" \ --data '{ "model": "JoyXiangLab/rnaseek-full", "prompt": "Once upon a time,", "max_tokens": 512, "temperature": 0.5 }'Use Docker
docker model run hf.co/JoyXiangLab/rnaseek-full
- SGLang
How to use JoyXiangLab/rnaseek-full with SGLang:
Install from pip and serve model
# Install SGLang from pip: pip install sglang # Start the SGLang server: python3 -m sglang.launch_server \ --model-path "JoyXiangLab/rnaseek-full" \ --host 0.0.0.0 \ --port 30000 # Call the server using curl (OpenAI-compatible API): curl -X POST "http://localhost:30000/v1/completions" \ -H "Content-Type: application/json" \ --data '{ "model": "JoyXiangLab/rnaseek-full", "prompt": "Once upon a time,", "max_tokens": 512, "temperature": 0.5 }'Use Docker images
docker run --gpus all \ --shm-size 32g \ -p 30000:30000 \ -v ~/.cache/huggingface:/root/.cache/huggingface \ --env "HF_TOKEN=<secret>" \ --ipc=host \ lmsysorg/sglang:latest \ python3 -m sglang.launch_server \ --model-path "JoyXiangLab/rnaseek-full" \ --host 0.0.0.0 \ --port 30000 # Call the server using curl (OpenAI-compatible API): curl -X POST "http://localhost:30000/v1/completions" \ -H "Content-Type: application/json" \ --data '{ "model": "JoyXiangLab/rnaseek-full", "prompt": "Once upon a time,", "max_tokens": 512, "temperature": 0.5 }' - Docker Model Runner
How to use JoyXiangLab/rnaseek-full with Docker Model Runner:
docker model run hf.co/JoyXiangLab/rnaseek-full
| # Copyright 2025 the LlamaFactory team. | |
| # | |
| # Licensed under the Apache License, Version 2.0 (the "License"); | |
| # you may not use this file except in compliance with the License. | |
| # You may obtain a copy of the License at | |
| # | |
| # http://www.apache.org/licenses/LICENSE-2.0 | |
| # | |
| # Unless required by applicable law or agreed to in writing, software | |
| # distributed under the License is distributed on an "AS IS" BASIS, | |
| # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. | |
| # See the License for the specific language governing permissions and | |
| # limitations under the License. | |
| from collections import defaultdict | |
| from dataclasses import asdict, dataclass | |
| from typing import TYPE_CHECKING, Any, Optional | |
| from ...extras import logging | |
| from ...extras.constants import IGNORE_INDEX | |
| from .processor_utils import DatasetProcessor, greedy_knapsack, infer_seqlen | |
| if TYPE_CHECKING: | |
| from ..mm_plugin import AudioInput, ImageInput, VideoInput | |
| logger = logging.get_logger(__name__) | |
| MAX_SU_SEQ_IDX = 2**32 # maximum sub-sequence index | |
| class PackingParams: | |
| r"""Metadata for a packed sequence: sub-sequence boundaries and multimodal data indices. | |
| - sequence_boundaries: cumulative token positions, e.g. [0, 100, 250, 512] means 3 sub-seqs | |
| with token ranges [0,100), [100,250), [250,512). Length = num_sub_seqs + 1. | |
| - image_subseq_ids / video_subseq_ids / audio_subseq_ids: for each mm item, the 0-based | |
| sub-sequence index it belongs to. Length = total number of that mm type in the packed sample. | |
| """ | |
| sequence_boundaries: list[int] | |
| image_subseq_ids: list[int] | |
| video_subseq_ids: list[int] | |
| audio_subseq_ids: list[int] | |
| right_padding_length: int | |
| class SupervisedDatasetProcessor(DatasetProcessor): | |
| def _encode_data_example( | |
| self, | |
| prompt: list[dict[str, str]], | |
| response: list[dict[str, str]], | |
| system: Optional[str], | |
| tools: Optional[str], | |
| images: list["ImageInput"], | |
| videos: list["VideoInput"], | |
| audios: list["AudioInput"], | |
| ) -> tuple[list[int], list[int]]: | |
| messages = self.template.mm_plugin.process_messages(prompt + response, images, videos, audios, self.processor) | |
| input_ids, labels = self.template.mm_plugin.process_token_ids( | |
| [], [], images, videos, audios, self.tokenizer, self.processor | |
| ) | |
| discarding_history_cot = self.data_args.mask_history and not self.template.preserve_thinking | |
| encoded_pairs = self.template.encode_multiturn(self.tokenizer, messages, system, tools, discarding_history_cot) | |
| total_length = len(input_ids) + (1 if self.template.efficient_eos else 0) | |
| if self.data_args.mask_history: | |
| encoded_pairs = encoded_pairs[::-1] # high priority for last turns | |
| for turn_idx, (source_ids, target_ids) in enumerate(encoded_pairs): | |
| if total_length >= self.data_args.cutoff_len: | |
| break | |
| source_len, target_len = infer_seqlen( | |
| len(source_ids), len(target_ids), self.data_args.cutoff_len - total_length | |
| ) | |
| source_ids = source_ids[:source_len] | |
| target_ids = target_ids[:target_len] | |
| total_length += source_len + target_len | |
| if self.data_args.train_on_prompt: | |
| source_label = source_ids | |
| elif self.template.efficient_eos and turn_idx != 0: | |
| source_label = [self.tokenizer.eos_token_id] + [IGNORE_INDEX] * (source_len - 1) | |
| else: | |
| source_label = [IGNORE_INDEX] * source_len | |
| if self.data_args.mask_history and turn_idx != 0: # train on the last turn only | |
| target_label = [IGNORE_INDEX] * target_len | |
| else: | |
| target_label = target_ids | |
| if self.data_args.mask_history: # reversed sequences | |
| input_ids = source_ids + target_ids + input_ids | |
| labels = source_label + target_label + labels | |
| else: | |
| input_ids += source_ids + target_ids | |
| labels += source_label + target_label | |
| if self.template.efficient_eos: | |
| input_ids += [self.tokenizer.eos_token_id] | |
| labels += [self.tokenizer.eos_token_id] | |
| return input_ids, labels | |
| def preprocess_dataset(self, examples: dict[str, list[Any]]) -> dict[str, list[Any]]: | |
| # build inputs with format `<bos> X Y <eos>` and labels with format `<ignore> ... <ignore> Y <eos>` | |
| # for multiturn examples, we only mask the prompt part in each prompt-response pair. | |
| model_inputs = defaultdict(list) | |
| for i in range(len(examples["_prompt"])): | |
| if len(examples["_prompt"][i]) % 2 != 1 or len(examples["_response"][i]) != 1: | |
| logger.warning_rank0( | |
| "Dropped invalid example: {}".format(examples["_prompt"][i] + examples["_response"][i]) | |
| ) | |
| continue | |
| input_ids, labels = self._encode_data_example( | |
| prompt=examples["_prompt"][i], | |
| response=examples["_response"][i], | |
| system=examples["_system"][i], | |
| tools=examples["_tools"][i], | |
| images=examples["_images"][i] or [], | |
| videos=examples["_videos"][i] or [], | |
| audios=examples["_audios"][i] or [], | |
| ) | |
| model_inputs["input_ids"].append(input_ids) | |
| model_inputs["attention_mask"].append([1] * len(input_ids)) | |
| model_inputs["labels"].append(labels) | |
| model_inputs["images"].append(examples["_images"][i]) | |
| model_inputs["videos"].append(examples["_videos"][i]) | |
| model_inputs["audios"].append(examples["_audios"][i]) | |
| return model_inputs | |
| def print_data_example(self, example: dict[str, list[int]]) -> None: | |
| valid_labels = list(filter(lambda x: x != IGNORE_INDEX, example["labels"])) | |
| print("input_ids:\n{}".format(example["input_ids"])) | |
| print("inputs:\n{}".format(self.tokenizer.decode(example["input_ids"], skip_special_tokens=False))) | |
| print("label_ids:\n{}".format(example["labels"])) | |
| print(f"labels:\n{self.tokenizer.decode(valid_labels, skip_special_tokens=False)}") | |
| class PackedSupervisedDatasetProcessor(SupervisedDatasetProcessor): | |
| def preprocess_dataset(self, examples: dict[str, list[Any]]) -> dict[str, list[Any]]: | |
| # TODO: use `position_ids` to achieve packing | |
| # build inputs with format `<bos> X1 Y1 <eos> <bos> X2 Y2 <eos>` | |
| # and labels with format `<ignore> ... <ignore> Y1 <eos> <ignore> ... <ignore> Y2 <eos>` | |
| valid_num = 0 | |
| batch_input_ids, batch_labels, batch_images, batch_videos, batch_audios = [], [], [], [], [] | |
| lengths = [] | |
| length2indexes = defaultdict(list) | |
| for i in range(len(examples["_prompt"])): | |
| if len(examples["_prompt"][i]) % 2 != 1 or len(examples["_response"][i]) != 1: | |
| logger.warning_rank0( | |
| "Dropped invalid example: {}".format(examples["_prompt"][i] + examples["_response"][i]) | |
| ) | |
| continue | |
| input_ids, labels = self._encode_data_example( | |
| prompt=examples["_prompt"][i], | |
| response=examples["_response"][i], | |
| system=examples["_system"][i], | |
| tools=examples["_tools"][i], | |
| images=examples["_images"][i] or [], | |
| videos=examples["_videos"][i] or [], | |
| audios=examples["_audios"][i] or [], | |
| ) | |
| length = len(input_ids) | |
| if length > self.data_args.cutoff_len: | |
| logger.warning_rank0(f"Dropped lengthy example with length {length} > {self.data_args.cutoff_len}.") | |
| else: | |
| lengths.append(length) | |
| length2indexes[length].append(valid_num) | |
| batch_input_ids.append(input_ids) | |
| batch_labels.append(labels) | |
| batch_images.append(examples["_images"][i] or []) | |
| batch_videos.append(examples["_videos"][i] or []) | |
| batch_audios.append(examples["_audios"][i] or []) | |
| valid_num += 1 | |
| model_inputs = defaultdict(list) | |
| requires_packing_params = self.data_args.neat_packing | |
| knapsacks = greedy_knapsack(lengths, self.data_args.cutoff_len) | |
| for knapsack in knapsacks: | |
| packed_input_ids, packed_attention_masks, packed_position_ids, packed_labels = [], [], [], [] | |
| packed_images, packed_videos, packed_audios = [], [], [] | |
| if requires_packing_params: | |
| sequence_boundaries = [0] | |
| image_subseq_ids: list[int] = [] | |
| video_subseq_ids: list[int] = [] | |
| audio_subseq_ids: list[int] = [] | |
| for i, length in enumerate(knapsack): | |
| index = length2indexes[length].pop() | |
| packed_input_ids += batch_input_ids[index] | |
| packed_position_ids += list(range(len(batch_input_ids[index]))) # NOTE: pad_to_multiple_of ignore this | |
| packed_labels += batch_labels[index] | |
| packed_images += batch_images[index] | |
| packed_videos += batch_videos[index] | |
| packed_audios += batch_audios[index] | |
| if requires_packing_params: | |
| n_img = len(batch_images[index]) | |
| n_vid = len(batch_videos[index]) | |
| n_aud = len(batch_audios[index]) | |
| sequence_boundaries.append(sequence_boundaries[-1] + len(batch_input_ids[index])) | |
| image_subseq_ids.extend([i] * n_img) | |
| video_subseq_ids.extend([i] * n_vid) | |
| audio_subseq_ids.extend([i] * n_aud) | |
| if self.data_args.neat_packing: | |
| packed_attention_masks += [i + 1] * len(batch_input_ids[index]) # start from 1 | |
| else: | |
| packed_attention_masks += [1] * len(batch_input_ids[index]) | |
| if len(packed_input_ids) < self.data_args.cutoff_len + 1: # avoid flash_attn drops attn mask | |
| pad_length = self.data_args.cutoff_len - len(packed_input_ids) + 1 | |
| packed_input_ids += [self.tokenizer.pad_token_id] * pad_length | |
| packed_position_ids += [0] * pad_length | |
| packed_labels += [IGNORE_INDEX] * pad_length | |
| if self.data_args.neat_packing: | |
| packed_attention_masks += [0] * pad_length | |
| else: | |
| packed_attention_masks += [1] * pad_length # more efficient flash_attn | |
| if requires_packing_params: | |
| sequence_boundaries.append(sequence_boundaries[-1] + pad_length) | |
| if len(packed_input_ids) != self.data_args.cutoff_len + 1: | |
| raise ValueError("The length of packed example should be identical to the cutoff length.") | |
| model_inputs["input_ids"].append(packed_input_ids) | |
| if requires_packing_params: | |
| packing_params = PackingParams( | |
| sequence_boundaries=sequence_boundaries, | |
| image_subseq_ids=image_subseq_ids or [MAX_SU_SEQ_IDX], # avoid dataset concat error | |
| video_subseq_ids=video_subseq_ids or [MAX_SU_SEQ_IDX], | |
| audio_subseq_ids=audio_subseq_ids or [MAX_SU_SEQ_IDX], | |
| right_padding_length=pad_length, | |
| ) | |
| model_inputs["packing_params"].append(asdict(packing_params)) | |
| model_inputs["attention_mask"].append(packed_attention_masks) | |
| model_inputs["position_ids"].append(packed_position_ids) | |
| model_inputs["labels"].append(packed_labels) | |
| model_inputs["images"].append(packed_images or None) | |
| model_inputs["videos"].append(packed_videos or None) | |
| model_inputs["audios"].append(packed_audios or None) | |
| return model_inputs | |