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. | |
| import json | |
| from enum import StrEnum, unique | |
| from typing import TYPE_CHECKING, Any, Optional, TypedDict, Union | |
| import fsspec | |
| from datasets import DatasetDict, concatenate_datasets, interleave_datasets | |
| from ..extras import logging | |
| if TYPE_CHECKING: | |
| from datasets import Dataset, IterableDataset | |
| from ..hparams import DataArguments | |
| logger = logging.get_logger(__name__) | |
| SLOTS = list[Union[str, set[str], dict[str, str]]] | |
| class Role(StrEnum): | |
| USER = "user" | |
| ASSISTANT = "assistant" | |
| SYSTEM = "system" | |
| FUNCTION = "function" | |
| OBSERVATION = "observation" | |
| class DatasetModule(TypedDict): | |
| train_dataset: Optional[Union["Dataset", "IterableDataset"]] | |
| eval_dataset: Optional[Union["Dataset", "IterableDataset", dict[str, "Dataset"]]] | |
| def merge_dataset( | |
| all_datasets: list[Union["Dataset", "IterableDataset"]], data_args: "DataArguments", seed: int | |
| ) -> Union["Dataset", "IterableDataset"]: | |
| r"""Merge multiple datasets to a unified dataset.""" | |
| if len(all_datasets) == 1: | |
| return all_datasets[0] | |
| elif data_args.mix_strategy == "concat": | |
| if data_args.streaming: | |
| logger.warning_rank0_once("The samples between different datasets will not be mixed in streaming mode.") | |
| return concatenate_datasets(all_datasets) | |
| elif data_args.mix_strategy.startswith("interleave"): | |
| if not data_args.streaming: | |
| logger.warning_rank0_once("We recommend using `mix_strategy=concat` in non-streaming mode.") | |
| strategy_map: str = { | |
| "interleave_under": "first_exhausted", | |
| "interleave_over": "all_exhausted", | |
| "interleave_once": "all_exhausted_without_replacement", | |
| }[data_args.mix_strategy] | |
| return interleave_datasets( | |
| datasets=all_datasets, | |
| probabilities=data_args.interleave_probs, | |
| seed=seed, | |
| stopping_strategy=strategy_map, # type: ignore | |
| ) | |
| else: | |
| raise ValueError(f"Unknown mixing strategy: {data_args.mix_strategy}.") | |
| def split_dataset( | |
| dataset: Optional[Union["Dataset", "IterableDataset"]], | |
| eval_dataset: Optional[Union["Dataset", "IterableDataset", dict[str, "Dataset"]]], | |
| data_args: "DataArguments", | |
| seed: int, | |
| ) -> tuple[dict, dict]: | |
| r"""Split the dataset and returns two dicts containing train set and validation set. | |
| Support both map dataset and iterable dataset. | |
| Returns: | |
| train_dict: Dictionary containing training data with key "train" | |
| eval_dict: Dictionary containing evaluation data with keys "validation" or "validation_{name}" | |
| """ | |
| if eval_dataset is not None and data_args.val_size > 1e-6: | |
| raise ValueError("Cannot specify `val_size` if `eval_dataset` is not None.") | |
| # the train and eval better to in dict dtype and separately return for cpode clearly and good handle outside | |
| train_dict, eval_dict = {}, {} | |
| if dataset is not None: | |
| if data_args.streaming: | |
| dataset = dataset.shuffle(buffer_size=data_args.buffer_size, seed=seed) | |
| if data_args.val_size > 1e-6: | |
| if data_args.streaming: | |
| eval_dict["validation"] = dataset.take(int(data_args.val_size)) | |
| train_dict["train"] = dataset.skip(int(data_args.val_size)) | |
| else: | |
| val_size = int(data_args.val_size) if data_args.val_size > 1 else data_args.val_size | |
| split_result = dataset.train_test_split(test_size=val_size, seed=seed) | |
| train_dict["train"] = split_result["train"] | |
| eval_dict["validation"] = split_result["test"] | |
| else: | |
| train_dict["train"] = dataset | |
| if eval_dataset is not None: | |
| if isinstance(eval_dataset, dict): | |
| for name, data in eval_dataset.items(): | |
| eval_dict[f"validation_{name}"] = data | |
| else: | |
| if data_args.streaming: | |
| eval_dataset = eval_dataset.shuffle(buffer_size=data_args.buffer_size, seed=seed) | |
| eval_dict["validation"] = eval_dataset | |
| return train_dict, eval_dict | |
| def get_dataset_module(dataset: Union["Dataset", "DatasetDict"]) -> "DatasetModule": | |
| r"""Convert dataset or dataset dict to dataset module.""" | |
| dataset_module: DatasetModule = {} | |
| if isinstance(dataset, DatasetDict): # dataset dict | |
| if "train" in dataset: | |
| dataset_module["train_dataset"] = dataset["train"] | |
| if "validation" in dataset: | |
| dataset_module["eval_dataset"] = dataset["validation"] | |
| else: | |
| eval_dataset = {} | |
| for key in dataset.keys(): | |
| if key.startswith("validation_"): | |
| eval_dataset[key[len("validation_") :]] = dataset[key] | |
| if len(eval_dataset): | |
| dataset_module["eval_dataset"] = eval_dataset | |
| else: # single dataset | |
| dataset_module["train_dataset"] = dataset | |
| return dataset_module | |
| def setup_fs(path: str, anon: bool = False) -> "fsspec.AbstractFileSystem": | |
| r"""Set up a filesystem object based on the path protocol.""" | |
| storage_options = {"anon": anon} if anon else {} | |
| if path.startswith("s3://"): | |
| fs = fsspec.filesystem("s3", **storage_options) | |
| elif path.startswith(("gs://", "gcs://")): | |
| fs = fsspec.filesystem("gcs", **storage_options) | |
| else: | |
| raise ValueError(f"Unsupported protocol in path: {path}. Use 's3://' or 'gs://'.") | |
| if not fs.exists(path): | |
| raise ValueError(f"Path does not exist: {path}.") | |
| return fs | |
| def _read_json_with_fs(fs: "fsspec.AbstractFileSystem", path: str) -> list[Any]: | |
| r"""Helper function to read JSON/JSONL files using fsspec.""" | |
| with fs.open(path, "r") as f: | |
| if path.endswith(".jsonl"): | |
| return [json.loads(line) for line in f if line.strip()] | |
| else: | |
| return json.load(f) | |
| def read_cloud_json(cloud_path: str) -> list[Any]: | |
| r"""Read a JSON/JSONL file from cloud storage (S3 or GCS). | |
| Args: | |
| cloud_path: str | |
| Cloud path in the format: | |
| - 's3://bucket-name/file.json' for AWS S3 | |
| - 'gs://bucket-name/file.jsonl' or 'gcs://bucket-name/file.jsonl' for Google Cloud Storage | |
| """ | |
| try: | |
| fs = setup_fs(cloud_path, anon=True) # try with anonymous access first | |
| except Exception: | |
| fs = setup_fs(cloud_path) # try again with credentials | |
| # filter out non-JSON files | |
| files = [x["Key"] for x in fs.listdir(cloud_path)] if fs.isdir(cloud_path) else [cloud_path] | |
| files = list(filter(lambda file: file.endswith(".json") or file.endswith(".jsonl"), files)) | |
| if not files: | |
| raise ValueError(f"No JSON/JSONL files found in the specified path: {cloud_path}.") | |
| return sum([_read_json_with_fs(fs, file) for file in files], []) | |