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 HuggingFace Inc. and the LlamaFactory team. | |
| # | |
| # This code is inspired by the HuggingFace's Transformers library. | |
| # https://github.com/huggingface/transformers/blob/v4.40.0/src/transformers/models/llava/modeling_llava.py | |
| # | |
| # 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 dataclasses import dataclass | |
| from typing import TYPE_CHECKING, Optional | |
| import torch | |
| import transformers | |
| import transformers.models | |
| from transformers.activations import ACT2FN | |
| from ...extras import logging | |
| if TYPE_CHECKING: | |
| from transformers import LlavaConfig, PretrainedConfig, PreTrainedModel | |
| from ...hparams import FinetuningArguments, ModelArguments | |
| logger = logging.get_logger(__name__) | |
| transformers_logger = transformers.utils.logging.get_logger(__name__) | |
| class CompositeModel: | |
| model_type: str | |
| projector_keys: list[str] | |
| vision_model_keys: list[str] | |
| language_model_keys: list[str] | |
| lora_conflict_keys: list[str] | |
| def get_projectors(self, module: "torch.nn.Module") -> list["torch.nn.Module"]: | |
| mm_projectors: list[torch.nn.Module] = [] | |
| for projector_key in self.projector_keys: | |
| project_module = module | |
| for key in projector_key.split("."): | |
| project_module = getattr(project_module, key, None) | |
| if project_module is None: # i,e gemma4 bigger one, there is no embed_audio | |
| logger.warning_rank0( | |
| f"Projector key {projector_key} not found in module {module.__class__.__name__}." | |
| ) | |
| break | |
| if isinstance(project_module, torch.nn.Module): | |
| mm_projectors.append(project_module) | |
| return mm_projectors | |
| COMPOSITE_MODELS: dict[str, "CompositeModel"] = {} | |
| def _register_composite_model( | |
| model_type: str, | |
| projector_keys: list[str] | None = None, | |
| vision_model_keys: Optional[list[str]] = None, | |
| language_model_keys: Optional[list[str]] = None, | |
| lora_conflict_keys: Optional[list[str]] = None, | |
| ): | |
| r"""Register a new composite model. | |
| Args: | |
| model_type: model type | |
| projector_keys: multi_modal_projector | |
| vision_model_keys: vision_tower | |
| language_model_keys: language_model | |
| lora_conflict_keys: None | |
| """ | |
| COMPOSITE_MODELS[model_type] = CompositeModel( | |
| model_type=model_type, | |
| projector_keys=projector_keys or ["multi_modal_projector"], | |
| vision_model_keys=vision_model_keys or ["vision_tower"], | |
| language_model_keys=language_model_keys or ["language_model", "lm_head"], | |
| lora_conflict_keys=lora_conflict_keys or [], | |
| ) | |
| class LlavaMultiModalProjectorForYiVL(torch.nn.Module): | |
| def __init__(self, config: "LlavaConfig") -> None: | |
| super().__init__() | |
| self.config = config | |
| if config is None: | |
| return | |
| self.linear_1 = torch.nn.Linear(config.vision_config.hidden_size, config.text_config.hidden_size, bias=True) | |
| self.linear_2 = torch.nn.LayerNorm(config.text_config.hidden_size, bias=True) | |
| self.linear_3 = torch.nn.Linear(config.text_config.hidden_size, config.text_config.hidden_size, bias=True) | |
| self.linear_4 = torch.nn.LayerNorm(config.text_config.hidden_size, bias=True) | |
| self.act = ACT2FN[config.projector_hidden_act] | |
| def forward(self, image_features: "torch.Tensor") -> "torch.Tensor": | |
| hidden_states = self.linear_1(image_features) | |
| hidden_states = self.linear_2(hidden_states) | |
| hidden_states = self.act(hidden_states) | |
| hidden_states = self.linear_3(hidden_states) | |
| hidden_states = self.linear_4(hidden_states) | |
| if hidden_states.dtype == torch.float32: | |
| if torch.is_autocast_enabled(): | |
| target_dtype = torch.get_autocast_gpu_dtype() | |
| elif hasattr(self.config, "_pre_quantization_dtype"): | |
| target_dtype = self.config._pre_quantization_dtype | |
| else: | |
| target_dtype = self.linear_1.weight.dtype | |
| transformers_logger.warning_once("The hidden states seems to be silently casted in float32.") | |
| hidden_states = hidden_states.to(target_dtype) | |
| return hidden_states | |
| class LlavaMultiModalProjectorForYiVLForVLLM(LlavaMultiModalProjectorForYiVL): | |
| def __init__(self, vision_hidden_size: int, text_hidden_size: int, projector_hidden_act: str) -> None: | |
| super().__init__(config=None) | |
| self.linear_1 = torch.nn.Linear(vision_hidden_size, text_hidden_size, bias=True) | |
| self.linear_2 = torch.nn.LayerNorm(text_hidden_size, bias=True) | |
| self.linear_3 = torch.nn.Linear(text_hidden_size, text_hidden_size, bias=True) | |
| self.linear_4 = torch.nn.LayerNorm(text_hidden_size, bias=True) | |
| self.act = ACT2FN[projector_hidden_act] | |
| def autocast_projector_dtype(model: "PreTrainedModel", model_args: "ModelArguments") -> None: | |
| r"""Cast projector output to half precision for fine-tuning quantized VLMs.""" | |
| def _mm_projector_forward_post_hook( | |
| module: "torch.nn.Module", args: tuple["torch.Tensor"], output: "torch.Tensor" | |
| ) -> "torch.Tensor": | |
| return output.to(model_args.compute_dtype) | |
| if getattr(model, "quantization_method", None): | |
| model_type = getattr(model.config, "model_type", None) | |
| if model_type in COMPOSITE_MODELS: | |
| mm_projectors = COMPOSITE_MODELS[model_type].get_projectors(model) | |
| else: | |
| return | |
| logger.info_rank0( | |
| f"Casting multimodal projector outputs in {model_args.compute_dtype}: " | |
| f"{COMPOSITE_MODELS[model_type].projector_keys}." | |
| ) | |
| for mm_projector in mm_projectors: | |
| mm_projector.register_forward_hook(_mm_projector_forward_post_hook) | |
| def configure_visual_model(config: "PretrainedConfig") -> None: | |
| r"""Patch VLMs before loading them.""" | |
| if getattr(config, "text_config", None) and not getattr(config, "hidden_size", None): | |
| # required for ds zero3 and valuehead models | |
| setattr(config, "hidden_size", getattr(config.text_config, "hidden_size", None)) | |
| if getattr(config, "is_yi_vl_derived_model", None): | |
| logger.info_rank0("Detected Yi-VL model, applying projector patch.") | |
| transformers.models.llava.modeling_llava.LlavaMultiModalProjector = LlavaMultiModalProjectorForYiVL | |
| def get_forbidden_modules(config: "PretrainedConfig", finetuning_args: "FinetuningArguments") -> set[str]: | |
| r"""Freeze vision tower and language model for VLM full/freeze tuning.""" | |
| model_type = getattr(config, "model_type", None) | |
| forbidden_modules = set() | |
| if model_type in COMPOSITE_MODELS: | |
| if finetuning_args.freeze_vision_tower: | |
| vision_model_keys = COMPOSITE_MODELS[model_type].vision_model_keys | |
| logger.info_rank0(f"Set vision model not trainable: {vision_model_keys}.") | |
| forbidden_modules.update(vision_model_keys) | |
| if finetuning_args.freeze_multi_modal_projector: | |
| projector_keys = COMPOSITE_MODELS[model_type].projector_keys | |
| logger.info_rank0(f"Set multi model projector not trainable: {projector_keys}.") | |
| forbidden_modules.update(projector_keys) | |
| if finetuning_args.freeze_language_model: | |
| language_model_keys = COMPOSITE_MODELS[model_type].language_model_keys | |
| logger.info_rank0(f"Set language model not trainable: {language_model_keys}.") | |
| forbidden_modules.update(language_model_keys) | |
| return forbidden_modules | |
| def patch_target_modules( | |
| model: "PreTrainedModel", finetuning_args: "FinetuningArguments", target_modules: list[str] | |
| ) -> list[str]: | |
| r"""Freeze vision tower for VLM LoRA tuning.""" | |
| model_type = getattr(model.config, "model_type", None) | |
| if model_type in COMPOSITE_MODELS: | |
| forbidden_modules = get_forbidden_modules(model.config, finetuning_args) | |
| forbidden_modules.update(COMPOSITE_MODELS[model_type].lora_conflict_keys) | |
| module_names = [] | |
| for name, _ in model.named_modules(): | |
| if any(target_module in name for target_module in target_modules) and not any( | |
| forbidden_module in name for forbidden_module in forbidden_modules | |
| ): | |
| module_names.append(name) | |
| return module_names | |
| else: | |
| return target_modules | |
| _register_composite_model( | |
| model_type="dots_ocr", | |
| projector_keys=["vision_tower.merger"], | |
| vision_model_keys=["vision_tower"], | |
| language_model_keys=["model", "lm_head"], | |
| lora_conflict_keys=["merger"], | |
| ) | |
| _register_composite_model( | |
| model_type="gemma3", | |
| ) | |
| _register_composite_model( | |
| model_type="gemma3n", | |
| vision_model_keys=["vision_tower", "audio_tower"], | |
| lora_conflict_keys=["timm_model", "subsample_conv_projection"], | |
| ) | |
| _register_composite_model( | |
| model_type="gemma4", | |
| projector_keys=["model.embed_vision", "model.embed_audio"], | |
| vision_model_keys=["vision_tower", "audio_tower"], | |
| lora_conflict_keys=["per_layer_projection_norm"], | |
| ) | |
| # copied from qwen2vl | |
| _register_composite_model( | |
| model_type="glm4v", | |
| projector_keys=["visual.merger"], | |
| vision_model_keys=["visual.patch_embed", "visual.blocks"], | |
| language_model_keys=["language_model", "lm_head"], | |
| lora_conflict_keys=["patch_embed"], | |
| ) | |
| _register_composite_model( | |
| model_type="glm4v_moe", | |
| projector_keys=["visual.merger"], | |
| vision_model_keys=["visual.patch_embed", "visual.blocks"], | |
| language_model_keys=["language_model", "lm_head"], | |
| lora_conflict_keys=["patch_embed"], | |
| ) | |
| _register_composite_model( | |
| model_type="glm_ocr", | |
| projector_keys=["visual.merger"], | |
| vision_model_keys=["visual.patch_embed", "visual.blocks"], | |
| language_model_keys=["language_model", "lm_head"], | |
| lora_conflict_keys=["patch_embed"], | |
| ) | |
| _register_composite_model( | |
| model_type="internvl", | |
| ) | |
| _register_composite_model( | |
| model_type="interns1", | |
| ) | |
| _register_composite_model( | |
| model_type="Keye", | |
| projector_keys=["mlp_AR"], | |
| vision_model_keys=["visual.vision_model.patch_embedding", "visual.vision_model.encoder"], | |
| language_model_keys=["model", "lm_head"], | |
| lora_conflict_keys=["patch_embedding"], | |
| ) | |
| _register_composite_model( | |
| model_type="kimi_vl", | |
| ) | |
| _register_composite_model( | |
| model_type="llama4", | |
| vision_model_keys=["vision_model"], | |
| ) | |
| _register_composite_model( | |
| model_type="llava", | |
| ) | |
| _register_composite_model( | |
| model_type="llava_next", | |
| ) | |
| _register_composite_model( | |
| model_type="llava_next_video", | |
| ) | |
| _register_composite_model( | |
| model_type="minicpmv", | |
| projector_keys=["resampler"], | |
| vision_model_keys=["vpm"], | |
| language_model_keys=["llm"], | |
| ) | |
| _register_composite_model( | |
| model_type="minicpmv4_6", | |
| projector_keys=["model.merger"], | |
| vision_model_keys=["model.vision_tower"], | |
| language_model_keys=["model.language_model", "lm_head"], | |
| ) | |
| _register_composite_model( | |
| model_type="minicpmo", | |
| projector_keys=["resampler"], | |
| vision_model_keys=["vpm", "apm", "audio_avg_pooler", "audio_projection_layer", "tts"], | |
| language_model_keys=["llm"], | |
| lora_conflict_keys=["audio_projection_layer"], | |
| ) | |
| _register_composite_model( | |
| model_type="mistral3", | |
| projector_keys=["model.multi_modal_projector"], | |
| ) | |
| _register_composite_model( | |
| model_type="moss_vl", | |
| projector_keys=["model.visual.merger", "model.separator_token"], | |
| vision_model_keys=["model.visual.pos_embed", "model.visual.patch_embed", "model.visual.blocks"], | |
| language_model_keys=["model.language_model", "lm_head"], | |
| lora_conflict_keys=["patch_embed"], | |
| ) | |
| _register_composite_model( | |
| model_type="mllama", | |
| vision_model_keys=["vision_model"], | |
| ) | |
| _register_composite_model( | |
| model_type="paligemma", | |
| ) | |
| _register_composite_model( | |
| model_type="qwen2_audio", | |
| vision_model_keys=["audio_tower"], | |
| ) | |
| _register_composite_model( | |
| model_type="qwen2_5_omni_thinker", | |
| projector_keys=["visual.merger", "audio_tower.proj"], | |
| vision_model_keys=["visual.patch_embed", "visual.blocks", "audio_tower"], | |
| language_model_keys=["model", "lm_head"], | |
| lora_conflict_keys=["patch_embed"], | |
| ) | |
| _register_composite_model( | |
| model_type="qwen2_vl", | |
| projector_keys=["visual.merger"], | |
| vision_model_keys=["visual.patch_embed", "visual.blocks"], | |
| language_model_keys=["language_model", "lm_head"], | |
| lora_conflict_keys=["patch_embed"], | |
| ) | |
| _register_composite_model( | |
| model_type="qwen2_5_vl", | |
| projector_keys=["visual.merger"], | |
| vision_model_keys=["visual.patch_embed", "visual.blocks"], | |
| language_model_keys=["language_model", "lm_head"], | |
| lora_conflict_keys=["patch_embed"], | |
| ) | |
| _register_composite_model( | |
| model_type="qwen3_vl", | |
| projector_keys=["visual.merger"], | |
| vision_model_keys=["visual.pos_embed", "visual.patch_embed", "visual.blocks", "visual.deepstack_merger_list"], | |
| language_model_keys=["language_model", "lm_head"], | |
| lora_conflict_keys=["patch_embed"], | |
| ) | |
| _register_composite_model( | |
| model_type="qwen3_vl_moe", | |
| projector_keys=["visual.merger"], | |
| vision_model_keys=["visual.pos_embed", "visual.patch_embed", "visual.blocks", "visual.deepstack_merger_list"], | |
| language_model_keys=["language_model", "lm_head"], | |
| lora_conflict_keys=["patch_embed"], | |
| ) | |
| _register_composite_model( | |
| model_type="qwen3_omni_moe_thinker", | |
| projector_keys=["visual.merger", "audio_tower.proj"], | |
| vision_model_keys=[ | |
| "visual.pos_embed", | |
| "visual.patch_embed", | |
| "visual.blocks", | |
| "visual.deepstack_merger_list", | |
| "audio_tower", | |
| ], | |
| language_model_keys=["language_model", "lm_head"], | |
| lora_conflict_keys=["patch_embed"], | |
| ) | |
| _register_composite_model( | |
| model_type="qwen3_5", | |
| projector_keys=["model.visual.merger"], | |
| vision_model_keys=["visual.pos_embed", "visual.patch_embed", "visual.blocks"], | |
| language_model_keys=["language_model", "lm_head"], | |
| lora_conflict_keys=["patch_embed"], | |
| ) | |
| _register_composite_model( | |
| model_type="qwen3_5_moe", | |
| projector_keys=["model.visual.merger"], | |
| vision_model_keys=["visual.pos_embed", "visual.patch_embed", "visual.blocks"], | |
| language_model_keys=["language_model", "lm_head"], | |
| lora_conflict_keys=["patch_embed"], | |
| ) | |
| _register_composite_model( | |
| model_type="video_llava", | |
| ) | |