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
File size: 6,114 Bytes
83ddd7e | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 | # 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 torch
from llamafactory.model.model_utils.embedding import (
_description_based_initialization,
_existing_embeddings,
_noisy_mean_initialization,
_resolve_new_token_ids,
)
class _StubTokenizer:
"""Minimal tokenizer stub mapping token strings to fixed IDs."""
unk_token_id = 0
def __init__(self, mapping: dict[str, int], desc_ids: list[int] | None = None):
self._mapping = mapping
self._desc_ids = desc_ids or []
def convert_tokens_to_ids(self, token: str) -> int:
return self._mapping.get(token, self.unk_token_id)
def __call__(self, desc, return_tensors=None, add_special_tokens=False):
return {"input_ids": torch.tensor([self._desc_ids], dtype=torch.long)}
class _StubModel:
"""Wraps an embedding matrix so ``get_input_embeddings()`` is a usable lookup."""
def __init__(self, embed_weight: "torch.Tensor"):
self._emb = torch.nn.Embedding.from_pretrained(embed_weight.clone(), freeze=True)
def get_input_embeddings(self):
return self._emb
def test_resolve_new_token_ids_returns_none_without_config():
tokenizer = _StubTokenizer({})
assert _resolve_new_token_ids(None, tokenizer, embed_size=100) is None
assert _resolve_new_token_ids([], tokenizer, embed_size=100) is None
def test_resolve_new_token_ids_filters_invalid_and_dedups():
# "<a>" valid, "<unk_like>" maps to unk_token_id (skipped), "<oob>" out of range (skipped)
tokenizer = _StubTokenizer({"<a>": 10, "<unk_like>": 0, "<oob>": 999, "<b>": 5})
# duplicates and unsorted input -> sorted unique in-range IDs
tokens = ["<a>", "<a>", "<unk_like>", "<oob>", "<b>"]
assert _resolve_new_token_ids(tokens, tokenizer, embed_size=100) == [5, 10]
# passing a dict iterates its keys (config compatibility)
assert _resolve_new_token_ids({"<a>": "desc"}, tokenizer, embed_size=100) == [10]
def test_existing_embeddings_excludes_new_token_ids():
embed_weight = torch.arange(10 * 2, dtype=torch.float32).reshape(10, 2)
# explicit ids take precedence and drop exactly those rows
existing = _existing_embeddings(embed_weight, num_new_tokens=3, new_token_ids=[2, 5])
assert existing.size(0) == 8
# tail fallback when no explicit ids
tail = _existing_embeddings(embed_weight, num_new_tokens=3, new_token_ids=None)
assert torch.allclose(tail, embed_weight[:-3])
# no resize and no ids -> use everything
everything = _existing_embeddings(embed_weight, num_new_tokens=0, new_token_ids=None)
assert torch.allclose(everything, embed_weight)
def test_noisy_mean_initialization_with_token_ids_targets_exact_rows():
"""New tokens placed by explicit IDs must hit those rows, even inside the padding zone."""
torch.manual_seed(0)
vocab_size, embedding_dim = 20, 8
embed_weight = torch.zeros(vocab_size, embedding_dim)
# existing rows carry a constant so the mean is well-defined and non-zero
embed_weight[:16] = 1.0
# num_new_tokens reflects the embedding resize delta (4 padded rows),
# but the real new tokens sit at IDs 16 and 17 (inside what the tail slice would miss/over-cover).
target_ids = [16, 17]
_noisy_mean_initialization(embed_weight, num_new_tokens=4, token_ids=target_ids)
# targeted rows are initialized around the mean (~1.0) and not left at zero
for tid in target_ids:
assert not torch.allclose(embed_weight[tid], torch.zeros(embedding_dim))
assert abs(embed_weight[tid].mean().item() - 1.0) < 0.5
# untouched padding rows (18, 19) must remain zero
assert torch.allclose(embed_weight[18], torch.zeros(embedding_dim))
assert torch.allclose(embed_weight[19], torch.zeros(embedding_dim))
def test_noisy_mean_initialization_tail_fallback():
"""Without token_ids, falls back to the last num_new_tokens rows."""
torch.manual_seed(0)
vocab_size, embedding_dim = 12, 8
embed_weight = torch.zeros(vocab_size, embedding_dim)
embed_weight[:10] = 1.0
_noisy_mean_initialization(embed_weight, num_new_tokens=2, token_ids=None)
# last two rows initialized, earlier rows untouched
assert not torch.allclose(embed_weight[-1], torch.zeros(embedding_dim))
assert not torch.allclose(embed_weight[-2], torch.zeros(embedding_dim))
assert torch.allclose(embed_weight[0], torch.ones(embedding_dim))
def test_description_init_excludes_new_token_ids_from_average():
"""Description tokens that are themselves new (uninitialized) must be excluded.
Reproduces the padding-zone bug: id 17 is a new token and must not pollute the
semantic average for id 16; only the valid existing token (id 5) should be used.
"""
vocab_size, embedding_dim = 20, 4
embed_weight = torch.zeros(vocab_size, embedding_dim)
embed_weight[5] = 3.0 # the only valid description token
# description for "<x>" tokenizes to [5 (existing), 17 (new -> must be skipped)]
tokenizer = _StubTokenizer({"<x>": 16}, desc_ids=[5, 17])
model = _StubModel(embed_weight)
_description_based_initialization(
embed_weight,
num_new_tokens=4,
descriptions={"<x>": "ignored, ids come from the stub"},
tokenizer=tokenizer,
model=model,
new_token_ids=[16, 17],
add_noise=False,
)
# row 16 must equal embedding of id 5 only (3.0), not the (5,17) average (1.5)
assert torch.allclose(embed_weight[16], torch.full((embedding_dim,), 3.0))
if __name__ == "__main__":
import pytest
pytest.main([__file__])
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