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
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#
# 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 inspect
import os
from collections import Counter
import pytest
import torch
from PIL import Image
from transformers import AutoConfig, AutoModelForImageTextToText
from llamafactory.data import get_template_and_fix_tokenizer
from llamafactory.data.collator import MultiModalDataCollatorForSeq2Seq, prepare_4d_attention_mask
from llamafactory.extras.constants import IGNORE_INDEX
from llamafactory.extras.packages import is_transformers_version_greater_than
from llamafactory.hparams import get_infer_args
from llamafactory.model import load_tokenizer
TINY_LLAMA3 = os.getenv("TINY_LLAMA3", "llamafactory/tiny-random-Llama-3")
@pytest.mark.runs_on(["cpu", "mps"])
def test_base_collator():
model_args, data_args, *_ = get_infer_args({"model_name_or_path": TINY_LLAMA3, "template": "default"})
tokenizer_module = load_tokenizer(model_args)
template = get_template_and_fix_tokenizer(tokenizer_module["tokenizer"], data_args)
data_collator = MultiModalDataCollatorForSeq2Seq(
template=template,
pad_to_multiple_of=8,
label_pad_token_id=IGNORE_INDEX,
**tokenizer_module,
)
p = tokenizer_module["tokenizer"].pad_token_id
q = IGNORE_INDEX
features = [
{
"input_ids": [0, 1, 2, 3, 4, 5],
"attention_mask": [1, 1, 1, 1, 1, 1],
"labels": [q, q, 2, 3, 4, 5],
},
{
"input_ids": [6, 7],
"attention_mask": [1, 1],
"labels": [q, 7],
},
]
batch_input = data_collator(features)
expected_input = {
"input_ids": [
[0, 1, 2, 3, 4, 5, p, p],
[6, 7, p, p, p, p, p, p],
],
"attention_mask": [
[1, 1, 1, 1, 1, 1, 0, 0],
[1, 1, 0, 0, 0, 0, 0, 0],
],
"labels": [
[q, q, 2, 3, 4, 5, q, q],
[q, 7, q, q, q, q, q, q],
],
}
for k in batch_input.keys():
assert batch_input[k].eq(torch.tensor(expected_input[k])).all()
@pytest.mark.runs_on(["cpu", "mps"])
def test_multimodal_collator():
model_args, data_args, *_ = get_infer_args(
{"model_name_or_path": "Qwen/Qwen2-VL-2B-Instruct", "template": "qwen2_vl"}
)
tokenizer_module = load_tokenizer(model_args)
template = get_template_and_fix_tokenizer(tokenizer_module["tokenizer"], data_args)
config = AutoConfig.from_pretrained(model_args.model_name_or_path)
with torch.device("meta"):
model = AutoModelForImageTextToText.from_config(config)
data_collator = MultiModalDataCollatorForSeq2Seq(
template=template,
model=model,
pad_to_multiple_of=4,
label_pad_token_id=IGNORE_INDEX,
**tokenizer_module,
)
p = tokenizer_module["tokenizer"].pad_token_id
q = IGNORE_INDEX
s = tokenizer_module["tokenizer"].convert_tokens_to_ids("<|vision_start|>")
e = tokenizer_module["tokenizer"].convert_tokens_to_ids("<|vision_end|>")
m = tokenizer_module["tokenizer"].convert_tokens_to_ids("<|image_pad|>")
fake_image = Image.new("RGB", (64, 64), (255, 255, 255))
features = [
{
"input_ids": [0, 1, 2, 3],
"attention_mask": [1, 1, 1, 1],
"labels": [0, 1, 2, 3],
},
]
batch_input = data_collator(features)
expected_input = {
"input_ids": [
[0, 1, 2, 3, s, m, m, m, m, e, p, p],
],
"attention_mask": [
[1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0],
],
"labels": [
[0, 1, 2, 3, q, q, q, q, q, q, q, q],
],
"position_ids": [[[0, 1, 2, 3, 0, 0, 0, 0, 0, 0, 0, 0]]] * 3,
"rope_deltas": [[0]],
**tokenizer_module["processor"].image_processor(fake_image),
}
if not is_transformers_version_greater_than("5.0.0"):
# adapt position_ids and rope_deltas for transformers < 5.0.0
# https://github.com/huggingface/transformers/pull/43972
expected_input["position_ids"] = [[[0, 1, 2, 3, 1, 1, 1, 1, 1, 1, 1, 1]]] * 3
expected_input["rope_deltas"] = [[-8]]
assert batch_input.keys() == expected_input.keys()
for k in batch_input.keys():
if k == "position_ids" and batch_input[k].dim() == 3 and batch_input[k].shape[0] == 4:
batch_input[k] = batch_input[k][1:]
assert batch_input[k].eq(torch.tensor(expected_input[k])).all()
def _make_packed_feature(
*,
packing_params: dict,
pad_token_id: int,
label_ignore_id: int,
fake_image: Image.Image,
vision_start_id: int | None = None,
vision_end_id: int | None = None,
image_pad_id: int | None = None,
) -> dict:
r"""Build one packed sample using the new PackingParams schema."""
sequence_boundaries = packing_params["sequence_boundaries"]
image_subseq_ids = packing_params["image_subseq_ids"]
video_subseq_ids = packing_params["video_subseq_ids"]
audio_subseq_ids = packing_params["audio_subseq_ids"]
unpadded_length = packing_params["unpadded_length"]
right_padding_length = packing_params["right_padding_length"] # which only preserved in tests
cutoff_plus_one = sequence_boundaries[-1]
content_len = unpadded_length
pad_len = right_padding_length
assert content_len + pad_len == cutoff_plus_one
assert sequence_boundaries[0] == 0
assert sequence_boundaries[-1] == cutoff_plus_one
content_ids = list(range(100, 100 + content_len))
if vision_start_id is not None and vision_end_id is not None and image_pad_id is not None:
image_counts_by_subseq = Counter(image_subseq_ids)
for subseq_idx, image_count in sorted(image_counts_by_subseq.items()):
if subseq_idx >= len(sequence_boundaries) - 1:
continue
subseq_start = sequence_boundaries[subseq_idx]
subseq_end = sequence_boundaries[subseq_idx + 1]
subseq_len = subseq_end - subseq_start
if subseq_len < 3:
continue
# Build repeated image groups while preserving at least 3 tokens for each remaining image.
injected_tokens: list[int] = []
remaining = subseq_len
for image_idx in range(image_count):
remaining_images = image_count - image_idx
min_reserved_for_rest = 3 * (remaining_images - 1)
current_group_len = min(6, remaining - min_reserved_for_rest)
if current_group_len < 3:
break
group = [vision_start_id] + [image_pad_id] * max(1, current_group_len - 2) + [vision_end_id]
injected_tokens.extend(group[:current_group_len])
remaining -= current_group_len
if injected_tokens:
insert_end = subseq_start + len(injected_tokens)
content_ids[subseq_start:insert_end] = injected_tokens
input_ids = content_ids + [pad_token_id] * pad_len
attention_mask = [1] * content_len + [0] * pad_len
labels = [label_ignore_id] * cutoff_plus_one
return {
"input_ids": input_ids,
"attention_mask": attention_mask,
"labels": labels,
"images": [fake_image] * len(image_subseq_ids),
"videos": [None] * len(video_subseq_ids),
"audios": [None] * len(audio_subseq_ids),
"packing_params": packing_params,
}
def _make_packed_features(
*,
packing_params: dict,
pad_token_id: int,
label_ignore_id: int,
fake_image: Image.Image,
vision_start_id: int,
vision_end_id: int,
image_pad_id: int,
) -> list[dict]:
r"""Build packed features from caller-provided packing_params."""
return [
_make_packed_feature(
packing_params=packing_params,
pad_token_id=pad_token_id,
label_ignore_id=label_ignore_id,
fake_image=fake_image,
vision_start_id=vision_start_id,
vision_end_id=vision_end_id,
image_pad_id=image_pad_id,
)
]
def _get_expected_position_ids(
packing_params,
get_rope_func,
input_ids,
attention_mask,
image_token_id: int | None = None,
video_token_id: int | None = None,
) -> torch.Tensor:
bound_list = packing_params["sequence_boundaries"]
input_ids_slices = [input_ids[bound_list[i] : bound_list[i + 1]] for i in range(len(bound_list) - 1)]
attention_mask_slices = [attention_mask[bound_list[i] : bound_list[i + 1]] for i in range(len(bound_list) - 1)]
img_counts_by_subseq = Counter(packing_params["image_subseq_ids"])
needs_mm_token_type_ids = "mm_token_type_ids" in inspect.signature(get_rope_func).parameters
all_position_ids = []
for i, input_ids_slice in enumerate(input_ids_slices):
img_cnt = img_counts_by_subseq[i]
if sum(attention_mask_slices[i]) == 0:
continue
input_ids_tensor = torch.tensor(input_ids_slice).unsqueeze(0)
rope_func_kwargs = {
"input_ids": input_ids_tensor,
"attention_mask": torch.tensor(attention_mask_slices[i]).unsqueeze(0),
"image_grid_thw": [torch.tensor([1, 4, 4])] * img_cnt,
}
if needs_mm_token_type_ids:
mm_token_type_ids = torch.zeros_like(input_ids_tensor)
if image_token_id is not None:
mm_token_type_ids[input_ids_tensor == image_token_id] = 1
if video_token_id is not None:
mm_token_type_ids[input_ids_tensor == video_token_id] = 2
rope_func_kwargs["mm_token_type_ids"] = mm_token_type_ids
position_ids, _ = get_rope_func(**rope_func_kwargs)
all_position_ids.append(position_ids)
return torch.cat(all_position_ids, dim=-1)
@pytest.mark.runs_on(["cpu", "mps"])
def test_multimodal_collator_with_packing():
model_args, data_args, *_ = get_infer_args(
{"model_name_or_path": "Qwen/Qwen2-VL-2B-Instruct", "template": "qwen2_vl"}
)
tokenizer_module = load_tokenizer(model_args)
template = get_template_and_fix_tokenizer(tokenizer_module["tokenizer"], data_args)
tokenizer_module["tokenizer"].padding_side = "right"
config = AutoConfig.from_pretrained(model_args.model_name_or_path)
with torch.device("meta"):
model = AutoModelForImageTextToText.from_config(config)
data_collator = MultiModalDataCollatorForSeq2Seq(
template=template,
model=model,
pad_to_multiple_of=4,
label_pad_token_id=IGNORE_INDEX,
**tokenizer_module,
)
tokenizer = tokenizer_module["tokenizer"]
packing_params = {
"sequence_boundaries": [0, 2, 10, 18, 28, 32],
"image_subseq_ids": [1, 2, 3],
"video_subseq_ids": [],
"audio_subseq_ids": [],
"unpadded_length": 28,
"right_padding_length": 4,
}
fake_image = Image.new("RGB", (64, 64), (255, 255, 255))
features = _make_packed_features(
packing_params=packing_params,
pad_token_id=tokenizer.pad_token_id,
label_ignore_id=IGNORE_INDEX,
fake_image=fake_image,
vision_start_id=tokenizer.convert_tokens_to_ids("<|vision_start|>"),
vision_end_id=tokenizer.convert_tokens_to_ids("<|vision_end|>"),
image_pad_id=tokenizer.convert_tokens_to_ids("<|image_pad|>"),
)
expected_position_ids = _get_expected_position_ids(
packing_params,
data_collator.get_rope_func,
features[0]["input_ids"],
features[0]["attention_mask"],
image_token_id=getattr(model.config, "image_token_id", None),
video_token_id=getattr(model.config, "video_token_id", None),
)
batch_input = data_collator(features) # [3, bsz, seq_len]
valid_len = expected_position_ids.shape[-1]
assert batch_input["position_ids"][1:, :, :valid_len].eq(expected_position_ids).all()
@pytest.mark.runs_on(["cpu"])
def test_4d_attention_mask():
o = 0.0
x = torch.finfo(torch.float16).min
attention_mask_with_indices = torch.tensor(
[
[1, 1, 2, 2, 2, 0],
[1, 2, 2, 3, 3, 3],
]
)
attention_mask_computed = prepare_4d_attention_mask(attention_mask_with_indices, torch.float16)
attention_mask_expected = torch.tensor(
[
[
[
[o, x, x, x, x, x],
[o, o, x, x, x, x],
[x, x, o, x, x, x],
[x, x, o, o, x, x],
[x, x, o, o, o, x],
[x, x, x, x, x, x],
]
],
[
[
[o, x, x, x, x, x],
[x, o, x, x, x, x],
[x, o, o, x, x, x],
[x, x, x, o, x, x],
[x, x, x, o, o, x],
[x, x, x, o, o, o],
]
],
],
dtype=torch.float16,
)
assert list(attention_mask_computed.size()) == [2, 1, 6, 6]
assert torch.all(attention_mask_computed == attention_mask_expected)
if __name__ == "__main__":
test_multimodal_collator()
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