biomed-Qwen2-VL-2B-Instruct

Adapting Multimodal Large Language Models to Domains via Post-Training (EMNLP 2025)

This repos contains the biomedicine MLLM developed from Qwen-2-VL-2B-Instruct in our paper: On Domain-Specific Post-Training for Multimodal Large Language Models. The correspoding training dataset is in medicine-visual-instructions.

The main project page is: Adapt-MLLM-to-Domains

1. To Chat with AdaMLLM

Our model architecture aligns with the base model: Qwen-2-VL-Instruct. We provide a usage example below, and you may refer to the official Qwen-2-VL-Instruct repository for more advanced usage instructions.

Note: For AdaMLLM, always place the image at the beginning of the input instruction in the messages.

<details> <summary> Click to expand </summary>

1. Set up

pip install qwen-vl-utils

1. Inference

from transformers import Qwen2VLForConditionalGeneration, AutoTokenizer, AutoProcessor
from qwen_vl_utils import process_vision_info

# default: Load the model on the available device(s)
model = Qwen2VLForConditionalGeneration.from_pretrained(
    "AdaptLLM/biomed-Qwen2-VL-2B-Instruct", torch_dtype="auto", device_map="auto"
)

# We recommend enabling flash_attention_2 for better acceleration and memory saving, especially in multi-image and video scenarios.
# model = Qwen2VLForConditionalGeneration.from_pretrained(
#     "AdaptLLM/biomed-Qwen2-VL-2B-Instruct",
#     torch_dtype=torch.bfloat16,
#     attn_implementation="flash_attention_2",
#     device_map="auto",
# )

# default processer
processor = AutoProcessor.from_pretrained("AdaptLLM/biomed-Qwen2-VL-2B-Instruct")

# The default range for the number of visual tokens per image in the model is 4-16384. You can set min_pixels and max_pixels according to your needs, such as a token count range of 256-1280, to balance speed and memory usage.
# min_pixels = 256*28*28
# max_pixels = 1280*28*28
# processor = AutoProcessor.from_pretrained("AdaptLLM/biomed-Qwen2-VL-2B-Instruct", min_pixels=min_pixels, max_pixels=max_pixels)


# NOTE: For AdaMLLM, always place the image at the beginning of the input instruction in the messages.
messages = [
    {
        "role": "user",
        "content": [
            {
                "type": "image",
                "image": "https://qianwen-res.oss-cn-beijing.aliyuncs.com/Qwen-VL/assets/demo.jpeg",
            },
            {"type": "text", "text": "Describe this image."},
        ],
    }
]

# Preparation for inference
text = processor.apply_chat_template(
    messages, tokenize=False, add_generation_prompt=True
)
image_inputs, video_inputs = process_vision_info(messages)
inputs = processor(
    text=[text],
    images=image_inputs,
    videos=video_inputs,
    padding=True,
    return_tensors="pt",
)
inputs = inputs.to("cuda")

# Inference: Generation of the output
generated_ids = model.generate(**inputs, max_new_tokens=128)
generated_ids_trimmed = [
    out_ids[len(in_ids) :] for in_ids, out_ids in zip(inputs.input_ids, generated_ids)
]
output_text = processor.batch_decode(
    generated_ids_trimmed, skip_special_tokens=True, clean_up_tokenization_spaces=False
)
print(output_text)

</details>

2. To Evaluate Any MLLM on Domain-Specific Benchmarks

Please refer to the biomed-VQA-benchmark to reproduce our results and evaluate many other MLLMs on domain-specific benchmarks.

3. To Reproduce this Domain-Adapted MLLM

See Post-Train Guide to adapt MLLMs to domains.

Citation

If you find our work helpful, please cite us.

Adapt MLLM to Domains (EMNLP 2025 Findings)

@article{adamllm,
  title={On Domain-Adaptive Post-Training for Multimodal Large Language Models},
  author={Cheng, Daixuan and Huang, Shaohan and Zhu, Ziyu and Zhang, Xintong and Zhao, Wayne Xin and Luan, Zhongzhi and Dai, Bo and Zhang, Zhenliang},
  journal={arXiv preprint arXiv:2411.19930},
  year={2024}
}

Adapt LLM to Domains (ICLR 2024)

@inproceedings{
cheng2024adapting,
title={Adapting Large Language Models via Reading Comprehension},
author={Daixuan Cheng and Shaohan Huang and Furu Wei},
booktitle={The Twelfth International Conference on Learning Representations},
year={2024},
url={https://openreview.net/forum?id=y886UXPEZ0}
}