| <h3 align="center"> |
| 🩺 MedEvalKit: A Unified Medical Evaluation Framework |
| </h3> |
|
|
| <p align="center"> |
| <a href="https://arxiv.org/abs/2506.07044" target="_blank">📖 arXiv Paper</a> • |
| <a href="https://huggingface.co/collections/lingshu-medical-mllm/lingshu-mllms-6847974ca5b5df750f017dad" target="_blank">🤗 Lingshu Models</a> • |
| <a href="https://alibaba-damo-academy.github.io/lingshu/" target="_blank">🌐 Lingshu Project Page</a> |
| </p> |
|
|
| <p align="center"> |
| <a href="https://opensource.org/license/apache-2-0"> |
| <img src="https://img.shields.io/badge/Code%20License-Apache_2.0-green.svg" alt="License"> |
| </a> |
| <a href="https://github.com/alibaba-damo-academy"> |
| <img src="https://img.shields.io/badge/Institution-DAMO-red" alt="Institution"> |
| </a> |
| <a> |
| <img src="https://img.shields.io/badge/PRs-Welcome-red" alt="PRs Welcome"> |
| </a> |
| </p> |
| |
| --- |
|
|
| ## 📌 Introduction |
| A comprehensive evaluation framework for **Large Medical Models (LMMs/LLMs)** in the healthcare domain. |
| We welcome contributions of new models, benchmarks, or enhanced evaluation metrics! |
|
|
| --- |
|
|
| ## Eval Results |
| ### MultiModal Eval Results |
| <p align="center"> |
| <a> |
| <img src="assets/mm_eval.png"> |
| </a> |
| </p> |
| |
| ### Text-Only Eval Results |
| <p align="center"> |
| <a> |
| <img src="assets/text_eval.png"> |
| </a> |
| </p> |
| |
|
|
|
|
|
|
| ## 🔥 Latest News |
| * **2025-06-12** - Initial release of MedEvalKit v1.0! |
| --- |
|
|
| ## 🧪 Supported Benchmarks |
|
|
| | Multimodal Medical Benchmarks | Text-Only Medical Benchmarks | |
| |-----------------------|----------------------| |
| | MMMU-Medical-test | MedQA-USMLE | |
| | MMMU-Medical-val | MedMCQA | |
| | PMC_VQA | PubMedQA | |
| | OmniMedVQA | Medbullets-op4 | |
| | IU XRAY | Medbullets-op5 | |
| | MedXpertQA-Multimodal | MedXpertQA-Text | |
| | CheXpert Plus | SuperGPQA | |
| | MIMIC-CXR | HealthBench | |
| | VQA-RAD | CMB | |
| | SLAKE | CMExam | |
| | PATH-VQA | CMMLU | |
| | MedFrameQA | MedQA-MCMLE | |
| |
| --- |
| |
| ## 🤖 Supported Models |
| ### HuggingFace Exclusive |
| <div style="column-count: 2;"> |
| |
| * BiMediX2 |
| * BiomedGPT |
| * HealthGPT |
| * Janus |
| * Med_Flamingo |
| * MedDr |
| * MedGemma |
| * NVILA |
| * VILA_M3 |
| |
| </div> |
| |
| ### HF + vLLM Compatible |
| <div style="column-count: 2;"> |
| |
| * HuatuoGPT-vision |
| * InternVL |
| * Llama_3.2-vision |
| * LLava |
| * LLava_Med |
| * Qwen2_5_VL |
| * Qwen2_VL |
|
|
| </div> |
|
|
| --- |
|
|
| ## 🛠️ Installation |
| ```bash |
| # Clone repository |
| git clone https://github.com/DAMO-NLP-SG/MedEvalKit |
| cd MedEvalKit |
| |
| # Install dependencies |
| pip install -r requirements.txt |
| pip install 'open_clip_torch[training]' |
| pip install flash-attn --no-build-isolation |
| |
| # For LLaVA-like models |
| git clone https://github.com/LLaVA-VL/LLaVA-NeXT.git |
| cd LLaVA-NeXT && pip install -e . |
| ``` |
|
|
| --- |
|
|
| ## 📂 Dataset Preparation |
| ### HuggingFace Datasets (Direct Access) |
| ```python |
| # Set DATASETS_PATH='hf' |
| VQA-RAD: flaviagiammarino/vqa-rad |
| SuperGPQA: m-a-p/SuperGPQA |
| PubMedQA: openlifescienceai/pubmedqa |
| PATHVQA: flaviagiammarino/path-vqa |
| MMMU: MMMU/MMMU |
| MedQA-USMLE: GBaker/MedQA-USMLE-4-options |
| MedQA-MCMLE: shuyuej/MedQA-MCMLE-Benchmark |
| Medbullets_op4: tuenguyen/Medical-Eval-MedBullets_op4 |
| Medbullets_op5: LangAGI-Lab/medbullets_op5 |
| CMMMU: haonan-li/cmmlu |
| CMExam: fzkuji/CMExam |
| CMB: FreedomIntelligence/CMB |
| MedFrameQA: SuhaoYu1020/MedFrameQA |
| ``` |
|
|
| ### Local Datasets (Manual Download Required) |
| | Dataset | Source | |
| |------------------|--------| |
| | MedXpertQA | [TsinghuaC3I](https://huggingface.co/datasets/TsinghuaC3I/MedXpertQA) | |
| | SLAKE | [BoKelvin](https://huggingface.co/datasets/BoKelvin/SLAKE) | |
| | PMCVQA | [RadGenome](https://huggingface.co/datasets/RadGenome/PMC-VQA) | |
| | OmniMedVQA | [foreverbeliever](https://huggingface.co/datasets/foreverbeliever/OmniMedVQA) | |
| | MIMIC_CXR | [MIMIC_CXR](https://physionet.org/content/mimic-cxr/2.1.0/) | |
| | IU_Xray | [IU_Xray](https://openi.nlm.nih.gov/faq?download=true) | |
| | CheXpert Plus | [CheXpert Plus](https://aimi.stanford.edu/datasets/chexpert-plus) | |
| | HealthBench | [Normal](https://openaipublic.blob.core.windows.net/simple-evals/healthbench/2025-05-07-06-14-12_oss_eval.jsonl),[Hard](https://openaipublic.blob.core.windows.net/simple-evals/healthbench/hard_2025-05-08-21-00-10.jsonl),[Consensus](https://openaipublic.blob.core.windows.net/simple-evals/healthbench/consensus_2025-05-09-20-00-46.jsonl) | |
|
|
| --- |
|
|
| ## 🚀 Quick Start |
| ### 1. Configure `eval.sh` |
| ```bash |
| #!/bin/bash |
| export HF_ENDPOINT=https://hf-mirror.com |
| # MMMU-Medical-test,MMMU-Medical-val,PMC_VQA,MedQA_USMLE,MedMCQA,PubMedQA,OmniMedVQA,Medbullets_op4,Medbullets_op5,MedXpertQA-Text,MedXpertQA-MM,SuperGPQA,HealthBench,IU_XRAY,CheXpert_Plus,MIMIC_CXR,CMB,CMExam,CMMLU,MedQA_MCMLE,VQA_RAD,SLAKE,PATH_VQA,MedFrameQA |
| EVAL_DATASETS="Medbullets_op4" |
| DATASETS_PATH="hf" |
| OUTPUT_PATH="eval_results/{}" |
| # TestModel,Qwen2-VL,Qwen2.5-VL,BiMediX2,LLava_Med,Huatuo,InternVL,Llama-3.2,LLava,Janus,HealthGPT,BiomedGPT,Vllm_Text,MedGemma,Med_Flamingo,MedDr |
| MODEL_NAME="Qwen2.5-VL" |
| MODEL_PATH="Qwen2.5-VL-7B-Instruct" |
| |
| #vllm setting |
| CUDA_VISIBLE_DEVICES="0" |
| TENSOR_PARALLEL_SIZE="1" |
| USE_VLLM="False" |
| |
| #Eval setting |
| SEED=42 |
| REASONING="False" |
| TEST_TIMES=1 |
| |
| |
| # Eval LLM setting |
| MAX_NEW_TOKENS=8192 |
| MAX_IMAGE_NUM=6 |
| TEMPERATURE=0 |
| TOP_P=0.0001 |
| REPETITION_PENALTY=1 |
| |
| # LLM judge setting |
| USE_LLM_JUDGE="True" |
| # gpt api model name |
| GPT_MODEL="gpt-4.1-2025-04-14" |
| OPENAI_API_KEY="" |
| |
| |
| # pass hyperparameters and run python sccript |
| python eval.py \ |
| --eval_datasets "$EVAL_DATASETS" \ |
| --datasets_path "$DATASETS_PATH" \ |
| --output_path "$OUTPUT_PATH" \ |
| --model_name "$MODEL_NAME" \ |
| --model_path "$MODEL_PATH" \ |
| --seed $SEED \ |
| --cuda_visible_devices "$CUDA_VISIBLE_DEVICES" \ |
| --tensor_parallel_size "$TENSOR_PARALLEL_SIZE" \ |
| --use_vllm "$USE_VLLM" \ |
| --max_new_tokens "$MAX_NEW_TOKENS" \ |
| --max_image_num "$MAX_IMAGE_NUM" \ |
| --temperature "$TEMPERATURE" \ |
| --top_p "$TOP_P" \ |
| --repetition_penalty "$REPETITION_PENALTY" \ |
| --reasoning "$REASONING" \ |
| --use_llm_judge "$USE_LLM_JUDGE" \ |
| --judge_gpt_model "$GPT_MODEL" \ |
| --openai_api_key "$OPENAI_API_KEY" \ |
| --test_times "$TEST_TIMES" |
| ``` |
|
|
| ### 2. Run Evaluation |
| ```bash |
| chmod +x eval.sh # Add execute permission |
| ./eval.sh |
| ``` |
|
|
| --- |
|
|
| ## 📜 Citation |
| ```bibtex |
| @article{xu2025lingshu, |
| title={Lingshu: A Generalist Foundation Model for Unified Multimodal Medical Understanding and Reasoning}, |
| author={Xu, Weiwen and Chan, Hou Pong and Li, Long and Aljunied, Mahani and Yuan, Ruifeng and Wang, Jianyu and Xiao, Chenghao and Chen, Guizhen and Liu, Chaoqun and Li, Zhaodonghui and others}, |
| journal={arXiv preprint arXiv:2506.07044}, |
| year={2025} |
| } |
| ``` |
|
|
| <div align="center"> |
| <sub>Built with ❤️ by the DAMO Academy Medical AI Team</sub> |
| </div> |
|
|
