Update README.md

README.md

@@ -7,4 +7,129 @@ library_name: transformers
 tags:
 - multimodal
 - Pathology
----
+- arxiv:2505.11404
+extra_gated_prompt: >-
+  The Patho-R1-3B model and its associated materials are released under the CC-BY-NC-ND 4.0 license. 
+  Access is restricted to non-commercial, academic research purposes only, with proper citation required. 
+  Any commercial usage, redistribution, or derivative work (including training models based on this model or generating datasets from its outputs) 
+  is strictly prohibited without prior written approval. 
+
+  Users must register with an official institutional email address (generic domains such as @gmail, @qq, @hotmail, etc. will not be accepted). 
+  By requesting access, you confirm that your information is accurate and current, and that you agree to comply with all terms listed herein. 
+  If other members of your organization wish to use the model, they must register independently and agree to the same terms.
+
+extra_gated_fields:
+  Full name (first and last): text
+  Institutional affiliation (no abbreviations): text
+  Role/Position:
+    type: select
+    options:
+      - Faculty/Principal Investigator
+      - PhD Student
+      - Postdoctoral Researcher
+      - Research Staff
+      - Other
+  Official institutional email (**must match your Hugging Face primary email; generic domains will be denied**): text
+  Intended research use (be specific): text
+  I agree to use this model only for non-commercial academic purposes: checkbox
+  I agree not to redistribute this model or share it outside of my individual usage: checkbox
+  I confirm that all submitted information is accurate and up to date: checkbox
+---
+## Introduction📝
+While vision-language models have shown impressive progress in general medical domains, pathology remains a challenging subfield due to its high-resolution image requirements and complex diagnostic reasoning.  
+
+To address this gap, we introduce **Patho-R1-3B**, a multimodal pathology reasoner designed to enhance diagnostic understanding through structured reasoning. **Patho-R1-3B** is trained using a three-stage pipeline:  
+1. *Continued pretraining* on **3.5M pathology figure-caption pairs** for domain knowledge acquisition  
+2. *Supervised fine-tuning* on **500k expert-annotated Chain-of-Thought samples** to encourage reasoning  
+3. *Reinforcement learning* with **Decoupled CLIP and Dynamic sAmpling Policy Optimization** to refine response quality  
+
+Experimental results show that **Patho-R1-3B** achieves strong performance across key pathology tasks, including **multiple choice questions** and **visual question answering**, highlighting its potential for real-world pathology AI applications.
+
+### Quickstart🏃
+Here we show a code snippet to show you how to use the chat model with `transformers` and `qwen_vl_utils`:
+
+```python
+from transformers import Qwen2_5_VLForConditionalGeneration, AutoProcessor
+from qwen_vl_utils import process_vision_info
+
+
+model = Qwen2_5_VLForConditionalGeneration.from_pretrained(
+    "WenchuanZhang/Patho-R1-3B",
+    torch_dtype="auto", device_map="auto"
+)
+processor = AutoProcessor.from_pretrained("WenchuanZhang/Patho-R1-3B")
+
+# example question from Pathmmu-test-dataset
+# ground truth: D
+
+messages = [
+    {   "role": "system",
+        "content": [
+            {
+                "type": "image",
+                "image": "./images/241.jpg",
+            },
+            {"type": "text", "text": "You are a pathology expert, your task is to answer question step by step. Use the following format:<think> Your step-by-step reasoning </think><answer> Your final answer </answer>"},
+        ],
+
+    },
+    {
+        "role": "user",
+        "content": [
+            {
+                "type": "image",
+                "image": "./images/241.jpg",
+            },
+            {"type": "text", "text": "What feature in the provided micrograph is indicative of chronic inflammation? /n A. Granuloma formation /n B. Multinucleated giant cells /n C. Neutrophilic infiltration /n D. Plasma cells with eccentrically placed nuclei"},       
+        ],
+    }
+]
+# 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(model.device)
+
+# Inference: Generation of the output
+generated_ids = model.generate(**inputs, max_new_tokens=2048)
+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)
+```
+## Acknowledgements🎖
+
+We gratefully acknowledge the contributions of the open-source community, particularly the following projects which laid the foundation for various components of this work:
+
+- [Qwen](https://github.com/QwenLM) for providing powerful vision language models that significantly advanced our multimodal understanding and generation capabilities.  
+- [DocLayout-YOLO](https://github.com/opendatalab/DocLayout-YOLO) for document layout detection.  
+- [PaddleOCR](https://github.com/PaddlePaddle/PaddleOCR) for comprehensive optical character recognition.  
+- [ModelScope Swift](https://github.com/modelscope/ms-swift) for efficient model serving and deployment tools.  
+- [LLaMA-Factory](https://github.com/hiyouga/LLaMA-Factory) for robust LLM training and fine-tuning pipelines.  
+- [VERL](https://github.com/volcengine/verl) for valuable visual-language pretraining resources.  
+- [DeepSeek](https://github.com/deepseek-ai) for high-quality models and infrastructure supporting text understanding.
+
+We thank the authors and contributors of these repositories for their dedication and impactful work, which made our development of Patho-R1-3B possible.
+
+## Citation❤️
+If you find our work helpful, a citation would be greatly appreciated:
+
+```
+@article{zhang2025patho,
+  title={Patho-R1: A Multimodal Reinforcement Learning-Based Pathology Expert Reasoner},
+  author={Zhang, Wenchuan and Zhang, Penghao and Guo, Jingru and Cheng, Tao and Chen, Jie and Zhang, Shuwan and Zhang, Zhang and Yi, Yuhao and Bu, Hong},
+  journal={arXiv preprint arXiv:2505.11404},
+  year={2025}
+}
+```