ChiPhan1110/ScaleReasoner-R1

[MICCAI 2026] Enhancing Pathological VLMs with Cross-scale Reasoning

Chi Phan*, Tianyi Zhang*, Qiaochu Xue, Yufeng Wu, Dan Hu, Zeyu Liu, Sudong Wang, Yueming Jin

🔬 Overview

Pathological diagnosis is inherently multi-scale: pathologists reason from global tissue architecture at low magnification down to cellular morphology at high magnification, integrating evidence across views before reaching a conclusion. While existing pathological datasets for vision-language models (VLMs) include various scales, they often lack explicit cross-scale reasoning objectives. This limitation prevents VLMs from capturing essential cross-scale representations and learning evidence-based reasoning.

We introduce the first cross-scale training and evaluation paradigm for pathological VLMs, along with:

• Scale-VQA - a high-quality benchmark of 4,685 leakage-aware multiple-choice questions grounded in multi-magnification pathology images across 15 organs and 5 clinically-aligned reasoning dimensions.
• ScaleReasoner-R1 - a pathology VLM trained with Group Relative Policy Optimization (GRPO) that achieves state-of-the-art performance on cross-scale multi-image VQA and transfers strongly to established single-image benchmarks.

🧩 Method

(a) Leakage-aware curation pipeline for Scale-VQA. (b) Dataset overview across organs and magnifications. (c) GRPO-based reinforcement learning framework for ScaleReasoner-R1.

Scale-VQA: Leakage-Aware Cross-Scale Benchmark

Naively constructed cross-scale VQA benchmarks suffer from text-only shortcut solutions — models can infer the correct answer from linguistic or biomedical priors without ever examining the images. Our curation pipeline eliminates these via three steps:

Step	Description
Scale-specific Feature Decomposition	Expert annotations are decomposed into per-scale evidence sets; initial visual-grounding and scale-dependency constraints are imposed.
Text-only Adversarial Screening	Gemini 3 Pro and Qwen3-Max act as text-only adversaries. If either model answers correctly without images, constraints are tightened and questions are regenerated.
Cross-scale MCQ Construction & Clinical Validation	Final MCQs are reviewed by senior pathologists to confirm that correct answers are visually grounded and distractors are clinically plausible.

ScaleReasoner-R1: Cross-scale Reasoning via RL

ScaleReasoner-R1 is initialized from Patho-R1-7B and fine-tuned with GRPO on Scale-VQA. Given a multi-scale image set I = {I_(10x), I_(40x), I_(200x)}, a question, and options, the model generates a structured response with a reasoning trace (<think>) followed by a final answer (<answer>).

Training Dynamics:

Training Reward	Validation Accuracy

🏆 Results

Cross-scale Multi-image VQA

Model	Corresp.	Confirm.	Localiz.	Explan.	Diagno.	AVG
Qwen2.5-VL-7B	41.79	47.26	71.14	44.28	63.68	53.63
Gemini 3 Flash	48.26	58.71	71.64	53.73	72.14	60.90
GPT-5.2	47.76	59.70	74.13	45.77	65.17	58.51
LLaVA-Med-7B	25.87	16.92	28.36	20.90	24.88	23.38
Quilt-LLaVA	32.34	14.43	45.27	30.35	29.35	30.35
CLOVER	37.31	61.69	73.13	46.27	65.77	56.82
Patho-R1	31.84	40.30	59.70	56.22	68.66	51.34
ScaleReasoner-R1	80.60	89.05	84.58	76.12	84.08	82.89

Single-image VQA (PathMMU)

Model	Overall	PubMed	SocialPath	EduContent	Atlas	PathCLS
Patho-R1	64.8	68.7	63.9	65.7	73.5	41.8
ScaleReasoner-R1	66.2	71.2	67.6	67.6	79.3	37.9

---

📁 Repository Structure

ScaleReasoner-R1/
├── assets/                          
├── data/                            # Cross-scale VQA json by split
├── preprocess/
│   ├── generate_vqa_data/           # Feature extraction, VQA generation, split creation
│   └── prompts/                     # Leakage-aware prompt templates and constraints
├── script/
│   ├── preprocess/                  # End-to-end preprocessing entrypoints
│   ├── train/                       # SFT and GRPO launch scripts
│   └── postprocess/                 # Postprocess after training
├── LLaMA-Factory/                   # SFT training framework          
└── verl/                            # RL training framework                            

🚀 Getting Started

Environment Setup

# Clone the repository
git clone https://github.com/iMVR-PL/ScaleReasoner-R1.git
cd ScaleReasoner-R1

# Set up environment variables
cp script/.env.example script/.env
# Edit script/.env with your paths and API keys

Configure script/.env:

# Data paths
DATA_DIR=/path/to/triplet_raw_data
ROOT=/path/to/ScaleReasoner-R1
PROCESSED_DIR=/path/to/processed_data

# Model paths
ACTOR_MODEL_DIR=/path/to/patho-r1-7b   # base model (Patho-R1-7B)
RESULTS_DIR=/path/to/results

# Logging
LOG_DIR=/path/to/logs
WANDB_DIR=/path/to/wandb

# API keys (for VQA generation pipeline)
GEMINI_API_KEY=...
OPENAI_API_KEY=...
DASHSCOPE_API_KEY=...
HF_TOKEN=...

RL environment (verl). ScaleReasoner-R1 is trained with verl. Please follow the verl installation guide to set up the environment, then install the local copy:

conda create -n verl python=3.10 -y && conda activate verl
pip install -e verl/

SFT environment (LLaMA-Factory). The SFT baseline uses LLaMA-Factory:

conda create -n sft python=3.10 -y && conda activate sft
pip install -e LLaMA-Factory/

Both environments require CUDA 12.1+ and PyTorch 2.3+. We recommend using separate conda environments for RL and SFT to avoid dependency conflicts.

🗂️ Dataset

Download Scale-VQA from HuggingFace. The data/ directory contains the train/val/test splits in JSON format. Each sample includes:

{
  "question": "...",
  "options": { "A": "...", "B": "...", "C": "...", "D": "..." },
  "answer": "D",
  "rationale": "...",
  "image_path": {
    "low_mag":  "wsi_id/rois/10_....jpg",
    "mid_mag":  "wsi_id/rois/40_....jpg",
    "high_mag": "wsi_id/rois/200_....jpg"
  }
}

🤖 Training & Inference

RL Training (ScaleReasoner-R1)

We use verl for GRPO-based RL training:

conda create -n verl python=3.10 -y && conda activate verl
pip install -e verl/

bash script/train/run_grpo_cross_scale_vqa.sh

Key hyperparameters: n=5 rollouts per question, total_epochs=5, train_batch_size=32. The custom reward function is at verl/verl/utils/reward_score/cross_scale_vqa.py.

SFT Baseline

We use LLaMA-Factory for supervised fine-tuning:

conda create -n sft python=3.10 -y && conda activate sft
pip install -e LLaMA-Factory/

bash script/train/run_sft_pathor1_new_triplet_mcq_think_only.sh

Inference

Download ScaleReasoner-R1 from HuggingFace. ScaleReasoner-R1 was trained to produce structured outputs using <think> and <answer> tags. To ensure reproducible results, pass the system prompt below:

SYSTEM_PROMPT = (
    "You are a pathology expert. Read the question and options about the image carefully. "
    "Think step by step inside <think> </think>. Then output ONLY the SINGLE best option letter "
    "inside <answer> </answer>.
"
    "Example: <think>Your reasoning</think> <answer>A</answer>. "
    "Do not include the option text or any extra words inside <answer> </answer> tags."
)

Option 1 — vLLM server (recommended for batched evaluation)

vllm serve <path/to/ScaleReasoner-R1> \
    --host 0.0.0.0 \
    --port 8000 \
    --tensor-parallel-size 1 \
    --max-model-len 8192 \
    --limit-mm-per-prompt.image 5 

Then query via the OpenAI-compatible client:

from openai import OpenAI
import base64

def encode_image(path):
    with open(path, "rb") as f:
        return base64.b64encode(f.read()).decode("utf-8")

client = OpenAI(base_url="http://localhost:8000/v1", api_key="token")

response = client.chat.completions.create(
    model="ChiPhan1110/ScaleReasoner-R1",
    messages=[{
        "role": "user",
        "content": [
            {"type": "image_url", "image_url": {"url": f"data:image/jpeg;base64,{encode_image('low_mag.jpg')}"}},
            {"type": "image_url", "image_url": {"url": f"data:image/jpeg;base64,{encode_image('mid_mag.jpg')}"}},
            {"type": "image_url", "image_url": {"url": f"data:image/jpeg;base64,{encode_image('high_mag.jpg')}"}},
            {"type": "text", "text": "<question>
(A) ...
(B) ...
(C) ...
(D) ..."},
        ]
    }],
    max_tokens=4096,
)
print(response.choices[0].message.content)

Option 2 — Hugging Face Transformers

from transformers import Qwen2_5_VLForConditionalGeneration, AutoProcessor
from qwen_vl_utils import process_vision_info

model = Qwen2_5_VLForConditionalGeneration.from_pretrained(
    "ChiPhan1110/ScaleReasoner-R1", torch_dtype="auto", device_map="auto"
)
processor = AutoProcessor.from_pretrained("ChiPhan1110/ScaleReasoner-R1")

messages = [{
    "role": "user",
    "content": [
        {"type": "image", "image": "low_mag.jpg"},
        {"type": "image", "image": "mid_mag.jpg"},
        {"type": "image", "image": "high_mag.jpg"},
        {"type": "text", "text": "<question>
(A) ...
(B) ...
(C) ...
(D) ..."},
    ]
}]

text = processor.apply_chat_template(messages, tokenize=False, add_generation_prompt=True)
image_inputs, _ = process_vision_info(messages)
inputs = processor(text=[text], images=image_inputs, return_tensors="pt").to(model.device)

output = model.generate(**inputs, max_new_tokens=4096)
print(processor.decode(output[0][len(inputs.input_ids[0]):], skip_special_tokens=True))

🙏 Acknowledgements

This work was supported by the Ministry of Education, Singapore, under the Tier 1 grant (24-1250-P0001) and Tier 2 grant (T2EP20224-0028), and by PuzzleLogic Pte Ltd, Singapore.

We gratefully acknowledge the open-source projects that made the development of ScaleReasoner-R1 possible:

• verl, for the reinforcement learning training framework.
• LLaMA-Factory, for the unified fine-tuning pipelines.
• vLLM, for efficient large language model inference and serving.

We also acknowledge the following open-source models used for comparison in our experiments: Qwen2.5-VL-7B, LLaVA-Med-7B, HuaTuoGPT-7B, Lingshu-7B, Quilt-LLaVA, CLOVER, and Patho-R1.

We sincerely thank the developers and contributors of these projects for their excellent work and for making their code and models publicly available to the research community.

❤️ Citation

If you find our work helpful, please consider citing our paper and the frameworks we build upon:

@article{phan2026enhancing,
  title={Enhancing Pathological VLMs with Cross-scale Reasoning},
  author={Phan, Chi and Zhang, Tianyi Beetroot and Xue, Qiaochu and Wu, Yufeng and Hu, Dan and Liu, Zeyu and Wang, Sudong and Jin, Yueming},
  journal={arXiv preprint arXiv:2606.17412},
  year={2026}
}