# MedReason: Eliciting Factual Medical Reasoning Steps in LLMs via Knowledge Graphs

arXiv: https://arxiv.org/abs/2504.00993 · HTML: https://mlsanity.com/paper/2504.00993/

## Key facts

- Cited by 110 papers in the map (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 34 of its 47 references that are in the map.
- First posted on arXiv 1 Apr 2025.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)

## Builds on (most cited first, 30 of 34)

- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [DeepSeekMath: Pushing the Limits of Mathematical Reasoning in Open Language Models](https://mlsanity.com/paper/2402.03300/) (2024)
- [Measuring Massive Multitask Language Understanding](https://mlsanity.com/paper/2009.03300/) (2020)
- [DeepSeek-R1: Incentivizing Reasoning Capability in LLMs via Reinforcement Learning](https://mlsanity.com/paper/2501.12948/) (2025)
- [Qwen2.5 Technical Report](https://mlsanity.com/paper/2412.15115/) (2024)
- [GPT-4o System Card](https://mlsanity.com/paper/2410.21276/) (2024)
- [MMLU-Pro: A More Robust and Challenging Multi-Task Language Understanding Benchmark](https://mlsanity.com/paper/2406.01574/) (2024)
- [A Survey on Hallucination in Large Language Models: Principles, Taxonomy, Challenges, and Open Questions](https://mlsanity.com/paper/2311.05232/) (2023)
- [What Disease does this Patient Have? A Large-scale Open Domain Question Answering Dataset from Medical Exams](https://mlsanity.com/paper/2009.13081/) (2020)
- [s1: Simple test-time scaling](https://mlsanity.com/paper/2501.19393/) (2025)
- [LLaVA-Med: Training a Large Language-and-Vision Assistant for Biomedicine in One Day](https://mlsanity.com/paper/2306.00890/) (2023)
- [ZeRO: Memory Optimizations Toward Training Trillion Parameter Models](https://mlsanity.com/paper/1910.02054/) (2019)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [Kimi k1.5: Scaling Reinforcement Learning with LLMs](https://mlsanity.com/paper/2501.12599/) (2025)
- [Towards Reasoning in Large Language Models: A Survey](https://mlsanity.com/paper/2212.10403/) (2022)
- [Do NOT Think That Much for 2+3=? On the Overthinking of o1-Like LLMs](https://mlsanity.com/paper/2412.21187/) (2024)
- [MedMCQA : A Large-scale Multi-Subject Multi-Choice Dataset for Medical domain Question Answering](https://mlsanity.com/paper/2203.14371/) (2022)
- [LIMO: Less is More for Reasoning](https://mlsanity.com/paper/2502.03387/) (2025)
- [Humanity's Last Exam](https://mlsanity.com/paper/2501.14249/) (2025)
- [From System 1 to System 2: A Survey of Reasoning Large Language Models](https://mlsanity.com/paper/2502.17419/) (2025)
- [BioMistral: A Collection of Open-Source Pretrained Large Language Models for Medical Domains](https://mlsanity.com/paper/2402.10373/) (2024)
- [O1-Pruner: Length-Harmonizing Fine-Tuning for O1-Like Reasoning Pruning](https://mlsanity.com/paper/2501.12570/) (2025)
- [HuatuoGPT-o1, Towards Medical Complex Reasoning with LLMs](https://mlsanity.com/paper/2412.18925/) (2024)
- [MedXpertQA: Benchmarking Expert-Level Medical Reasoning and Understanding](https://mlsanity.com/paper/2501.18362/) (2025)
- [Imitate, Explore, and Self-Improve: A Reproduction Report on Slow-thinking Reasoning Systems](https://mlsanity.com/paper/2412.09413/) (2024)
- [Evaluation of OpenAI o1: Opportunities and Challenges of AGI](https://mlsanity.com/paper/2409.18486/) (2024)
- [Benchmarking Large Language Models on Answering and Explaining Challenging Medical Questions](https://mlsanity.com/paper/2402.18060/) (2024)
- [OpenR: An Open Source Framework for Advanced Reasoning with Large Language Models](https://mlsanity.com/paper/2410.09671/) (2024)
- [Towards Building Multilingual Language Model for Medicine](https://mlsanity.com/paper/2402.13963/) (2024)
- [O1 Replication Journey -- Part 2: Surpassing O1-preview through Simple Distillation, Big Progress or Bitter Lesson?](https://mlsanity.com/paper/2411.16489/) (2024)

## Built on by (most cited first, 30 of 110)

- [Lingshu: A Generalist Foundation Model for Unified Multimodal Medical Understanding and Reasoning](https://mlsanity.com/paper/2506.07044/) (2025)
- [A Survey of Agentic Reasoning for Large Language Models: Towards Recursively Self-Improving and Collective Agents](https://mlsanity.com/paper/2601.12538/) (2026)
- [The Avengers: A Simple Recipe for Uniting Smaller Language Models to Challenge Proprietary Giants](https://mlsanity.com/paper/2505.19797/) (2025)
- [A Survey of Scientific Large Language Models: From Data Foundations to Agent Frontiers](https://mlsanity.com/paper/2508.21148/) (2025)
- [MedCaseReasoning: Evaluating and learning diagnostic reasoning from clinical case reports](https://mlsanity.com/paper/2505.11733/) (2025)
- [MedFrameQA: A Multi-Image Medical VQA Benchmark for Clinical Reasoning](https://mlsanity.com/paper/2505.16964/) (2025)
- [MedVLThinker: Simple Baselines for Multimodal Medical Reasoning](https://mlsanity.com/paper/2508.02669/) (2025)
- [MedAgentGym: A Scalable Agentic Training Environment for Code-Centric Reasoning in Biomedical Data Science](https://mlsanity.com/paper/2506.04405/) (2025)
- [Learning to Orchestrate Agents in Natural Language with the Conductor](https://mlsanity.com/paper/2512.04388/) (2025)
- [Disentangling Reasoning and Knowledge in Medical Large Language Models](https://mlsanity.com/paper/2505.11462/) (2025)
- [EHR-R1: A Reasoning-Enhanced Foundational Language Model for Electronic Health Record Analysis](https://mlsanity.com/paper/2510.25628/) (2025)
- [Improving Medical Reasoning with Curriculum-Aware Reinforcement Learning](https://mlsanity.com/paper/2505.19213/) (2025)
- [MedMO: Grounding and Understanding Multimodal Large Language Model for Medical Images](https://mlsanity.com/paper/2602.06965/) (2026)
- [Counteraction-Aware Multi-Teacher On-Policy Distillation for General Capability Recovery with Domain Preservation](https://mlsanity.com/paper/2605.27115/) (2026)
- [Knowledge or Reasoning? A Close Look at How LLMs Think Across Domains](https://mlsanity.com/paper/2506.02126/) (2025)
- [InfiMed-ORBIT: Aligning LLMs on Open-Ended Complex Tasks via Rubric-Based Incremental Training](https://mlsanity.com/paper/2510.15859/) (2025)
- [MedSynapse-V: Bridging Visual Perception and Clinical Intuition via Latent Memory Evolution](https://mlsanity.com/paper/2604.26283/) (2026)
- [Medical Reasoning in the Era of LLMs: A Systematic Review of Enhancement Techniques and Applications](https://mlsanity.com/paper/2508.00669/) (2025)
- [Token Hidden Reward: Steering Exploration-Exploitation in Group Relative Deep Reinforcement Learning](https://mlsanity.com/paper/2510.03669/) (2025)
- [OctoMed: Data Recipes for State-of-the-Art Multimodal Medical Reasoning](https://mlsanity.com/paper/2511.23269/) (2025)
- [MASPOB: Bandit-Based Prompt Optimization for Multi-Agent Systems with Graph Neural Networks](https://mlsanity.com/paper/2603.02630/) (2026)
- [MedReflect: Teaching Medical LLMs to Self-Improve via Reflective Correction](https://mlsanity.com/paper/2510.03687/) (2025)
- [Agentic Unlearning: When LLM Agent Meets Machine Unlearning](https://mlsanity.com/paper/2602.17692/) (2026)
- [Building a Human-Verified Clinical Reasoning Dataset via a Human LLM Hybrid Pipeline for Trustworthy Medical AI](https://mlsanity.com/paper/2505.06912/) (2025)
- [DEEPMED: Building a Medical DeepResearch Agent via Multi-hop Med-Search Data and Turn-Controlled Agentic Training & Inference](https://mlsanity.com/paper/2601.18496/) (2026)
- [From Seeing to Thinking: Decoupling Perception and Reasoning Improves Post-Training of Vision-Language Models](https://mlsanity.com/paper/2605.20177/) (2026)
- [Context-Free Synthetic Data Mitigates Forgetting](https://mlsanity.com/paper/2505.13811/) (2025)
- [MedPAIR: Measuring Physicians and AI Relevance Alignment in Medical Question Answering](https://mlsanity.com/paper/2505.24040/) (2025)
- [Improving Clinical Diagnosis with Counterfactual Multi-Agent Reasoning](https://mlsanity.com/paper/2603.27820/) (2026)
- [Adaptive Reinforcement for Open-ended Medical Reasoning via Semantic-Guided Reward Collapse Mitigation](https://mlsanity.com/paper/2508.12957/) (2025)

## Abstract (arXiv)

Medical tasks such as diagnosis and treatment planning require precise and complex reasoning, particularly in life-critical domains. Unlike mathematical reasoning, medical reasoning demands meticulous, verifiable thought processes to ensure reliability and accuracy. However, there is a notable lack of datasets that provide transparent, step-by-step reasoning to validate and enhance the medical reasoning ability of AI models. To bridge this gap, we introduce MedReason, a large-scale high-quality medical reasoning dataset designed to enable faithful and explainable medical problem-solving in large language models (LLMs). We utilize a structured medical knowledge graph (KG) to convert clinical QA pairs into logical chains of reasoning, or ``thinking paths'', which trace connections from question elements to answers via relevant KG entities. Each path is validated for consistency with clinical logic and evidence-based medicine. Our pipeline generates detailed reasoning for various medical questions from 7 medical datasets, resulting in a dataset of 32,682 question-answer pairs, each with detailed, step-by-step explanations. Experiments demonstrate that fine-tuning with our dataset consistently boosts medical problem-solving capabilities, achieving significant gains of up to 7.7% for DeepSeek-Ditill-8B. Our top-performing model, MedReason-8B, outperforms the Huatuo-o1-8B, a state-of-the-art medical reasoning model, by up to 4.2% on the clinical benchmark MedBullets. We also engage medical professionals from diverse specialties to assess our dataset's quality, ensuring MedReason offers accurate and coherent medical reasoning. Our data, models, and code is available at https://github.com/UCSC-VLAA/MedReason.