# MedicalAgentsBench for Complex Medical Reasoning: Comparing Internalized Reasoning Models versus Externalized Agent-based Frameworks

arXiv: https://arxiv.org/abs/2503.07459 · HTML: https://mlsanity.com/paper/2503.07459/

## Key facts

- Cited by 40 papers in the map (data through 14 Oct 2026).
- Placed in Clinical and biomedical applications, one of 17 directions in LLM reasoning.
- Builds on 38 of its 49 references that are in the map.
- First posted on arXiv 10 Mar 2025.

## Placed in

- LLM reasoning / [Clinical and biomedical applications](https://mlsanity.com/lr/clinical-and-biomedical-applications/)
- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

## Builds on (most cited first, 30 of 38)

- [GPT-4 Technical Report](https://mlsanity.com/paper/2303.08774/) (2023)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [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)
- [Self-Consistency Improves Chain of Thought Reasoning in Language Models](https://mlsanity.com/paper/2203.11171/) (2022)
- [Self-Refine: Iterative Refinement with Self-Feedback](https://mlsanity.com/paper/2303.17651/) (2023)
- [MMLU-Pro: A More Robust and Challenging Multi-Task Language Understanding Benchmark](https://mlsanity.com/paper/2406.01574/) (2024)
- [Large Language Models Encode Clinical Knowledge](https://mlsanity.com/paper/2212.13138/) (2022)
- [What Disease does this Patient Have? A Large-scale Open Domain Question Answering Dataset from Medical Exams](https://mlsanity.com/paper/2009.13081/) (2020)
- [PubMedQA: A Dataset for Biomedical Research Question Answering](https://mlsanity.com/paper/1909.06146/) (2019)
- [Capabilities of GPT-4 on Medical Challenge Problems](https://mlsanity.com/paper/2303.13375/) (2023)
- [MedMCQA : A Large-scale Multi-Subject Multi-Choice Dataset for Medical domain Question Answering](https://mlsanity.com/paper/2203.14371/) (2022)
- [PathVQA: 30000+ Questions for Medical Visual Question Answering](https://mlsanity.com/paper/2003.10286/) (2020)
- [AFlow: Automating Agentic Workflow Generation](https://mlsanity.com/paper/2410.10762/) (2024)
- [Benchmarking Retrieval-Augmented Generation for Medicine](https://mlsanity.com/paper/2402.13178/) (2024)
- [Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine](https://mlsanity.com/paper/2311.16452/) (2023)
- [MedAgents: Large Language Models as Collaborators for Zero-shot Medical Reasoning](https://mlsanity.com/paper/2311.10537/) (2023)
- [MedAlpaca -- An Open-Source Collection of Medical Conversational AI Models and Training Data](https://mlsanity.com/paper/2304.08247/) (2023)
- [MEDITRON-70B: Scaling Medical Pretraining for Large Language Models](https://mlsanity.com/paper/2311.16079/) (2023)
- [Unleashing the Emergent Cognitive Synergy in Large Language Models: A Task-Solving Agent through Multi-Persona Self-Collaboration](https://mlsanity.com/paper/2307.05300/) (2023)
- [MedXpertQA: Benchmarking Expert-Level Medical Reasoning and Understanding](https://mlsanity.com/paper/2501.18362/) (2025)
- [Can large language models reason about medical questions?](https://mlsanity.com/paper/2207.08143/) (2022)
- [MedCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval](https://mlsanity.com/paper/2307.00589/) (2023)
- [A Study of Generative Large Language Model for Medical Research and Healthcare](https://mlsanity.com/paper/2305.13523/) (2023)
- [MDAgents: An Adaptive Collaboration of LLMs for Medical Decision-Making](https://mlsanity.com/paper/2404.15155/) (2024)
- [emrQA: A Large Corpus for Question Answering on Electronic Medical Records](https://mlsanity.com/paper/1809.00732/) (2018)
- [Empowering Biomedical Discovery with AI Agents](https://mlsanity.com/paper/2404.02831/) (2024)
- [Benchmarking Large Language Models on Answering and Explaining Challenging Medical Questions](https://mlsanity.com/paper/2402.18060/) (2024)
- [HEAD-QA: A Healthcare Dataset for Complex Reasoning](https://mlsanity.com/paper/1906.04701/) (2019)
- [AI Hospital: Benchmarking Large Language Models in a Multi-agent Medical Interaction Simulator](https://mlsanity.com/paper/2402.09742/) (2024)

## Built on by (most cited first, 30 of 40)

- [Multimodal Chain-of-Thought Reasoning: A Comprehensive Survey](https://mlsanity.com/paper/2503.12605/) (2025)
- [From LLM Reasoning to Autonomous AI Agents: A Comprehensive Review](https://mlsanity.com/paper/2504.19678/) (2025)
- [A Survey of Agentic Reasoning for Large Language Models: Towards Recursively Self-Improving and Collective Agents](https://mlsanity.com/paper/2601.12538/) (2026)
- [MMedAgent-RL: Optimizing Multi-Agent Collaboration for Multimodal Medical Reasoning](https://mlsanity.com/paper/2506.00555/) (2025)
- [Beyond Distillation: Pushing the Limits of Medical LLM Reasoning with Minimalist Rule-Based RL](https://mlsanity.com/paper/2505.17952/) (2025)
- [MedAgentBoard: Benchmarking Multi-Agent Collaboration with Conventional Methods for Diverse Medical Tasks](https://mlsanity.com/paper/2505.12371/) (2025)
- [Med-PRM: Medical Reasoning Models with Stepwise, Guideline-verified Process Rewards](https://mlsanity.com/paper/2506.11474/) (2025)
- [MedAgentGym: A Scalable Agentic Training Environment for Code-Centric Reasoning in Biomedical Data Science](https://mlsanity.com/paper/2506.04405/) (2025)
- [Automating Expert-Level Medical Reasoning Evaluation of Large Language Models](https://mlsanity.com/paper/2507.07988/) (2025)
- [MIRA: Multimodal Iterative Reasoning Agent for Image Editing](https://mlsanity.com/paper/2511.21087/) (2025)
- [HealthFlow: A Self-Evolving AI Agent with Meta Planning for Autonomous Healthcare Research](https://mlsanity.com/paper/2508.02621/) (2025)
- [MementoGUI: Learning Agentic Multimodal Memory Control for Long-Horizon GUI Agents](https://mlsanity.com/paper/2605.18652/) (2026)
- [Medical Reasoning in the Era of LLMs: A Systematic Review of Enhancement Techniques and Applications](https://mlsanity.com/paper/2508.00669/) (2025)
- [MedSentry: Understanding and Mitigating Safety Risks in Medical LLM Multi-Agent Systems](https://mlsanity.com/paper/2505.20824/) (2025)
- [Real Money, Fake Models: Deceptive Model Claims in Shadow APIs](https://mlsanity.com/paper/2603.01919/) (2026)
- [CHI-Bench: Can AI Agents Automate End-to-End, Long-Horizon, Policy-Rich Healthcare Workflows?](https://mlsanity.com/paper/2605.16679/) (2026)
- [MedXIAOHE: A Comprehensive Recipe for Building Medical MLLMs](https://mlsanity.com/paper/2602.12705/) (2026)
- [GSEM: Graph-based Self-Evolving Memory for Experience Augmented Clinical Reasoning](https://mlsanity.com/paper/2603.22096/) (2026)
- [MedPlan: A Two-Stage RAG-Based System for Personalized Medical Plan Generation](https://mlsanity.com/paper/2503.17900/) (2025)
- [Agentic Systems in Radiology: Design, Applications, Evaluation, and Challenges](https://mlsanity.com/paper/2510.09404/) (2025)
- [Medical thinking with multiple images](https://mlsanity.com/paper/2604.16506/) (2026)
- [Beyond Classification Accuracy: Neural-MedBench and the Need for Deeper Reasoning Benchmarks](https://mlsanity.com/paper/2509.22258/) (2025)
- [Grounded in Reality: Learning and Deploying Proactive LLM from Offline Logs](https://mlsanity.com/paper/2510.25441/) (2025)
- [ESTAR: Early-Stopping Token-Aware Reasoning For Efficient Inference](https://mlsanity.com/paper/2602.10004/) (2026)
- [TAGS: A Test-Time Generalist-Specialist Framework with Retrieval-Augmented Reasoning and Verification](https://mlsanity.com/paper/2505.18283/) (2025)
- [Silence is Not Consensus: Disrupting Agreement Bias in Multi-Agent LLMs via Catfish Agent for Clinical Decision Making](https://mlsanity.com/paper/2505.21503/) (2025)
- [ConfAgents: A Conformal-Guided Multi-Agent Framework for Cost-Efficient Medical Diagnosis](https://mlsanity.com/paper/2508.04915/) (2025)
- [Empowering Real-World: A Survey on the Technology, Practice, and Evaluation of LLM-driven Industry Agents](https://mlsanity.com/paper/2510.17491/) (2025)
- [MedInsightBench: Evaluating Medical Analytics Agents Through Multi-Step Insight Discovery in Multimodal Medical Data](https://mlsanity.com/paper/2512.13297/) (2025)
- [MedCoG: Maximizing LLM Inference Density in Medical Reasoning via Meta-Cognitive Regulation](https://mlsanity.com/paper/2602.07905/) (2026)

## Abstract (arXiv)

Complex medical reasoning requires integrating heterogeneous clinical evidence across multiple inference steps. Large language models (LLMs) now approach this through two routes: internalized reasoning and externalized agent scaffolding (frameworks that decompose problems collaboratively amongst multiple LLMs). To determine whether these routes are exclusive or complementary, we introduce MedicalAgentsBench, a filtered benchmark of 862 complex clinical questions drawn from the union of eight medical datasets via difficulty-aware curation and contamination screening. Evaluating three internalized reasoning models (DeepSeek-R1, o1-mini, and o3-mini), seven base models, and nine externalized agent-based methods, we find that internalized and externalized approaches each independently improve performance, and that their benefits compound: the highest accuracy is achieved by layering agent workflows onto an internalized reasoning model (i.e., o3-mini + MDAgents with 35.1%). Pareto analysis shows this combination dominates the cost-performance frontier; moreover, lightweight optimization on inexpensive models offers an entry point for resource-constrained settings. Our benchmark is at https://github.com/gersteinlab/MedicalAgentsBench.