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We introduce MedAgentGym, a scalable and interactive training environment designed to enhance coding-based biomedical reasoning capabilities in large language model (LLM) agents.
An overview of the bioasq large-scale biomedical semantic indexing and question answering competition
George Tsatsaronis, Georgios Balikas, Prodromos Malakasiotis, Ioannis Partalas, Matthias Zschunke, Michael R Alvers, Dirk Weissenborn, Anastasia Krithara, Sergios Petridis, Dimitris Polychronopoulos, et al · 2015
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Mimic-iii, a freely accessible critical care database
Alistair EW Johnson, Tom J Pollard, Lu Shen, Li-wei H Lehman, Mengling Feng, Mohammad Ghassemi, Benjamin Moody, Peter Szolovits, Leo Anthony Celi, and Roger G Mark · 2016
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Decoupled weight decay regularization
Ilya Loshchilov and Frank Hutter · 2017
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Proximal policy optimization algorithms
John Schulman, Filip Wolski, Prafulla Dhariwal, Alec Radford, and Oleg Klimov · 2017
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The eicu collaborative research database, a freely available multi-center database for critical care research
Tom J Pollard, Alistair EW Johnson, Jesse D Raffa, Leo A Celi, Roger G Mark, and Omar Badawi · 2018
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PubMedQA: A dataset for biomedical research question answering
Qiao Jin, Bhuwan Dhingra, Zhengping Liu, William Cohen, and Xinghua Lu · 2019
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Text-to-sql generation for question answering on electronic medical records
Ping Wang, Tian Shi, and Chandan K Reddy · 2020
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Evaluating large language models trained on code
Mark Chen, Jerry Tworek, Heewoo Jun, Qiming Yuan, Henrique Ponde De Oliveira Pinto, Jared Kaplan, Harri Edwards, Yuri Burda, Nicholas Joseph, Greg Brockman, et al · 2021
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Training verifiers to solve math word problems
Karl Cobbe, Vineet Kosaraju, Mohammad Bavarian, Mark Chen, Heewoo Jun, Lukasz Kaiser, Matthias Plappert, Jerry Tworek, Jacob Hilton, Reiichiro Nakano, et al · 2021
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What disease does this patient have? a large-scale open domain question answering dataset from medical exams
Di Jin, Eileen Pan, Nassim Oufattole, Wei-Hung Weng, Hanyi Fang, and Peter Szolovits · 2021
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Patient triage system for supporting the operation of dispatch centres and rescue teams
Acrapol Nimmolrat, Krongkarn Sutham, and Orawit Thinnukool · 2021
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Ehrsql: A practical text-to-sql benchmark for electronic health records
Gyubok Lee, Hyeonji Hwang, Seongsu Bae, Yeonsu Kwon, Woncheol Shin, Seongjun Yang, Minjoon Seo, Jong-Yeup Kim, and Edward Choi · 2022
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Medmcqa: A large-scale multi-subject multi-choice dataset for medical domain question answering
Ankit Pal, Logesh Kumar Umapathi, and Malaikannan Sankarasubbu · 2022
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Mlagentbench: Evaluating language agents on machine learning experimentation
Qian Huang, Jian Vora, Percy Liang, and Jure Leskovec · 2023
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Agentbench: Evaluating llms as agents
Xiao Liu, Hao Yu, Hanchen Zhang, Yifan Xu, Xuanyu Lei, Hanyu Lai, Yu Gu, Hangliang Ding, Kaiwen Men, Kejuan Yang, et al · 2023
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The imperative for regulatory oversight of large language models (or generative ai) in healthcare
Bertalan Meskó and Eric J Topol · 2023
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Foundation models for generalist medical artificial intelligence
Michael Moor, Oishi Banerjee, Zahra Shakeri Hossein Abad, Harlan M Krumholz, Jure Leskovec, Eric J Topol, and Pranav Rajpurkar · 2023
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Large language models encode clinical knowledge
Karan Singhal, Shekoofeh Azizi, Tao Tu, S Sara Mahdavi, Jason Wei, Hyung Won Chung, Nathan Scales, Ajay Tanwani, Heather Cole-Lewis, Stephen Pfohl, et al · 2023
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Xiangru Tang, Yuliang Liu, Zefan Cai, Yanjun Shao, Junjie Lu, Yichi Zhang, Zexuan Deng, Helan Hu, Kaikai An, Ruijun Huang, et al · 2023
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Mle-bench: Evaluating machine learning agents on machine learning engineering
Jun Shern Chan, Neil Chowdhury, Oliver Jaffe, James Aung, Dane Sherburn, Evan Mays, Giulio Starace, Kevin Liu, Leon Maksin, Tejal Patwardhan, et al · 2024
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Huatuogpt-o1, towards medical complex reasoning with llms
Junying Chen, Zhenyang Cai, Ke Ji, Xidong Wang, Wanlong Liu, Rongsheng Wang, Jianye Hou, and Benyou Wang · 2024
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The browsergym ecosystem for web agent research
De Chezelles, Thibault Le Sellier, Maxime Gasse, Alexandre Lacoste, Alexandre Drouin, Massimo Caccia, Léo Boisvert, Megh Thakkar, Tom Marty, Rim Assouel, et al · 2024
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Workarena: How capable are web agents at solving common knowledge work tasks?
Alexandre Drouin, Maxime Gasse, Massimo Caccia, Issam H. Laradji, Manuel Del Verme, Tom Marty, David Vazquez, Nicolas Chapados, and Alexandre Lacoste · 2024
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Abhimanyu Dubey, Abhinav Jauhri, Abhinav Pandey, Abhishek Kadian, Ahmad Al-Dahle, Aiesha Letman, Akhil Mathur, Alan Schelten, Amy Yang, Angela Fan, et al · 2024
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DS-agent: Automated data science by empowering large language models with case-based reasoning
Siyuan Guo, Cheng Deng, Ying Wen, Hechang Chen, Yi Chang, and Jun Wang · 2024
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Qwen2. 5-coder technical report
Binyuan Hui, Jian Yang, Zeyu Cui, Jiaxi Yang, Dayiheng Liu, Lei Zhang, Tianyu Liu, Jiajun Zhang, Bowen Yu, Keming Lu, et al · 2024
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Aaron Hurst, Adam Lerer, Adam P Goucher, Adam Perelman, Aditya Ramesh, Aidan Clark, AJ Ostrow, Akila Welihinda, Alan Hayes, Alec Radford, et al · 2024
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Agentmd: Empowering language agents for risk prediction with large-scale clinical tool learning
Qiao Jin, Zhizheng Wang, Yifan Yang, Qingqing Zhu, Donald Wright, Thomas Huang, W John Wilbur, Zhe He, Andrew Taylor, Qingyu Chen, et al · 2024
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Researcharena: Benchmarking llms’ ability to collect and organize information as research agents
Hao Kang and Chenyan Xiong · 2024
Cited alongside, same era.
Medcalc-bench: Evaluating large language models for medical calculations
Nikhil Khandekar, Qiao Jin, Guangzhi Xiong, Soren Dunn, Serina Applebaum, Zain Anwar, Maame Sarfo-Gyamfi, Conrad Safranek, Abid Anwar, Andrew Zhang, et al · 2024
Cited alongside, same era.
MDAgents: An Adaptive Collaboration of LLMs for Medical Decision-Making
Yubin Kim, Chanwoo Park, Hyewon Jeong, Yik Siu Chan, Xuhai Xu, Daniel McDuff, Hyeonhoon Lee, Marzyeh Ghassemi, Cynthia Breazeal, and Hae Won Park · 2024
Cited alongside, same era.
EHRCon: Dataset for checking consistency between unstructured notes and structured tables in electronic health records
Yeonsu Kwon, Jiho Kim, Gyubok Lee, Seongsu Bae, Daeun Kyung, Wonchul Cha, Tom Pollard, ALISTAIR JOHNSON, and Edward Choi · 2024
Cited alongside, same era.
Mmedagent: Learning to use medical tools with multi-modal agent
Binxu Li, Tiankai Yan, Yuanting Pan, Jie Luo, Ruiyang Ji, Jiayuan Ding, Zhe Xu, Shilong Liu, Haoyu Dong, Zihao Lin, et al · 2024
DSBench: How far are data science agents from becoming data science experts?
Liqiang Jing, Zhehui Huang, Xiaoyang Wang, Wenlin Yao, Wenhao Yu, Kaixin Ma, Hongming Zhang, Xinya Du, and Dong Yu · 2025
Closest in time.
Med-r1: Reinforcement learning for generalizable medical reasoning in vision-language models
Yuxiang Lai, Jike Zhong, Ming Li, Shitian Zhao, and Xiaofeng Yang · 2025
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Wuyang Lan, Wenzheng Wang, Changwei Ji, Guoxing Yang, Yongbo Zhang, Xiaohong Liu, Song Wu, and Guangyu Wang · 2025
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Aligning llms to ask good questions a case study in clinical reasoning
Shuyue Stella Li, Jimin Mun, Faeze Brahman, Jonathan S Ilgen, Yulia Tsvetkov, and Maarten Sap · 2025
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Paper2agent: Reimagining research papers as interactive and reliable ai agents
alphaXiv searches the wider corpus for related work and actual follow-ups.
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Cited alongside, same era.
Reflectool: Towards reflection-aware tool-augmented clinical agents
Yusheng Liao, Shuyang Jiang, Yanfeng Wang, and Yu Wang · 2024
Cited alongside, same era.
Can large language models reason about medical questions?
Valentin Liévin, Christoffer Egeberg Hother, Andreas Geert Motzfeldt, and Ole Winther · 2024
Cited alongside, same era.
Ehr-seqsql: A sequential text-to-sql dataset for interactively exploring electronic health records
Jaehee Ryu, Seonhee Cho, Gyubok Lee, and Edward Choi · 2024
Cited alongside, same era.
Agentclinic: a multimodal agent benchmark to evaluate ai in simulated clinical environments
Samuel Schmidgall, Rojin Ziaei, Carl Harris, Eduardo Reis, Jeffrey Jopling, and Michael Moor · 2024
Cited alongside, same era.
Medadapter: Efficient test-time adaptation of large language models towards medical reasoning
Wenqi Shi, Ran Xu, Yuchen Zhuang, Yue Yu, Haotian Sun, Hang Wu, Carl Yang, and May D Wang · 2024
Cited alongside, same era.
EHRAgent: Code empowers large language models for few-shot complex tabular reasoning on electronic health records
Wenqi Shi, Ran Xu, Yuchen Zhuang, Yue Yu, Jieyu Zhang, Hang Wu, Yuanda Zhu, Joyce C. Ho, Carl Yang, and May Dongmei Wang · 2024
Cited alongside, same era.
Large language models are poor medical coders—benchmarking of medical code querying
Ali Soroush, Benjamin S Glicksberg, Eyal Zimlichman, Yiftach Barash, Robert Freeman, Alexander W Charney, Girish N Nadkarni, and Eyal Klang · 2024
Cited alongside, same era.
Jiacheng Miao, Joe R Davis, Jonathan K Pritchard, and James Zou · 2025
Closest in time.
Un ministral, des ministraux
Ministral · 2025
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Bixbench: a comprehensive benchmark for llm-based agents in computational biology
Ludovico Mitchener, Jon M Laurent, Benjamin Tenmann, Siddharth Narayanan, Geemi P Wellawatte, Andrew White, Lorenzo Sani, and Samuel G Rodriques · 2025
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Mlgym: A new framework and benchmark for advancing ai research agents
Deepak Nathani, Lovish Madaan, Nicholas Roberts, Nikolay Bashlykov, Ajay Menon, Vincent Moens, Amar Budhiraja, Despoina Magka, Vladislav Vorotilov, Gaurav Chaurasia, et al · 2025
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Training software engineering agents and verifiers with SWE-gym
Jiayi Pan, Xingyao Wang, Graham Neubig, Navdeep Jaitly, Heng Ji, Alane Suhr, and Yizhe Zhang · 2025
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Smart: Self-aware agent for tool overuse mitigation
Cheng Qian, Emre Can Acikgoz, Hongru Wang, Xiusi Chen, Avirup Sil, Dilek Hakkani-Tür, Gokhan Tur, and Heng Ji · 2025
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Jiahao Qiu, Xuan Qi, Tongcheng Zhang, Xinzhe Juan, Jiacheng Guo, Yifu Lu, Yimin Wang, Zixin Yao, Qihan Ren, Xun Jiang, Xing Zhou, Dongrui Liu, Ling Yang, Yue Wu, Kaixuan Huang, Shilong Liu, Hongru Wang, and Mengdi Wang · 2025
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N-power ai: A specialized agent framework for automated sample size and power analysis in clinical trial design
Peifeng Ruan, Ismael Villanueva-Miranda, Jialiang Liu, Donghan M Yang, Qinbo Zhou, Guanghua Xiao, and Yang Xie · 2025
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Agentrxiv: Towards collaborative autonomous research
Samuel Schmidgall and Michael Moor · 2025
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Agent laboratory: Using llm agents as research assistants, 2025
Samuel Schmidgall, Yusheng Su, Ze Wang, Ximeng Sun, Jialian Wu, Xiaodong Yu, Jiang Liu, Zicheng Liu, and Emad Barsoum · 2025
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Hybridflow: A flexible and efficient rlhf framework
Guangming Sheng, Chi Zhang, Zilingfeng Ye, Xibin Wu, Wang Zhang, Ru Zhang, Yanghua Peng, Haibin Lin, and Chuan Wu · 2025
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Reasoning gym: Reasoning environments for reinforcement learning with verifiable rewards, 2025
Zafir Stojanovski, Oliver Stanley, Joe Sharratt, Richard Jones, Abdulhakeem Adefioye, Jean Kaddour, and Andreas Kopf · 2025
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Medagentsbench: Benchmarking thinking models and agent frameworks for complex medical reasoning
Xiangru Tang, Daniel Shao, Jiwoong Sohn, Jiapeng Chen, Jiayi Zhang, Jinyu Xiang, Fang Wu, Yilun Zhao, Chenglin Wu, Wenqi Shi, et al · 2025
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NovelSeek Team, Bo Zhang, Shiyang Feng, Xiangchao Yan, Jiakang Yuan, Zhiyin Yu, Xiaohan He, Songtao Huang, Shaowei Hou, Zheng Nie, et al · 2025
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Disentangling reasoning and knowledge in medical large language models
Rahul Thapa, Qingyang Wu, Kevin Wu, Harrison Zhang, Angela Zhang, Eric Wu, Haotian Ye, Suhana Bedi, Nevin Aresh, Joseph Boen, et al · 2025
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Mmedagent-rl: Optimizing multi-agent collaboration for multimodal medical reasoning
Peng Xia, Jinglu Wang, Yibo Peng, Kaide Zeng, Xian Wu, Xiangru Tang, Hongtu Zhu, Yun Li, Shujie Liu, Yan Lu, et al · 2025
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Swe-smith: Scaling data for software engineering agents, 2025
John Yang, Kilian Leret, Carlos E. Jimenez, Alexander Wettig, Kabir Khandpur, Yanzhe Zhang, Binyuan Hui, Ofir Press, Ludwig Schmidt, and Diyi Yang · 2025
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Ailing Yu, Lan Yao, Jingnan Liu, Zhe Chen, Jiajun Yin, Yuan Wang, Xinhao Liao, Zhiling Ye, Ji Li, Yun Yue, et al · 2025
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Dolphin: Closed-loop open-ended auto-research through thinking, practice, and feedback
Jiakang Yuan, Xiangchao Yan, Botian Shi, Tao Chen, Wanli Ouyang, Bo Zhang, Lei Bai, Yu Qiao, and Bowen Zhou · 2025
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Sirius: Self-improving multi-agent systems via bootstrapped reasoning
Wanjia Zhao, Mert Yuksekgonul, Shirley Wu, and James Zou · 2025
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Medgr: Breaking the data barrier for medical reasoning via generative reward learning
Weihai Zhi, Jiayan Guo, and Shangyang Li · 2025
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Yinghao Zhu, Ziyi He, Haoran Hu, Xiaochen Zheng, Xichen Zhang, Zixiang Wang, Junyi Gao, Liantao Ma, and Lequan Yu · 2025
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Medxpertqa: Benchmarking expert-level medical reasoning and understanding
Yuxin Zuo, Shang Qu, Yifei Li, Zhangren Chen, Xuekai Zhu, Ermo Hua, Kaiyan Zhang, Ning Ding, and Bowen Zhou · 2025
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