Home | Wenqi Shi

Hello! I am a Tenure-Track Assistant Professor in the Department of Health Data Science and Biostatistics at UT Southwestern Medical Center. I am also a faculty member of the Quantitative Biomedical Research Center at UTSW. I received my Ph.D. from Bio-Medical Informatics and Bioimaging Lab (MIBLab) at Georgia Institute of Technology (GT) under the supervision of Dr. May D. Wang.

My research interest lies at the intersection of artificial intelligence (AI) and healthcare, advancing both fundamental algorithms and applied systems for precision and personalized medicine. With a dedicated focus on pediatric healthcare, cancer, and rare diseases, I actively work on developing large language models for translational medicine, advancing agentic AI for biomedical discovery, and promoting responsible AI practices to improve real-world clinical research and practice.

News

[--Pinned--] Prospective students: I am always looking for strong and motivated students to join our group. I am also happy to host remote graduate / undergraduate visitors and actively looking for Ph.D. students. If you are interested, please contact me via email!
[2025/06] Introducing MedAgentGym, an interactive gym-style platform designed specifically for training LLM agents in coding-based medical reasoning!
[01/2025] [2025/03] We are grateful to receive the NVIDIA Academic Grant to support our research on improving fundamental agent capabilities of LLMs in biomedicine.

Selected Publications and Manuscripts

Please refer to publications or my Google Scholar profile for the full list. ("*" stands for equal contribution)

MedAgentGym: Training LLM Agents for Code-Based Medical Reasoning at Scale

Ran Xu, Yuchen Zhuang, Yishan Zhong, Yue Yu, Xiangru Tang, Hang Wu, May D. Wang, Peifeng Ruan, Donghan Yang, Tao Wang, Guanghua Xiao, Carl Yang, Yang Xie, Wenqi Shi

arXiv Paper Webpage Code Data QbitAI/量子位

WorkForceAgent-R1: Incentivizing Reasoning Capability in LLM-based Web Agents via Reinforcement Learning

Yuchen Zhuang, Di Jin, Jiaao Chen, Wenqi Shi, Hanrui Wang, Chao Zhang

arXiv Paper Code

Collab-rag: Boosting retrieval-augmented generation for complex question answering via white-box and black-box llm collaboration

Ran Xu*, Wenqi Shi*, Yuchen Zhuang, Yue Yu, Joyce C Ho, Haoyu Wang, Carl Yang

COLM'25 Paper Code

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, Arman Cohan, Mark Gerstein

arXiv Paper Code Data

Fairness artificial intelligence in clinical decision support: Mitigating effect of health disparity

Hang Wu, Yuanda Zhu, Wenqi Shi, Li Tong, May D. Wang

JBHI'24 Paper

MedAssist: LLM-Empowered Medical Assistant for Assisting the Scrutinization and Comprehension of Electronic Health Records

Ran Xu, Wenqi Shi, Jonathan Wang, Jasmine Zhou, Carl Yang

WWW'25 Paper

Predicting pediatric patient rehabilitation outcomes after spinal deformity surgery with artificial intelligence

Wenqi Shi, Felipe O. Giuste, Yuanda Zhu, Ben J. Tamo, Micky C. Nnamdi, Andrew Hornback, Ashley M. Carpenter, Coleman Hilton, Henry J. Iwinski, J. Michael Wattenbarger, May D. Wang

Nature Communication Medicine Paper

Clinical decision making under uncertainty: a bootstrapped counterfactual inference approach

Hang Wu, Wenqi Shi, Anirudh Choudhary, May D. Wang

BMC Medical Informatics and Decision Making Paper

Developing a novel causal inference algorithm for personalized biomedical causal graph learning using meta machine learning

Hang Wu, Wenqi Shi, May D. Wang

BMC Medical Informatics and Decision Making Paper

MIMIR: A Customizable Agent Tuning Platform for Enhanced Scientific Applications

Xiangru Tang, Chunyuan Deng, Hanminwang Hanminwang, Haoran Wang, Yilun Zhao, Wenqi Shi, Yi Fung, Wangchunshu Zhou, Jiannan Cao, Heng Ji, Arman Cohan, Mark Gerstein

EMNLP'24 Paper Code

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, May D. Wang

EMNLP'24 Paper Code

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, May D. Wang

EMNLP'24 Paper Code

BMRetriever: Tuning Large Language Models as Better Biomedical Text Retrievers

Ran Xu*, Wenqi Shi*, Yue Yu, Yuchen Zhuang, Yanqiao Zhu, May D. Wang, Joyce C. Ho, Chao Zhang, Carl Yang

EMNLP'24 Paper Model

RAM-EHR: Retrieval Augmentation Meets Clinical Predictions on Electronic Health Records

Ran Xu*, Wenqi Shi*, Yue Yu, Yuchen Zhuang, Bowen Jin, May D. Wang, Joyce C. Ho, Carl Yang

ACL'24 Paper Code

Knowledge-Infused Prompting: Assessing and Advancing Clinical Text Data Generation with Large Language Models

Ran Xu, Hejie Cui, Yue Yu, Xuan Kan, Wenqi Shi, Yuchen Zhuang, Wei Jin, Joyce Ho, Carl Yang

ACL Findings'24 Paper Code

Retrieval-Augmented Large Language Models for Adolescent Idiopathic Scoliosis Patients in Shared Decision-Making

Wenqi Shi, Yuchen Zhuang, Yuanda Zhu, Henry Iwinski, Michael Wattenbarger, May D. Wang

BCB'23 (Best Paper) Paper

Choice Over Effort: Mapping and Diagnosing Augmented Whole Slide Image Datasets with Training Dynamics

Wenqi Shi, Benoit Marteau, Felipe Giuste, May D. Wang

BCB'23 Paper

Explainable synthetic image generation to improve risk assessment of rare pediatric heart transplant rejection

Felipe O. Giuste, Ryan Sequeira, Vikranth Keerthipati, Peter Lais, Ali Mirzazadeh, Arshawn Mohseni, Yuanda Zhu, Wenqi Shi, Benoit Marteau, Yishan Zhong, Li Tong, Bibhuti Das, Bahig M. Shehata, Shriprasad R. Deshpande, May D. Wang

JBI Paper

Explainable Artificial Intelligence Methods in Combating Pandemics: A Systematic Review

Felipe Giuste, Wenqi Shi, Yuanda Zhu, Tarun Naren, Monica Isgut, Ying Sha, Li Tong, Mitali Gupte, May D. Wang

RBME Paper

Academic Services

Organization Committee: IEEE BHI 2025, ACM BCB 2025.
Area Chair: ACM BCB 2025.
PC Member: ACL, NAACL, EMNLP, ICML, ICLR, NeurIPS, COLM, AISTATS, KDD.
Journal Reviewer: Nature medicine, npj digital medicine, TBME, RBME, JBHI, JAMIA, JBI.

Selected Awards

NVIDIA Academic Grant Program Award (2025);
Best Student Paper Award in ACM BCB (2024);
Outstanding Reviewer for EMNLP 2024 (2024);
AMIA 2023 AI Evaluation Showcase Stage I-III (2023);
Best SIGBio Paper Award in ACM BCB (2023);
Rising Star in EECS (2023);
Finalist of the John H. Moe Award for Best Basic Science E-Poster at the SRS 57th Annual Meeting (2022);
Best Poster Award in IEEE Healthcare Summit (2021).