Wenqi Shi

Wenqi Shi

Tenure-Track Assistant Professor
Peter O'Donnell Jr. School of Public Health, UT Southwestern Medical Center

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 (QBRC), the Clinical Informatics Center (CIC), and a graduate faculty of the Biomedical Engineering (BME) Graduate Program.

My research lies at the intersection of AI and healthcare. I develop agentic large language model systems—integrating search, tools, multimodal clinical data, and verification pipelines—to enable transparent, safe, and auditable AI in clinical settings. I collaborate closely with clinicians to design, evaluate, and deploy AI-enabled decision support for precision and personalized medicine. Before joining UTSW, I received my Ph.D. from Bio-Medical Informatics and Bioimaging Lab (Bio-MIBLab) at Georgia Institute of Technology, advised by Dr. May D. Wang, in 2024.

wenqi.shi@utsouthwestern.edu Dallas, Texas

Openings

I am actively looking for Ph.D. students and Postdoctoral researchers to join my group. I am open to discussing research opportunities with motivated students who have strong backgrounds in machine learning and/or health informatics. Please reach out only if you are ready to devote time and effort in a research project. If interested, please email me at wenqi.shi@utsouthwestern.edu with your CV and a brief description of your research interests.

News

  • Mar 2026 Our tutorial on "Large Language Models and Agentic AI for Biomedical Informatics" has been accepted at ISMB 2026.
  • Mar 2026 Our tutorial on multi-agent language model systems has been accepted at ACL 2026.
  • Feb 2026 Grateful to receive the Google Gemini Academic Program Award ($10,000). Thank you Google for supporting our research!
  • Jan 2026 Our paper "MedAgentGym" has been accepted at ICLR 2026 as an Oral presentation (top 1.18%).
  • Jan 2026 Paper accepted at CVPR 2026 on scaling agentic reinforcement learning for tool-integrated reasoning in VLMs.
  • Jan 2026 Best Paper Award at AI4Research Workshop at AAAI 2026 for CellForge.
  • Dec 2025 Our paper "AceSearcher" has been accepted at NeurIPS 2025 as a Spotlight (top 3.2%).
  • Mar 2025 Grateful to receive the NVIDIA Academic Grant Program Award. Thank you NVIDIA for supporting our research!

Selected Publications

MedAgentGym: A Scalable Agentic Training Environment for Code-Centric Reasoning in Biomedical Data Science
Ran Xu, Yuchen Zhuang, Yishan Zhong, Yue Yu, Zifeng Wang, Xiangru Tang, Hang Wu, May D Wang, Peifeng Ruan, Donghan Yang, Tao Wang, Guanghua Xiao, Xin Liu, Carl Yang, Yang Xie†, Wenqi Shi†
International Conference on Learning Representations (ICLR), 2026 Oral, top 1.18%
Paper GitHub HuggingFace News
Scaling Agentic Reinforcement Learning for Tool-Integrated Reasoning in VLMs
Meng Lu, Ran Xu, Yi Fang, Wenxuan Zhang, Yue Yu, Gaurav Srivastava, Yuchen Zhuang, Mohamed Elhoseiny, Charles Fleming, Carl Yang, Zhengzhong Tu, Yang Xie, Guanghua Xiao, Hanrui Wang, Di Jin†, Wenqi Shi†, Xuan Wang†
IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2026
Paper GitHub
AceSearcher: Bootstrapping Reasoning and Search for LLMs via Self-Play Reinforcement Fine-Tuning
Ran Xu, Yuchen Zhuang, Zihan Dong, Jonathan Wang, Yue Yu, Joyce C Ho, Linjun Zhang, Haoyu Wang, Wenqi Shi†, Carl Yang†
Conference on Neural Information Processing Systems (NeurIPS), 2025 Spotlight, top 3.2%
Paper GitHub HuggingFace
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
Conference on Empirical Methods in Natural Language Processing (EMNLP), 2024
Paper GitHub HuggingFace
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
Conference on Empirical Methods in Natural Language Processing (EMNLP), 2024
Paper GitHub
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
Conference on Empirical Methods in Natural Language Processing (EMNLP), 2024
Paper GitHub HuggingFace

View all publications →

Education

Georgia Institute of Technology, College of Engineering
Ph.D. in Electrical and Computer Engineering
Advisor: Dr. May D. Wang, Bio-Medical Informatics and Bio-Imaging Laboratory (Bio-MIB Lab)
Aug 2019 – May 2024
Beijing Normal University, School of Artificial Intelligence
B.S. in Information Science and Technology
Advisor: Dr. Libao Zhang, Geoscience and Remote Sensing Lab
Aug 2015 – July 2019

Misc

  • 🐱 In my spare time, I mainly stay with my four cats — they are the real bosses of the house! 🐾🐾🐾🐾
  • 🎮 Passionate Dota 2 enjoyer. Huge fan of Ame, XXS, and Team XG! GG go next! 🏆🔥💪