About

Wenqi Shi is an Assistant Professor in the Department of Health Data Science and Biostatistics at UT Southwestern Medical Center, with joint appointments at the Quantitative Biomedical Research Center (QBRC) and the Clinical Informatics Center (CIC). Before joining UTSW, she received her Ph.D. from Bio-Medical Informatics and Bioimaging Lab (Bio-MIBLab) at Georgia Institute of Technology, advised by Dr. May D. Wang, in 2024.

Her lab focuses on scaling agentic intelligence toward autonomous co-scientists in biomedical data science, building search- and tool-augmented AI systems capable of reasoning over domain knowledge, executing reproducible research workflows, and continuously improving through interaction with biomedical environments. Lab research spans knowledge-grounded biomedical reasoning, code-empowered autonomous agents, scalable agentic training environments, and knowledge-guided synthetic data generation, with applications in both clinical informatics and biomedical discovery. Her research aims to accelerate precision and personalized medicine while ensuring AI systems in clinical and scientific settings remain transparent, auditable, and safe under meaningful human oversight.

Openings

I am actively looking for self-motivated Ph.D. students and Postdoctoral researchers to join my group. I am open to discussing research opportunities with 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

  • 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 Grateful to receive the Thinking Machines Lab Tinker Research and Teaching Grant.
  • 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 Information Science and Technology
B.S. in Electrical Information Science and Technology
Advisor: Dr. Libao Zhang, AI for Geoscience and Remote Sensing Lab
Aug 2015 – July 2019

Misc

  • 🐱 In my spare time, I mainly stay with my fur friends — they are the real bosses of the house! 🐾🐾🐾🐾
  • 🎮 Passionate Dota 2 enjoyer. Huge fan of Ame, XXS, and Team XG! GG go next! 🏆🔥💪 PudgeAxeJuggernautCrystal Maiden
  • 🗼 Slay the Spire on the side. Rebooting my beloved Defect (the “Chicken Pot” 🍲🤖). Slow to start, but proudly the 4th-strongest of all four characters! ⚙️
  • 👑 Currently scheming through Road to Empress II. Still, as always, holding out hope for 4599. 🎬