Wenqi Shi, Ph.D. Assistant Professor School School of Public Health Department Public Health Biography Dr. Wenqi Shi is an Assistant Professor at the Peter O’Donnell Jr. School of Public Health at UT Southwestern Medical Center (UTSW). Prior to joining UTSW, she received her Ph.D. from the Georgia Institute of Technology. Her research lies at the intersection of artificial intelligence (AI) and healthcare, advancing both fundamental algorithms and applied systems for precision and personalized medicine. She has extensive experience working with real-world multi-modal patient data, including Electronic Health Records (EHRs), medical notes, imaging, genomics, and more. With a dedicated focus on pediatric healthcare, cancer, and rare diseases, she actively works on developing large language models for translational medicine, advancing agentic AI and generative models for biomedical discovery, and promoting responsible AI practices to improve clinical outcomes. Research Interest Clinical Decision Support System Clinical Informatics Large Language Models and Foundation Models Personalized and Precision Medicine Publications Featured Publications Clinical decision making under uncertainty: a bootstrapped counterfactual inference approach. Wu H, Shi W, Choudhary A, Wang MD, BMC Med Inform Decis Mak 2024 Sep 24 1 275 Developing a novel causal inference algorithm for personalized biomedical causal graph learning using meta machine learning. Wu H, Shi W, Wang MD, BMC Med Inform Decis Mak 2024 May 24 1 137 Optimized Clinical Feature Analysis for Improved Cardiovascular Disease Risk Screening. Vyshnya S, Epperson R, Giuste F, Shi W, Hornback A, Wang MD, IEEE Open J Eng Med Biol 2024 5 816-827 MIMIR: A Customizable Agent Tuning Platform for Enhanced Scientific Applications Xiangru Tang, Chunyuan Deng, Hanmin Wang, Haoran Wang, Yilun Zhao, Wenqi Shi, Yi Fung, Wangchunshu Zhou, Jiannan Cao, Heng Ji, Arman Cohan, Mark Gerstein EMNLP 2024 486-496 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 Ho, Carl Yang, May D Wang EMNLP 2024 22315–22339 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 Dongmei Wang EMNLP 2024 22294–22314 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 2024 22234–22254 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 2024 754–765 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, May Dongmei Wang, Wei Jin, Joyce Ho, Carl Yang ACL 2024 15496–15523 Early and fair COVID-19 outcome risk assessment using robust feature selection. Giuste FO, He L, Lais P, Shi W, Zhu Y, Hornback A, Tsai C, Isgut M, Anderson B, Wang MD, Sci Rep 2023 Nov 13 1 18981 Results 1-10 of 15 1 2 Next Last Honors & Awards Best Student Paper Award in The 15th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB) (2024) AMIA 2023 AI Evaluation Showcase Stage I-III (2023) Best SIGBio Paper Award in the 14th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (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) Professional Associations/Affiliations ACM Special Interest Group on Bioinformatics, Computational Biology, and Biomedical Informatics (SIGBio) (2019) American Medical Informatics Association (2021) Association for Computational Linguistics (ACL) (2024) IEEE Engineering in Medicine and Biology Society (EMBS) (2019) Scoliosis Research Society (SRS) (2022)
