Selected Publications

^* denotes equal contribution first author ^† denotes equal contribution corresponding author

Full list is available on Google Scholar.

2026

MultiMed-RAG: Leveraging Multi-Source Knowledge and Agent Collaboration for Medical Tasks Yuxing Lu, Sin Yee Goi, Xukai Zhao, J. Ben Tamo, Wenqi Shi, Micky C. Nnamdi, May D. Wang, Jinzhuo Wang npj Digital Medicine, 2026.

MedicalAgentsBench for Complex Medical Reasoning: Comparing Internalized Reasoning Models versus Externalized Agent-based Frameworks Yanjun Shao, Xiangru Tang, Jiwoong Sohn, Jiapeng Chen, Yuxuan Liao, Jiayi Zhang, Jinyu Xiang, Fang Wu, Yilun Zhao, Chenglin Wu, Wenqi Shi, Arman Cohan, Mark Gerstein Cell Patterns, 2026.

RAG in the Wild: On the (In)effectiveness of LLMs with Mixture-of-Knowledge Retrieval Augmentation Ran Xu, Yuchen Zhuang, Yue Yu, Haoyu Wang, Wenqi Shi^†, Carl Yang^† Findings of the Association for Computational Linguistics (ACL), 2026.

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^† Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2026.

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^† Proceedings of the Fourteenth International Conference on Learning Representations (ICLR), 2026.Oral, top 1.18%

Multi-level Asymmetric Contrastive Learning for Volumetric Medical Image Segmentation Pre-training Shuang Zeng, Lei Zhu, Xinliang Zhang, Qian Chen, Hangzhou He, Lujia Jin, Zifeng Tian, Zhaoheng Xie, Micky C Nnamdi, Wenqi Shi, J Ben Tamo, May D. Wang, Yanye Lu IEEE Journal of Biomedical and Health Informatics (JBHI), 2026.

Human Experiences and Reflections (HEARs) Data Connector Protocol: Development and Validation of an AI-Based Tool to Improve Discovery and Reuse of Archived Qualitative Data Tammy Leonard, Jim P. Stimpson, Miguel Ángel Canod, Wenqi Shi, Ada Abaragua, Song Zhang JMIR Research Protocols (JRP), 2026.

Advancing Problem-Based Learning in Biomedical Engineering in the Era of Generative AI Micky C Nnamdi, J Ben Tamo, Wenqi Shi^†, May D Wang^† IEEE Transactions on Education (ToE), 2026.

PKAttn: Pharmacokinetics-Inspired Fusion of DCE-MRI and Clinical Data for Accurate Breast Cancer Recurrence Prediction Xinling Li, Yang Gu, Cheng Zhang, Ruoyu Wang, Xizhe Huang, Erin Cargin, Micky C Nnamdi, Junior Ben Tamo, Wenqi Shi, May Dongmei Wang IEEE International Symposium on Biomedical Imaging (ISBI), 2026.

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 Findings in Proceedings of the European Chapter of the Association for Computational Linguistics (EACL), 2026.

CellForge: Agentic Design of Virtual Cell Models Xiangru Tang, Zhuoyun Yu, Jiapeng Chen, Yan Cui, Daniel Shao, Weixu Wang, Fang Wu, Yuchen Zhuang, Wenqi Shi, Zhi Huang, Arman Cohan, Xihong Lin, Fabian Theis, Smita Krishnaswamy, Mark Gerstein AAAI 2026 Workshop on AI for Scientific Research, 2026.Oral, Best Paper Award

2025

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^† Proceedings of the Conference on Neural Information Processing Systems (NeurIPS), 2025.Spotlight, top 3.2%

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 Proceedings of the Conference on Language Modeling (COLM), 2025.

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 Proceedings of the ACM on Web Conference (WWW), 2025.

SBDH-Reader: a Large Language Model-Powered Method for Extracting Social and Behavioral Determinants of Health from Clinical Notes Zifan Gu, Lesi He, Awais Naeem, Pui Man Chan, Asim Mohamed, Hafsa Khalil, Yujia Guo, Jingwei Huang, Ismael Villanueva-Miranda, Ying Ding, Wenqi Shi, Matthew E Dupre, Guanghua Xiao, Eric D Peterson, Yang Xie, Ann Marie Navar, Donghan M Yang Journal of the American Medical Informatics Association (JAMIA), 2025.

Novel extraction of discriminative fine-grained feature to improve retinal vessel segmentation Shuang Zeng, Chee Hong Lee, Micky C. Nnamdi, Wenqi Shi, J Ben Tamo, Hangzhou He, Xinliang Zhang, Qian Chen, May D Wang, Lei Zhu, Yanye Lu, Qiushi Ren Image and Vision Computing, Volume 163, 2025.

Advancing Sleep Disorder Diagnostics: A Transformer-based EEG Model for Sleep Stage Classification and OSA Prediction Cheng Wan, Micky C Nnamdi, Wenqi Shi, Benjamin Smith, Chad Purnell, May D Wang IEEE Journal of Biomedical and Health Informatics (JBHI), vol. 29, no. 2, 2025.

Fairness Artificial Intelligence in Clinical Decision Support: Mitigating Effect of Health Disparity Hang Wu, Yuanda Zhu, Wenqi Shi, Li Tong, May D Wang IEEE Journal of Biomedical and Health Informatics (JBHI), vol. 29, no. 2, 2025.

Predicting Pediatric Patient Rehabilitation Outcomes After Spinal Deformity Surgery with Artificial Intelligence Wenqi Shi, Felipe 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 Communications Medicine, vol. 5, no. 1, 2025.

2024

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 Proceedings of the Conference on Empirical Methods in Natural Language Processing (EMNLP), 2024.

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 Proceedings of the Conference on Empirical Methods in Natural Language Processing (EMNLP), 2024.

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 Proceedings of the Conference on Empirical Methods in Natural Language Processing (EMNLP), 2024.

MIMIR: A Customizable Agent Tuning Platform for Enhanced Scientific Applications Xiangru Tang, Chunyuan Deng, Hanminwang, Haoran Wang, Yilun Zhao, Wenqi Shi, Yi Fung, Wangchunshu Zhou, Jiannan Cao, Heng Ji, Arman Cohan, Mark Gerstein Proceedings of the Conference on Empirical Methods in Natural Language Processing (EMNLP), 2024.

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 Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics (ACL), 2024.

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 D Wang, Wei Jin, Joyce C Ho, Carl Yang Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics (ACL), 2024.

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, vol. 24, no. 1, 2024.

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, vol. 24, no. 1, 2024.

Optimized Clinical Feature Analysis for Improved Cardiovascular Disease Risk Screening Sofiya Vyshnya, Rachel Epperson, Felipe Giuste, Wenqi Shi, Andrew Hornback, May D Wang IEEE Open Journal of Engineering in Medicine and Biology (OJEMB), vol 5, 2024.

2023 & Earlier

Improving Explainable AI with Patch Perturbation-based Evaluation Pipeline: a COVID-19 X-ray Image Analysis Case Study Jimin Sun^*, Wenqi Shi^*, Felipe Giuste, Yog S Vaghani, Lingzi Tang, May D Wang Scientific Reports, vol 13, issue 1, 2023.

Integrating Multi-omics Data with EHR for Precision Medicine Using Advanced Artificial Intelligence Li Tong, Wenqi Shi, Monica Isgut, Yishan Zhong, Peter Lais, Logan Gloster, Jimin Sun, Aniketh Swain, Felipe Giuste, May D Wang IEEE Reviews in Biomedical Engineering (RBME), vol 17, 2023.

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 Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB), 2023.Best SIGBio Paper Award, 1/191

Choice Over Effort: Mapping and Diagnosing Augmented Whole Slide Image Datasets with Training Dynamics Wenqi Shi, Benoit Marteau, Felipe Giuste, May D Wang Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB), 2023.

Explainable Synthetic Image Generation to Improve Risk Assessment of Rare Pediatric Heart Transplant Rejection Felipe Giuste, Ryan Sequeira, Vikranth Keerthipati, Peter Lais, Ali Mirzazadeh, Arshawn Mohseni, Yuanda Zhu, Wenqi Shi, Benoit Marteau, Yishan Zhong, Li Tong, Bibhuti Das, Bahig Shehata, Shriprasad Deshpande, May D Wang Journal of Biomedical Informatics (JBI), vol 139, 2023.

Early and fair COVID-19 outcome risk assessment using robust feature selection Felipe Giuste, Lawrence He, Peter Lais, Wenqi Shi, Yuanda Zhu, Andrew Hornback, Chiche Tsai, Monica Isgut, Blake Anderson, May D Wang Scientific Reports, vol 13, issue 1, 2023.

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 IEEE Reviews in Biomedical Engineering (RBME), vol 16, 2022.Annual Featured Article

A FHIR-compliant Application for Multi-site and Multi-modality Pediatric Scoliosis Patient Rehabilitation Wenqi Shi, Felipe Giuste, Yuanda Zhu, Ashley M Carpenter, Henry J Iwinski, Coleman Hilton, J Michael Wattenbarger, May D Wang IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2022.