Publications

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

Full list also available on Google Scholar.

Preprints

Hang Zhang, Ruheng Wang, Yuelyu Ji, Mingu Kwak, Xizhi Wu, Chenyu Li, Li Zhang, Wenqi Shi, Yifan Peng, Yanshan Wang
Scaling Medical Reasoning Verification via Tool-Integrated Reinforcement Learning
arXiv preprint arXiv:2601.20221, 2026.
Meng Lu, Yuxing Lu, Yuchen Zhuang, Megan Mullins, Yang Xie, Guanghua Xiao, Charles Fleming, Wenqi Shi†, Xuan Wang†
MEDVISTAGYM: A Scalable Training Environment for Thinking with Medical Images via Tool-Integrated Reinforcement Learning
arXiv preprint arXiv:2601.07107, 2026.
Ran Xu, Yuchen Zhuang, Yue Yu, Haoyu Wang, Wenqi Shi†, Carl Yang†
RAG in the Wild: On the (In)effectiveness of LLMs with Mixture-of-Knowledge Retrieval Augmentation
arXiv preprint arXiv:2507.20059, 2025.
Jingwei Huang, Kuroush Nezafati, et al., Donghan M Yang†, Wenqi Shi†, Yang Xie†
Multi-Agent LLMs Ensemble for Efficient Atrial Fibrillation Annotation of ECG Reports
arXiv preprint arXiv:2410.16543, 2025.
Xiangru Tang, Daniel Shao, et al., Wenqi Shi, Arman Cohan, Mark Gerstein
MedAgentsBench: Benchmarking Thinking Models and Agent Frameworks for Complex Medical Reasoning
arXiv preprint arXiv:2503.07459, 2025.
Matthew Chen, Micky Nnamdi, et al., Wenqi Shi†, May D Wang†
MENDR: Manifold Explainable Neural Data Representations
arXiv preprint arXiv:2508.04956, 2025.

2026

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†
Scaling Agentic Reinforcement Learning for Tool-Integrated Reasoning in VLMs
Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR), 2026.
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†
MedAgentGym: A Scalable Agentic Training Environment for Code-Centric Reasoning in Biomedical Data Science
Proceedings of the Fourteenth International Conference on Learning Representations (ICLR), 2026. Oral, top 1.18%
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
Multi-level Asymmetric Contrastive Learning for Volumetric Medical Image Segmentation Pre-training
IEEE Journal of Biomedical and Health Informatics (JBHI), 2026.
Tammy Leonard, Jim P. Stimpson, Miguel Ángel Canod, Wenqi Shi, Ada Abaragua, Song Zhang
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
JMIR Research Protocols (JRP), 2026.
Micky C Nnamdi, J Ben Tamo, Wenqi Shi†, May D Wang†
Advancing Problem-Based Learning in Biomedical Engineering in the Era of Generative AI
IEEE Transactions on Education (ToE), 2026.
Xinling Li, Yang Gu, Cheng Zhang, Ruoyu Wang, Xizhe Huang, Erin Cargin, Micky C Nnamdi, Junior Ben Tamo, Wenqi Shi, May Dongmei Wang
PKAttn: Pharmacokinetics-Inspired Fusion of DCE-MRI and Clinical Data for Accurate Breast Cancer Recurrence Prediction
IEEE International Symposium on Biomedical Imaging (ISBI), 2026.
Yuchen Zhuang, Di Jin, Jiaao Chen, Wenqi Shi, Hanrui Wang, Chao Zhang
WorkForceAgent-R1: Incentivizing Reasoning Capability in LLM-based Web Agents via Reinforcement Learning
Findings in Proceedings of the European Chapter of the Association for Computational Linguistics (EACL), 2026.
J Ben Tamo, Nishant S Chouhan, Micky C Nnamdi, Yining Yuan, Shreya S Chivilkar, Wenqi Shi, Steven W Hwang, B Randall Brenn, May D Wang
Causal Machine Learning for Surgical Interventions
Big Data Mining and Analytics, 2026.
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
CellForge: Agentic Design of Virtual Cell Models
AAAI 2026 Workshop on AI for Scientific Research, 2026. Oral, Best Paper Award

2025

Ran Xu, Yuchen Zhuang, Zihan Dong, Jonathan Wang, Yue Yu, Joyce C Ho, Linjun Zhang, Haoyu Wang, Wenqi Shi†, Carl Yang†
AceSearcher: Bootstrapping Reasoning and Search for LLMs via Self-Play Reinforcement Fine-Tuning
Proceedings of the Conference on Neural Information Processing Systems (NeurIPS), 2025. Spotlight, top 3.2%
Ran Xu*, Wenqi Shi*, Yuchen Zhuang, Yue Yu, Joyce C Ho, Haoyu Wang, Carl Yang
Collab-RAG: Boosting Retrieval-Augmented Generation for Complex Question Answering via White-Box and Black-Box LLM Collaboration
Proceedings of the Conference on Language Modeling (COLM), 2025.
Ran Xu, Wenqi Shi, Jonathan Wang, Jasmine Zhou, Carl Yang
MedAssist: LLM-Empowered Medical Assistant for Assisting the Scrutinization and Comprehension of Electronic Health Records
Proceedings of the ACM on Web Conference (WWW), 2025.
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
SBDH-Reader: a Large Language Model-Powered Method for Extracting Social and Behavioral Determinants of Health from Clinical Notes
Journal of the American Medical Informatics Association (JAMIA), 2025.
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
Novel extraction of discriminative fine-grained feature to improve retinal vessel segmentation
Image and Vision Computing, Volume 163, 2025.
Cheng Wan, Micky C Nnamdi, Wenqi Shi, Benjamin Smith, Chad Purnell, May D Wang
Advancing Sleep Disorder Diagnostics: A Transformer-based EEG Model for Sleep Stage Classification and OSA Prediction
IEEE Journal of Biomedical and Health Informatics (JBHI), vol. 29, no. 2, 2025.
Hang Wu, Yuanda Zhu, Wenqi Shi, Li Tong, May D Wang
Fairness Artificial Intelligence in Clinical Decision Support: Mitigating Effect of Health Disparity
IEEE Journal of Biomedical and Health Informatics (JBHI), vol. 29, no. 2, 2025.
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
Predicting Pediatric Patient Rehabilitation Outcomes After Spinal Deformity Surgery with Artificial Intelligence
Nature Communications Medicine, vol. 5, no. 1, 2025.
Pooja M Datta Roy, Jens Cuba, Kyle Milligan, Wenqi Shi, May D Wang, Michelle C LaPlaca
Sex Dimorphism Influences Cortical Microglial Morphological and Phenotypic Marker Profile After Closed Head Mild Traumatic Brain Injury in Rats
Neurotrauma Reports, vol. 6, no. 1, 2025.
B Vaibhav Mallya, Micky C Nnamdi, J Ben Tamo, Matthew Chen, Yishan Zhong, Wenqi Shi, May D Wang
ResSwinUnet3D: Developing A New Residual-Based SwinUnet3D Model for Enhanced 3D Medical Image Segmentation
IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI), 2025.
Micky C. Nnamdi, Wenqi Shi, Cheng Wan, J. Ben Tamo, Benjamin M Smith, Chad A. Purnell, May D Wang
KindSleep: Knowledge-Informed Diagnosis of Obstructive Sleep Apnea from Oximetry
Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB), 2025.
Yishan Zhong, Wenqi Shi, J. Ben Tamo, Micky C. Nnamdi, Yining Yuan, May D Wang
Multi-Agent LLM Reasoning for Clinical Procedure Sequencing from High-Granularity EHR Data
Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB), 2025. Best Paper Honorable Mention, 3/170
Nishant Singh Chouhan, J. Ben Tamo, Oankar R. Patil, Wenqi Shi, Micky C. Nnamdi, Steven Hwang, Kamran Shazand, May D Wang
From Association to Mechanism: Causal Graph-Based Fine-Mapping of Regulatory SNPs for Functional Validation
Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB), 2025.
Yining Yuan, J. Ben Tamo, Wenqi Shi, Yishan Zhong, Micky C. Nnamdi, B. Randall Brenn, Steven W. Hwang, May D Wang
Developing Fairness-Aware Task Decomposition to Improve Equity in Post-Spinal Fusion Complication Prediction
Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB), 2025.
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†
MedAgentGym: Training LLM Agents for Code-Based Medical Reasoning at Scale
GenAI4Health Workshop at NeurIPS, 2025.

2024

Wenqi Shi*, Ran Xu*, Yuchen Zhuang, Yue Yu, Jieyu Zhang, Hang Wu, Yuanda Zhu, Joyce C Ho, Carl Yang, May D Wang
EHRAgent: Code Empowers Large Language Models for Few-Shot Complex Tabular Reasoning on Electronic Health Records
Proceedings of the Conference on Empirical Methods in Natural Language Processing (EMNLP), 2024.
Wenqi Shi*, Ran Xu*, Yuchen Zhuang, Yue Yu, Haotian Sun, Hang Wu, Carl Yang, May D Wang
MedAdapter: Efficient Test-Time Adaptation of Large Language Models towards Medical Reasoning
Proceedings of the Conference on Empirical Methods in Natural Language Processing (EMNLP), 2024.
Ran Xu*, Wenqi Shi*, Yue Yu, Yuchen Zhuang, Yanqiao Zhu, May D Wang, Joyce C Ho, Chao Zhang, Carl Yang
BMRetriever: Tuning Large Language Models as Better Biomedical Text Retrievers
Proceedings of the Conference on Empirical Methods in Natural Language Processing (EMNLP), 2024.
Xiangru Tang, Chunyuan Deng, Hanminwang, Haoran Wang, Yilun Zhao, Wenqi Shi, Yi Fung, Wangchunshu Zhou, Jiannan Cao, Heng Ji, Arman Cohan, Mark Gerstein
MIMIR: A Customizable Agent Tuning Platform for Enhanced Scientific Applications
Proceedings of the Conference on Empirical Methods in Natural Language Processing (EMNLP), 2024.
Ran Xu*, Wenqi Shi*, Yue Yu, Yuchen Zhuang, Bowen Jin, May D Wang, Joyce C Ho, Carl Yang
RAM-EHR: Retrieval Augmentation Meets Clinical Predictions on Electronic Health Records
Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics (ACL), 2024.
Ran Xu, Hejie Cui, Yue Yu, Xuan Kan, Wenqi Shi, Yuchen Zhuang, May D Wang, Wei Jin, Joyce C Ho, Carl Yang
Knowledge-infused Prompting: Assessing and Advancing Clinical Text Data Generation with Large Language Models
Proceedings of the 62nd Annual Meeting of the Association for Computational Linguistics (ACL), 2024.
Hang Wu*, Wenqi Shi*, Anirudh Choudhary, May D Wang
Clinical Decision Making under Uncertainty: A Bootstrapped Counterfactual Inference Approach
BMC Medical Informatics and Decision Making, vol. 24, no. 1, 2024.
Hang Wu*, Wenqi Shi*, May D Wang
Developing a Novel Causal Inference Algorithm for Personalized Biomedical Causal Graph Learning Using Meta Machine Learning
BMC Medical Informatics and Decision Making, vol. 24, no. 1, 2024.
Sofiya Vyshnya, Rachel Epperson, Felipe Giuste, Wenqi Shi, Andrew Hornback, May D Wang
Optimized Clinical Feature Analysis for Improved Cardiovascular Disease Risk Screening
IEEE Open Journal of Engineering in Medicine and Biology (OJEMB), vol 5, 2024.
J Ben Tamo, Micky C Nnamdi, Andrew Hornback, Matthew Chen, Wenqi Shi, Yuanda Zhu, Henry J Iwinski, May D Wang
Heterogeneous Treatment Effects of Spinal Fusion Surgery for Adolescent Idiopathic Scoliosis Patients
Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB), 2024. Best Student Paper Award, 2/201

2023

Jimin Sun*, Wenqi Shi*, Felipe Giuste, Yog S Vaghani, Lingzi Tang, May D Wang
Improving Explainable AI with Patch Perturbation-based Evaluation Pipeline: a COVID-19 X-ray Image Analysis Case Study
Scientific Reports, vol 13, issue 1, 2023.
Li Tong, Wenqi Shi, Monica Isgut, Yishan Zhong, Peter Lais, Logan Gloster, Jimin Sun, Aniketh Swain, Felipe Giuste, May D Wang
Integrating Multi-omics Data with EHR for Precision Medicine Using Advanced Artificial Intelligence
IEEE Reviews in Biomedical Engineering (RBME), vol 17, 2023.
Wenqi Shi, Yuchen Zhuang, Yuanda Zhu, Henry Iwinski, Michael Wattenbarger, May D Wang
Retrieval-augmented Large Language Models for Adolescent Idiopathic Scoliosis Patients in Shared Decision-Making
Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB), 2023. Best SIGBio Paper Award, 1/191
Wenqi Shi, Benoit Marteau, Felipe Giuste, May D Wang
Choice Over Effort: Mapping and Diagnosing Augmented Whole Slide Image Datasets with Training Dynamics
Proceedings of the 14th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB), 2023.
Felipe Giuste, Ryan Sequeira, Vikranth Keerthipati, Peter Lais, Ali Mirzazadeh, Arshawn Mohseni, Yuanda Zhu, Wenqi Shi, et al., May D Wang
Explainable Synthetic Image Generation to Improve Risk Assessment of Rare Pediatric Heart Transplant Rejection
Journal of Biomedical Informatics (JBI), vol 139, 2023.
Felipe Giuste, Lawrence He, Peter Lais, Wenqi Shi, Yuanda Zhu, Andrew Hornback, et al., May D Wang
Early and fair COVID-19 outcome risk assessment using robust feature selection
Scientific Reports, vol 13, issue 1, 2023.

2022

Felipe Giuste*, Wenqi Shi*, Yuanda Zhu, Tarun Naren, Monica Isgut, Ying Sha, Li Tong, Mitali Gupte, May D Wang
Explainable Artificial Intelligence Methods in Combating Pandemics: A Systematic Review
IEEE Reviews in Biomedical Engineering (RBME), vol 16, 2022. Annual Featured Article
Wenqi Shi, Felipe Giuste, Yuanda Zhu, Ashley M Carpenter, Henry J Iwinski, Coleman Hilton, J Michael Wattenbarger, May D Wang
A FHIR-compliant Application for Multi-site and Multi-modality Pediatric Scoliosis Patient Rehabilitation
IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2022.
Wenqi Shi, Mitali S Gupte, May D Wang
Learning from Heterogeneous Data via Contrastive Learning: An Application in Multi-source Covid-19 Radiography
IEEE EMBS International Conference on Biomedical and Health Informatics (BHI), 2022.
Andrew Hornback, Wenqi Shi, Felipe Giuste, Yuanda Zhu, et al., May D Wang
Development of a Generalizable Multi-site and Multi-modality Clinical Data Cloud Infrastructure for Pediatric Patient Care
Proceedings of the 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB), 2022.

2021 & Earlier

Wenqi Shi, Li Tong, Yuanda Zhu, May D Wang
COVID-19 Automatic Diagnosis with Radiographic Imaging: Explainable Attention Transfer Deep Neural Networks
IEEE Journal of Biomedical and Health Informatics (JBHI), vol 25, issue 7, 2021.
Wenqi Shi, Li Tong, Yuchen Zhuang, Yuanda Zhu, May D Wang
EXAM: an Explainable Attention-based Model for Covid-19 Automatic Diagnosis
Proceedings of the 11th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics (BCB), 2020.
Qijian Zhang, Wenqi Shi, Libao Zhang, Yue Liu
Integrating Sparse Reconstruction Saliency and Target-Aware Active Contour Model for Airport Extraction
25th IEEE International Conference on Image Processing (ICIP), 2018.