Our Research Publications

Explore our contributions to AI in clinical research, published in leading journals and conferences.

Benchmark

TrialPanorama: Developing Large Language Models for Clinical Research Using One Million Clinical Trials

Benchmark

Clinical trials

Systematic Review

Trial Design

Database

Source Preprint

Authors Zifeng Wang, Qiao Jin, Jiacheng Lin, Junyi Gao, Jathurshan Pradeepkumar, Pengcheng Jiang, Benjamin Danek, Zhiyong Lu, Jimeng Sun

Can Large Language Models Replace Data Scientists in Biomedical Research?

LLM

Data Science

Biomedical Research

AI Assistant

Benchmark

Source Preprint

Authors Zifeng Wang, Benjamin Danek, Ziwei Yang, Zheng Chen, Jimeng Sun

BIODSA-1K: Benchmarking Data Science Agents for Biomedical Research

Benchmark

Data Science

Biomedical Research

AI Agent

LLM

Source Preprint

Authors Zifeng Wang, Benjamin Danek, Jimeng Sun

Clinical Trial Foundation Model

Panacea: A foundation model for clinical trial search, summarization, design, and recruitment

LLM

Clinical trials

Foundation model

Source Preprint

Authors Jiacheng Lin, Hanwen Xu, Zifeng Wang, Sheng Wang, Jimeng Sun

Systematic Literature Review

Accelerating clinical evidence synthesis with large language models

LLM

Medical Literature Mining

Systematic Review

Source NPJ Digital Medicine

Authors Wang, Zifeng and Cao, Lang and Danek, Benjamin and Jin, Qiao and Lu, Zhiyong and Sun, Jimeng

A foundation model for human-AI collaboration in medical literature mining

LLM

Medical Literature Mining

Systematic Review

Human-AI Collaboration

Source Nature Communications

Authors Zifeng Wang, Lang Cao, Qiao Jin, Joey Chan, Nicholas Wan, Behdad Afzali, Hyun-Jin Cho, Chang-In Choi, Mehdi Emamverdi, Manjot K. Gill, Sun-Hyung Kim, Yijia Li, Yi Liu, Hanley Ong, Justin Rousseau, Irfan Sheikh, Jenny J. Wei, Ziyang Xu, Christopher M. Zallek, Kyungsang Kim, Yifan Peng, Zhiyong Lu, Jimeng Sun

Patient Recruitment

Matching patients to clinical trials with large language models

LLM

Prompting

Patient-Trial Matching

Source Nature Communications

Authors Qiao Jin, Zifeng Wang, Charalampos S. Floudas, Fangyuan Chen, Changlin Gong, Dara Bracken-Clarke, Elisabetta Xue, Yifan Yang, Jimeng Sun & Zhiyong Lu

COMPOSE: Cross-modal pseudo-siamese network for patient trial matching

Patient-Trial Matching

EHR

Source KDD'20

Authors Junyi Gao, Cao Xiao, Lucas M. Glass, Jimeng Sun

Doctor2Vec: Dynamic Doctor Representation Learning for Clinical Trial Recruitment

Patient-Trial Matching

EHR

Source AAAI'20

Authors Junyi Gao, Cao Xiao, Lucas M. Glass, Jimeng Sun

Trial Design

AutoTrial: Prompting Language Models for Clinical Trial Design

LLM

Instruction Tuning

Eligibility Criteria

Source EMNLP'23

Authors Zifeng Wang, Cao Xiao, Jimeng Sun

Trial2Vec: Zero-Shot Clinical Trial Document Similarity Search using Self-Supervision

Trial Search

Contrastive Learning

Dense Retrieval

Source EMNLP'22

Authors Zifeng Wang, Jimeng Sun

SPOT: Sequential Predictive Modeling of Clinical Trial Outcome with Meta-Learning

Trial Outcome

Sequential Learning

Source ACM-BCB'23

Authors Zifeng Wang, Jimeng Sun

HINT: Hierarchical Interaction Network for Clinical Trial Outcome Predictions

Trial Outcome

Graph Neural Network

Source Patterns

Authors Zifeng Wang, Jimeng Sun

Multimodal Model

BioBridge: Bridging Biomedical Foundation Models via Knowledge Graph

Foundation Model

Multimodal AI

Biomedical AI

Knowledge Graph

Source ICLR'24

Authors Zifeng Wang, Zichen Wang, Balasubramaniam Srinivasan, Vassilis N. Ioannidis, Huzefa Rangwala, Rishita Anubhai

MedCLIP: Contrastive Learning from Unpaired Medical Images and Text

Vision-Language Model

Multimodal AI

Clinical Note

X-Ray

Source EMNLP'22

Authors Zifeng Wang, Jimeng Sun

Clinical Predictive Model

UniPredict: Large Language Models are Universal Tabular Predictors

Tabular Learning

Patient Outcome

LLM

Instruction Tuning

Source Preprint

Authors Ruiyu Wang, Zifeng Wang, Jimeng Sun

MediTab: Scaling Medical Tabular Data Predictors via Data Consolidation, Enrichment, and Refinement

Tabular Learning

Patient Outcome

LLM

Data-Centric AI

Source IJCAI'24

Authors Zifeng Wang, Chufan Gao,Cao Xiao, Jimeng Sun

TransTab: Learning Transferable Tabular Transformers Across Tables

Tabular Learning

Patient Outcome

Transfer Learning

Source NeurIPS'22

Authors Zifeng Wang, Jimeng Sun

STAN: Spatio-Temporal Attention Network for Pandemic Prediction using Real-World Evidence

Pandemic Prediction

Graph Neural Network

Real-World Evidence

Source JAMIA'21

Authors Junyi Gao, Rakshith Sharma, Cheng Qian, Lucas M Glass, Jeffrey Spaeder, Justin Romberg, Jimeng Sun, Cao Xiao

Evidence-driven spatiotemporal COVID-19 hospitalization prediction with Ising dynamics

Pandemic Prediction

Spatio-temporal Prediction

Source Nature Communications

Authors Junyi Gao, Joerg Heintz, Christina Mack, Lucas Glass, Adam Cross & Jimeng Sun

PopNet: Real-Time Population-Level Disease Prediction with Data Latency

Population Health Prediction

Graph Neural Network

Spatio-temporal Prediction

Source WWW'22

Authors Junyi Gao, Cao Xiao, Lucas M. Glass, Jimeng Sun

Improving medical machine learning models with generative balancing for equity and excellence

Predictive Modeling

Data Augmentation

Data Synthesis

Source npj Digital Medicine'25

Authors Brandon Theodorou, Benjamin Danek, Venkat Tummala, Shivam Pankaj Kumar, Bradley Malin, Jimeng Sun

Synthetic Patient Generation

TWIN: Personalized Clinical Trial Digital Twin Generation

Digital Twin

Variational Autoencoder

Source KDD'23

Authors Trisha Das, Zifeng Wang, Jimeng Sun

Synthesize high-dimensional longitudinal electronic health records via hierarchical autoregressive language model

Synthetic Data

EHR

Language Model

Longitudinal Data

Source Nature Communications

Authors Brandon Theodorou, Cao Xiao, Jimeng Sun