Our Research Publications

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

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Benchmark

TRIALPANORAMA: Database and Benchmark for Systematic Review and Design of Clinical Trials

Source: Preprint

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

Keywords:

Benchmark

Clinical trials

Systematic Review

Trial Design

Database

Project Website

Can Large Language Models Replace Data Scientists in Biomedical Research?

Source: Preprint

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

Keywords:

LLM

Data Science

Biomedical Research

AI Assistant

Benchmark

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

Source: Preprint

Authors: Zifeng Wang, Benjamin Danek, Jimeng Sun

Keywords:

Benchmark

Data Science

Biomedical Research

AI Agent

LLM

Project Website

Clinical Trial Foundation Model

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

Source: Preprint

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

Keywords:

LLM

Clinical trials

Foundation model

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Systematic Literature Review

Accelerating clinical evidence synthesis with large language models

Source: Preprint

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

Keywords:

LLM

Medical Literature Mining

Systematic Review

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

Source: Preprint

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

Keywords:

LLM

Medical Literature Mining

Systematic Review

Human-AI Collaboration

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Patient Recruitment

Matching patients to clinical trials with large language models

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

Keywords:

LLM

Prompting

Patient-Trial Matching

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

Source: KDD'20

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

Keywords:

Patient-Trial Matching

EHR

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Doctor2Vec: Dynamic Doctor Representation Learning for Clinical Trial Recruitment

Source: AAAI'20

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

Keywords:

Patient-Trial Matching

EHR

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Trial Design

AutoTrial: Prompting Language Models for Clinical Trial Design

Source: EMNLP'23

Authors: Zifeng Wang, Cao Xiao, Jimeng Sun

Keywords:

LLM

Instruction Tuning

Eligibility Criteria

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

Source: EMNLP'22

Authors: Zifeng Wang, Jimeng Sun

Keywords:

Trial Search

Contrastive Learning

Dense Retrieval

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

Source: ACM-BCB'23

Authors: Zifeng Wang, Jimeng Sun

Keywords:

Trial Outcome

Sequential Learning

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HINT: Hierarchical Interaction Network for Clinical Trial Outcome Predictions

Source: Patterns

Authors: Zifeng Wang, Jimeng Sun

Keywords:

Trial Outcome

Graph Neural Network

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Multimodal Model

BioBridge: Bridging Biomedical Foundation Models via Knowledge Graph

Source: ICLR'24

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

Keywords:

Foundation Model

Multimodal AI

Biomedical AI

Knowledge Graph

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MedCLIP: Contrastive Learning from Unpaired Medical Images and Text

Source: EMNLP'22

Authors: Zifeng Wang, Jimeng Sun

Keywords:

Vision-Language Model

Multimodal AI

Clinical Note

X-Ray

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Clinical Predictive Model

UniPredict: Large Language Models are Universal Tabular Predictors

Source: Preprint

Authors: Ruiyu Wang, Zifeng Wang, Jimeng Sun

Keywords:

Tabular Learning

Patient Outcome

LLM

Instruction Tuning

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

Source: IJCAI'24

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

Keywords:

Tabular Learning

Patient Outcome

LLM

Data-Centric AI

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TransTab: Learning Transferable Tabular Transformers Across Tables

Source: NeurIPS'22

Authors: Zifeng Wang, Jimeng Sun

Keywords:

Tabular Learning

Patient Outcome

Transfer Learning

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

Source: JAMIA'21

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

Keywords:

Pandemic Prediction

Graph Neural Network

Real-World Evidence

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

Source: Nature Communications

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

Keywords:

Pandemic Prediction

Spatio-temporal Prediction

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

Source: WWW'22

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

Keywords:

Population Health Prediction

Graph Neural Network

Spatio-temporal Prediction

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

Source: npj Digital Medicine'25

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

Keywords:

Predictive Modeling

Data Augmentation

Data Synthesis

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Synthetic Patient Generation

TWIN: Personalized Clinical Trial Digital Twin Generation

Source: KDD'23

Authors: Trisha Das, Zifeng Wang, Jimeng Sun

Keywords:

Digital Twin

Variational Autoencoder

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

Source: Nature Communications 2023

Authors: Brandon Theodorou, Cao Xiao, Jimeng Sun

Keywords:

Synthetic Data

EHR

Language Model

Longitudinal Data

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