Research Publications
Explore our contributions to AI in drug discovery and development, published in leading journals and conferences.
Making large language models reliable data science programming copilots for biomedical research
Zifeng Wang, Benjamin Danek, Ziwei Yang, Zheng Chen, Jimeng Sun
BIODSA-1K: Benchmarking Data Science Agents for Biomedical Research
Zifeng Wang, Benjamin Danek, Jimeng Sun
Benchmarking and Developing Large Language Models Using One Million Clinical Trials (TrialPanorama)
Zifeng Wang, Jiacheng Lin, Qiao Jin, Junyi Gao, Jathurshan Pradeepkumar, Pengcheng Jiang, Zhiyong Lu, Jimeng Sun
Panacea: A foundation model for clinical trial search, summarization, design, and recruitment
Jiacheng Lin, Hanwen Xu, Zifeng Wang, Sheng Wang, Jimeng Sun
Empowering Biomedical Evidence Exploration and Synthesis with Deep Knowledge Graph Research
Zifeng Wang, Zheng Chen, Ziwei Yang, Xiao Wang, Qiao Jin, Yifan Peng, Zhiyong Lu, Jimeng Sun
Tutorial: guidance on the use of large language models for medical research
Qiao Jin, Nicholas Wan, Robert Leaman, Shubo Tian, Zhizheng Wang, Yifan Yang, Zifeng Wang, Guangzhi Xiong, Po-Ting Lai, Qingqing Zhu, Benjamin Hou, Maame Sarfo-Gyamfi, Gongbo Zhang, Aidan Gilson, Balu Bhasuran, Zhe He, Aidong Zhang, Jimeng Sun, Chunhua Weng, Ronald M. Summers, Qingyu Chen, Yifan Peng, Zhiyong Lu
Accelerating clinical evidence synthesis with large language models
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
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
FRAMM: Fair ranking with missing modalities for clinical trial site selection
Brandon Theodorou, Lucas Glass, Cao Xiao, Jimeng Sun
Matching patients to clinical trials with large language models
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
Junyi Gao, Cao Xiao, Lucas M. Glass, Jimeng Sun
Doctor2Vec: Dynamic Doctor Representation Learning for Clinical Trial Recruitment
Junyi Gao, Cao Xiao, Lucas M. Glass, Jimeng Sun
AutoTrial: Prompting Language Models for Clinical Trial Design
Zifeng Wang, Cao Xiao, Jimeng Sun
Trial2Vec: Zero-Shot Clinical Trial Document Similarity Search using Self-Supervision
Zifeng Wang, Jimeng Sun
SPOT: Sequential Predictive Modeling of Clinical Trial Outcome with Meta-Learning
Zifeng Wang, Jimeng Sun
HINT: Hierarchical Interaction Network for Clinical Trial Outcome Predictions
Zifeng Wang, Jimeng Sun
TrialBench: Multi-Modal AI-Ready Datasets for Clinical Trial Prediction
Jintai Chen, Yaojun Hu, Mingchen Cai, Yingzhou Lu, Yue Wang, Xu Cao, Miao Lin, Hongxia Xu, Jian Wu, Xiao Cao, Jimeng Sun, Yuqiang Li, Lucas Glass, Kexin Huang, Marinka Zitnik, Tianfan Fu
MLOmics: Cancer Multi-Omics Database for Machine Learning
Ziwei Yang, Rikuto Kotoge, Xihao Piao, Zheng Chen, Lingwei Zhu, Peng Gao, Yasuko Matsubara, Yasushi Sakurai, Jimeng Sun
BioBridge: Bridging Biomedical Foundation Models via Knowledge Graph
Zifeng Wang, Zichen Wang, Balasubramaniam Srinivasan, Vassilis N. Ioannidis, Huzefa Rangwala, Rishita Anubhai
MedCLIP: Contrastive Learning from Unpaired Medical Images and Text
Zifeng Wang, Jimeng Sun
UniPredict: Large Language Models are Universal Tabular Predictors
Ruiyu Wang, Zifeng Wang, Jimeng Sun
MediTab: Scaling Medical Tabular Data Predictors via Data Consolidation, Enrichment, and Refinement
Zifeng Wang, Chufan Gao,Cao Xiao, Jimeng Sun
STAN: Spatio-Temporal Attention Network for Pandemic Prediction using Real-World Evidence
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
Junyi Gao, Joerg Heintz, Christina Mack, Lucas Glass, Adam Cross & Jimeng Sun
PopNet: Real-Time Population-Level Disease Prediction with Data Latency
Junyi Gao, Cao Xiao, Lucas M. Glass, Jimeng Sun
Improving medical machine learning models with generative balancing for equity and excellence
Brandon Theodorou, Benjamin Danek, Venkat Tummala, Shivam Pankaj Kumar, Bradley Malin, Jimeng Sun
TWIN: Personalized Clinical Trial Digital Twin Generation
Trisha Das, Zifeng Wang, Jimeng Sun
Synthesize high-dimensional longitudinal electronic health records via hierarchical autoregressive language model
Brandon Theodorou, Cao Xiao, Jimeng Sun
PromptEHR: Conditional Electronic Healthcare Records Generation with Prompt Learning
Zifeng Wang, Jimeng Sun
Clinical trial outcome prediction with multi-modal generative AI
Brandon Theodorou, Zifeng Wang, Jimeng Sun
How LLM Training Actually Works: a practical guide to open-weight model training and evaluation
Jimeng Sun