Publications

Methods for designing more feasible trials, simulating outcomes, and creating analysis-ready evidence for statistical teams.

• EMNLP'23

  AutoTrial: Prompting Language Models for Clinical Trial Design

  Zifeng Wang, Cao Xiao, Jimeng Sun

  LLMInstruction TuningEligibility Criteria

• EMNLP'22

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

  Zifeng Wang, Jimeng Sun

  Trial SearchContrastive LearningDense Retrieval

• KDD'23

  TWIN: Personalized Clinical Trial Digital Twin Generation

  Trisha Das, Zifeng Wang, Jimeng Sun

  Digital TwinVariational Autoencoder

• Patterns

  Clinical trial outcome prediction with multi-modal generative AI

  Brandon Theodorou, Zifeng Wang, Jimeng Sun

  Digital TwinGenerative AITrial OutcomeMulti-Modal

Reliable methods for cohort analysis, longitudinal patient modeling, comparative effectiveness, and safety studies on real-world data.

• Preprint

  UniPredict: Large Language Models are Universal Tabular Predictors

  Ruiyu Wang, Zifeng Wang, Jimeng Sun

  Tabular LearningPatient OutcomeLLMInstruction Tuning

• IJCAI'24

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

  Zifeng Wang, Chufan Gao,Cao Xiao, Jimeng Sun

  Tabular LearningPatient OutcomeLLMData-Centric AI

• NeurIPS'22

  TransTab: Learning Transferable Tabular Transformers Across Tables

  Zifeng Wang, Jimeng Sun

  Tabular LearningPatient OutcomeTransfer Learning

• JAMIA'21

  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

  Pandemic PredictionGraph Neural NetworkReal-World Evidence

• Nature Comm

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

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

  Pandemic PredictionSpatio-temporal Prediction

• WWW'22

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

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

  Population Health PredictionGraph Neural NetworkSpatio-temporal Prediction

• npj Digital Med

  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

  Predictive ModelingData AugmentationData Synthesis

• Nature Comm

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

  Brandon Theodorou, Cao Xiao, Jimeng Sun

  Synthetic DataEHRLanguage ModelLongitudinal Data

• EMNLP'22

  PromptEHR: Conditional Electronic Healthcare Records Generation with Prompt Learning

  Zifeng Wang, Jimeng Sun

  Synthetic DataEHRPrompt LearningConditional Generation

Clinical-trial foundation models and predictive methods for landscape analysis, probability of success, and evidence-backed portfolio decisions.

• npj Digital Med

  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

  BenchmarkClinical trialsSystematic ReviewTrial DesignDatabase

• Preprint

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

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

  LLMClinical trialsFoundation model

• ACM-BCB'23

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

  Zifeng Wang, Jimeng Sun

  Trial OutcomeSequential Learning

• Patterns

  HINT: Hierarchical Interaction Network for Clinical Trial Outcome Predictions

  Zifeng Wang, Jimeng Sun

  Trial OutcomeGraph Neural Network

• Scientific Data

  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

  BenchmarkClinical TrialsMulti-ModalAI

Research that improves site selection, patient-trial matching, recruitment, and the operational decisions that determine whether a trial finishes.

• Patterns

  FRAMM: Fair ranking with missing modalities for clinical trial site selection

  Brandon Theodorou, Lucas Glass, Cao Xiao, Jimeng Sun

  Site SelectionFair RankingClinical TrialsMissing DataMulti-Modal

• Nature Comm

  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

  LLMPromptingPatient-Trial Matching

• KDD'20

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

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

  Patient-Trial MatchingEHR

• AAAI'20

  Doctor2Vec: Dynamic Doctor Representation Learning for Clinical Trial Recruitment

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

  Patient-Trial MatchingEHR

Human-AI evidence synthesis methods for systematic reviews, reproducible screening, and evidence bases that can stand up to health technology assessment (HTA) review.

• Nature Mach Intell

  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

  Knowledge GraphEvidence SynthesisLLMBiomedical AI

• npj Digital Med

  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

  LLMMedical Literature MiningSystematic Review

• Nature Comm

  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

  LLMMedical Literature MiningSystematic ReviewHuman-AI Collaboration

Foundational AI, including drug-discovery and multimodal methods, plus data-science agents that help investigators run reproducible biomedical studies.

• Nature BME

  Making large language models reliable data science programming copilots for biomedical research

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

  LLMData ScienceBiomedical ResearchAI CopilotProgramming

• Preprint

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

  Zifeng Wang, Benjamin Danek, Jimeng Sun

  BenchmarkData ScienceBiomedical ResearchAI AgentLLM

• Nature Protocols

  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

  LLMMedical ResearchTutorialGuidance

• Scientific Data

  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

  Multi-OmicsCancerBenchmark DatasetMachine Learning

• ICLR'24

  BioBridge: Bridging Biomedical Foundation Models via Knowledge Graph

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

  Foundation ModelMultimodal AIBiomedical AIKnowledge Graph

• EMNLP'22

  MedCLIP: Contrastive Learning from Unpaired Medical Images and Text

  Zifeng Wang, Jimeng Sun

  Vision-Language ModelMultimodal AIClinical NoteX-Ray

• Technical brochure

  TrialMind for Biometric Teams

  Keiji AI

  BiometricsTrial DesignStatistical ProgrammingDigital TwinSimulation

• Presentation

  TrialMind for Biometric Teams — slide deck

  Keiji AI

  BiometricsTrial DesignStatistical ProgrammingDigital Twin

• Technical brochure

  TrialMind for Real-World Data and Evidence

  Keiji AI

  Real-World EvidenceFeasibilityComparative EffectivenessTreatment PatternsCohort Extraction

• Presentation

  TrialMind for Real-World Data and Evidence — slide deck

  Keiji AI

  Real-World EvidenceFeasibilityComparative EffectivenessSafety Signals

• Technical brochure

  How LLM Training Actually Works: a practical guide to open-weight model training and evaluation

  Jimeng Sun

  LLM TrainingOpen-Weight ModelsDistillationEvaluationFine-Tuning

• Presentation

  How LLM Training Actually Works — slide deck

  Jimeng Sun

  LLM TrainingOpen-Weight ModelsDistillationEvaluation