Group Members


Join Us
<a href=Marinka Zitnik" />

Marinka Zitnik

Assistant Professor

<a href=Shvat Messica" />

Shvat Messica

PhD Student
Harvard AIM

<a href=Ada Fang" />

Ada Fang

PhD Student
Harvard CCB

<a href=Yepeng Huang" />

Yepeng Huang

PhD Student
Harvard BBS

<a href=Katya Ivshina" />

Katya Ivshina

PhD Student
Harvard Applied Mathematics

<a href=Kevin Li" />

Kevin Li

PhD Student
Harvard-MIT HST

<a href=Walker Rickord " />

Walker Rickord

PhD Student
Harvard-MIT HST

<a href=Robert Calef" />

Robert Calef

PhD Student
MIT EECS

<a href=Yasha Ektefaie" />

Yasha Ektefaie

PhD Student
Harvard BIG

<a href=Michael Sun" />

Michael Sun

PhD Student
MIT EECS

<a href=Valentina Giunchiglia" />

Valentina Giunchiglia

PhD Student
Imperial College London

<a href=Aarthi Venkat" />

Aarthi Venkat

Postdoctoral Fellow
Eric and Wendy Schmidt Fellow

<a href=Grey Kuling" />

Grey Kuling

Postdoctoral Fellow
Curriculum Fellow

<a href=Intae Moon" />

Intae Moon

Postdoctoral Fellow

<a href=Michelle M. Li" />

Michelle M. Li

Postdoctoral Fellow
Harvard Berkowitz Fellow

<a href=Ruth Johnson" />

Ruth Johnson

Postdoctoral Fellow
Harvard Berkowitz Fellow

<a href=Shanghua Gao" />

Shanghua Gao

Postdoctoral Fellow

<a href=Wanxiang Shen" />

Wanxiang Shen

Postdoctoral Fellow

<a href=Xiang Lin" />

Xiang Lin

Postdoctoral Fellow

<a href=Xiaorui Su" />

Xiaorui Su

Postdoctoral Fellow

<a href=Ying Jin" />

Ying Jin

Postdoctoral Fellow
Harvard Data Science Fellow

<a href=Zhenglun Kong" />

Zhenglun Kong

Postdoctoral Fellow

<a href=Kexin Chen" />

Kexin Chen

Visiting PhD Student

<a href=Pengwei Sui" />

Pengwei Sui

Research Associate

<a href=Michelle Dai" />

Michelle Dai

Research Associate

<a href=Alejandro Velez Arce" />

Alejandro Velez Arce

Research Associate

<a href=Andrew Shen" />

Andrew Shen

Graduate Researcher

<a href=Iñaki Arango" />

Iñaki Arango

Undergraduate Researcher
Harvard

<a href=Richard Zhu" />

Richard Zhu

Undergraduate Researcher
Harvard

<a href=Ayush Noori" />

Ayush Noori

Undergraduate Researcher
Harvard

Lab alumni

2024:
  • Zaixi Zhang (Visiting PhD Student → Postdoctoral Fellow, Princeton University)
  • Owen Queen (Research Associate → Computer Science PhD Student, Stanford University)
  • Varun Ullanat (HMS)
  • Ivy Liang (Harvard College)
  • Tianlong Chen (Postdoctoral Fellow → Assistant Professor, University of North Carolina at Chapel Hill)
2023:
  • Guadalupe Gonzalez (Visiting PhD Student → Research Scientist, Prescient Design, Genentech, Roche)
  • Tom Cobley (Undergraduate Researcher → Machine Learning Engineer, Google DeepMind)
  • Ziyuan Zhao (Undergraduate Researcher → Systems Biology PhD Student, Harvard Medical School)
  • Nicholas Ho (Undergraduate Researcher → Computer Science PhD Student, Carnegie Mellon University)
  • Yepeng Huang (Graduate Researcher at Harvard Chan → Biological and Medical Sciences PhD Student, Harvard Medical School)
  • Marissa Sumathipala (Undergraduate Researcher at Harvard College; Gates Cambridge Scholarship; Churchill Scholarship; Cambridge University → Neuroscience PhD Student, Harvard University)
  • Julia Balla (Undergraduate Researcher at MIT → Computer Science PhD Student, MIT)
  • Jiali Cheng (Undergraduate Researcher → Computer Science PhD Student, UMass Lowell)
  • Isuru Herath (Undergraduate Researcher → Data Scientist, Merck)
  • Jean-Guillaume Brasier (Harvard IACS Graduate Student → Data Scientist, Moderna)
2022:
  • Marie Zhang (HMS)
  • Man Qing Liang (HMS → Data Scientist, Dandelion)
  • Payal Chandak (Undergraduate Researcher → Harvard-MIT HST PhD Student, Harvard University & MIT)
  • Xiang Zhang (Postdoctoral Fellow → Assistant Professor, UNC Charlotte)
  • Chirag Agarwal (Postdoctoral Fellow, HMS → Assistant Professor, University of Virginia)
  • Josh Pan (Postdoctoral Fellow, Broad Institute → Research Scientist, DeepMind)
  • Michelle Lu (Harvard College)
  • Raunak Chowdhuri (MIT)
  • Marie Zhang (HMS)
  • Satvik Tripathi (Undergraduate Researcher, Drexel University)
  • Varun Tekur (Undergraduate Researcher)
  • Lydia Fozo (Undergraduate Researcher, Johns Hopkins University)
2021:
  • Kexin Huang (Harvard Chan → Computer Science PhD Student, Stanford University)
  • Haoxin Li (Harvard Chan)
  • Yucong Lin (Harvard Chan → Beijing Institute of Technology)
  • Mert Erden (Tufts University)
  • Jingyi Liu (HMS)
2020:
  • Yujie Shao (HMS)
  • Stone Chen (HMS)
  • Kathleen Sucipto (HMS)
  • Min Jean Cho (Undergraduate Researcher, Brown University)

Latest News

Feb 2025:   MedTok: Unlocking Medical Codes for GenAI

Meet MedTok, a multimodal medical code tokenizer that transforms how AI understands structured medical data. By integrating textual descriptions and relational contexts, MedTok enhances tokenization for transformer-based models—powering everything from EHR foundation models to medical QA. [Project website]

Feb 2025:   What If You Could Rewrite Biology? Meet CLEF

What if we could anticipate molecular and medical changes before they happen? Introducing CLEF, an approach for counterfactual generation in biological and medical sequence models. [Project website]

Feb 2025:   Digital Twins as Global Health and Disease Models

Jan 2025:   LLM and KG+LLM agent papers at ICLR

Jan 2025:   Artificial Intelligence in Medicine 2

Excited to share our new graduate course on Artificial Intelligence in Medicine 2.

Jan 2025:   ProCyon AI Highlighted by Kempner

Thanks to Kempner Institute for highlighting our latest research, ProCyon, our protein-text foundation model for modeling protein functions.

Jan 2025:   AI Design of Proteins for Therapeutics

Dec 2024:   Unified Clinical Vocabulary Embeddings

New paper: A unified resource provides a new representation of clinical knowledge by unifying medical vocabularies. (1) Phenotype risk score analysis across 4.57 million patients, (2) Inter-institutional clinician panels evaluate alignment with clinical knowledge across 90 diseases and 3,000 clinical codes.

Dec 2024:   SPECTRA in Nature Machine Intelligence

Are biomedical AI models truly as smart as they seem? SPECTRA is a framework that evaluates models by considering the full spectrum of cross-split overlap: train-test similarity. SPECTRA reveals gaps in benchmarks for molecular sequence data across 19 models, including LLMs, GNNs, diffusion models, and conv nets.

Nov 2024:   Ayush Noori Selected as a Rhodes Scholar

Congratulations to Ayush Noori on being named a Rhodes Scholar! Such an incredible achievement!

Nov 2024:   PocketGen in Nature Machine Intelligence

Oct 2024:   Activity Cliffs in Molecular Properties

Oct 2024:   Knowledge Graph Agent for Medical Reasoning

Sep 2024:   Three Papers Accepted to NeurIPS

Exciting projects include a unified multi-task time series model, a flow-matching approach for generating protein pockets using geometric priors, and a tokenization method that produces invariant molecular representations for integration into large language models.

Sep 2024:   TxGNN Published in Nature Medicine

Aug 2024:   Graph AI in Medicine

Excited to share a new perspective on Graph Artificial Intelligence in Medicine in Annual Reviews.

Aug 2024:   How Proteins Behave in Context

Harvard Medicine News on our new AI tool that captures how proteins behave in context. Kempner Institute on how context matters for foundation models in biology.

Jul 2024:   PINNACLE in Nature Methods

PINNACLE contextual AI model is published in Nature Methods. Paper. Research Briefing. Project website.

Zitnik Lab  ·  Artificial Intelligence in Medicine and Science  ·  Harvard  ·  Department of Biomedical Informatics