Publications


Google Scholar

‘*’ Those authors contributed equally.

Latest News

Jul 2025:   Launching TxAgent Evaluation Portal

Launched TxAgent evaluation portal, our global evaluation of AI for drug decision-making and therapeutic reasoning. Participate in TxAgent evaluations! [TxAgent project]

Jul 2025:   SPATIA Model of Spatial Cell Phenotypes

Jul 2025:   AI-Enabled Drug Discovery Reaches Clinical Milestone

Jun 2025:   Knowledge Tracing for Biomedical AI Education

New preprint on biologically inspired architecture for knowledge tracing. The study on the use of generative AI in education with prospective evaluation of knowledge tracing in the classroom.

Jun 2025:   Few shot learning for rare disease diagnosis

Jun 2025:   One Patient, Many Contexts: Scaling Medical AI

Jun 2025:   ToolUniverse - 211+ Tools for "AI Scientist" Agents

ToolUniverse now offers access to over 211 cutting-edge biological and medical tools, all integrated with Model Context Protocol (MCP). Any “AI Scientist” agent can tap into these tools for biomedical research. [Tutorial] [ToolUniverse] [TxAgent]

May 2025:   What Perturbation Can Reverse Disease Effects?

In press at Nature Biomedical Engineering: PDGrapher AI predicts chemicals to reverse disease phenotypic effects — with applications to drug target identification.

May 2025:   Decision Transformers for Cell Reprogramming

New preprint: Decision transformers for generating reach-avoid policies in sequential decision making — with applications from robotics to cell reprogramming.

May 2025:   COMPASS: Immunotherapy Outcome Prediction

Apr 2025:   ATOMICA and TxAgent on the Kempner Blog

Check out the Kempner Deeper Learning posts describing our latest ATOMICA and TxAgent AI models.

Apr 2025:   ATOMICA - A Universal Model of Molecular Interactions

Mar 2025:   On Biomedical AI in Harvard Gazette

Read about AI in medicine in the latest Harvard Gazette and New York Times.

Mar 2025:   TxAgent: AI Agent for Therapeutic Reasoning

TxAgent is an AI agent for therapeutic reasoning that consolidates 211 tools from trusted sources, including all US FDA-approved drugs since 1939 and validated clinical insights. [Project website] [TxAgent] [ToolUniverse]

Mar 2025:   Multimodal AI predicts clinical outcomes of drug combinations from preclinical data

Mar 2025:   KGARevion: AI Agent for Knowledge-Intensive Biomedical QA

KGARevion is an AI agent designed for complex biomedical QA that integrates the non-codified knowledge of LLMs with the structured, codified knowledge found in knowledge graphs. [ICLR 2025 publication]

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

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