Artificial Intelligence for Medicine and Science


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AI for Medicine | Individualized Diagnosis and Treatment

The state of a person is described with increasing precision incorporating modalities like genetic code, cellular atlases, molecular datasets, and therapeutics—the challenge is how to reason over these data to develop powerful disease diagnostics and empower new kinds of therapies. Our research creates new avenues for fusing knowledge and patient data to give the right patient the right treatment at the right time and have medicinal effects that are consistent from person to person and with results in the laboratory.

AI for Science | Scientific Discovery and Therapeutic Science

For centuries, the method of discovery—the fundamental practice of science that scientists use to explain the natural world systematically and logically—has remained largely the same. We are using AI to change that. The natural world is interconnected, from the various facets of genome regulation to the molecular and organismal levels. These interactions across different levels yield a bewildering degree of complexity. Our research seeks to disentangle this complexity, developing AI models that advance drug design and help develop new kinds of therapies.

Latest News

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

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

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