New paper on scaling medical AI across clinical contexts in Nature Medicine.

Much of the world’s knowledge lies outside public web text accessible to LLMs, including internal ontologies, curated catalogs, drug safety tables, patient health data, and lab knowledge bases. ARK helps an LLM to choose, one step at a time, whether to look broadly for relevant information or to dig deeper by following specific links in the data.

New preprint on Medea, an omics AI agent for therapeutic discovery. [Project website]

Excited about this academic collaboration with Anthropic on adding connectors to ToolUniverse to make Claude even more powerful for scientific discovery.

Pairing AI with experiments: Our latest PROTON AI generates neurological hypotheses that we validated across molecular, organoid, and clinical systems. [Project website]

New preprint on Greater than the Sum of Its Parts: Building Substructure into Protein Encoding Models. [Project website]

A piece in Harvard Gazette on digital twins, cellular chatbots, and building digital twins at a cellular scale.

We are excited to meet hundreds of researchers attending our AI Virtual Cells and Instruments: A New Era in Drug Discovery and Development workshop at NeurIPS 2025.

Excited to see 1,622 researchers from around the world entering our CUREBench Challenge with 398 participating teams that made 3,383 submissions to the competition and submitted 8,457,500+ AI reasoning traces for therapeutics. Join us at the Award Ceremony at NeurIPS.

Join us and hundreds of other scientists at the 6th AI for Science workshop at NeurIPS.

New preprint introducing GeoBPE - Protein structure tokenization via geometric byte pair encoding.

New preprint introducing CONCERT, a niche-aware generative model that predicts perturbation effects across spatial tissue contexts.

A piece in Science explores how AI cell models could transform biomedicine (if they work as promised) and highlights ToolUniverse. ToolUniverse lets AI co-scientists test, analyze, and build on AI cell models.

A piece in Nature explores how AI sycophancy, in which models agree too much with users instead of reasoning on its own, could affect the use of AI in medical research.

A news story about PDGrapher in Harvard Crimson. ToolUniverse featured on the Kempner Institute blog.

A piece on AI agents in Nature highlights ongoing projects in our group, including methods for evaluating scientific hypotheses, challenges in benchmarking AI agents, and the open ToolUniverse ecosystem.

New paper: ToolUniverse introduces an open ecosystem for building AI scientists with 600+ scientific and biomedical tools. Build your AI co-scientists at https://aiscientist.tools.

Our new initiative: Use Tool Universe to build an AI scientist for yourself from any language or reasoning model, whether open or closed. https://aiscientist.tools

Collaboration with Ben and Girish on clinical phenotype resolution through deep geometric learning on electronic health records published in Nature Communications.

New paper in Nature Biomedical Engineering introducing PDGrapher, a model for phenotype-based target discovery. [Harvard Medicine News]