Computational biology in the age of AI agents
James Zou, PhD
Professor of Biomedical Data Science and, by courtesy, of Computer Science and Electrical Engineering, Stanford University
Abstract
AI agents—large language models equipped with tools and reasoning capabilities—are emerging as powerful research enablers. This talk will explore how computational biology is particularly well-positioned to benefit from rapid advances in agentic AI. I’ll first introduce the Virtual Lab—a collaborative team of AI scientist agents conducting in silico research meetings to tackle open-ended research projects. As an example application, the Virtual Lab designed new nanobody binders to recent Covid variants that we experimentally validated. Then I will present CellVoyager, a data science agent that analyzes complex genomics data to derive new insights. Finally, I will discuss using AI agents to discover and explain new biological concepts encoded by large protein foundation models (interPLM). I will conclude by discussing limits of agents and a roadmap for human researcher-AI collaboration.
Bio
James Zou, PhD is an associate professor of Biomedical Data Science, CS and EE at Stanford University. He works on developing cutting-edge AI for biomedical applications. His group developed many widely used innovations including EchoNet AI (FDA cleared for assessing cardiac function), Gradio (used by over a million developers), and SyntheMol (NY Times 2024 Good Tech). He has received the Overton Prize, Sloan Fellowship, NSF CAREER Award, two Chan-Zuckerberg Investigator Awards, a Top Ten Clinical Achievement Award, best paper awards at ICML and other AI conferences, and faculty awards from Google, Amazon, Adobe and Apple.
