Pankaj Mehta (Boston University): Schmidt AI in Science Speaker Series

Organized by the University of Chicago’s Eric and Wendy Schmidt AI in Science Fellowship Program.

Agenda
4:00pm – 4:45pm:  Presentation
4:45pm – 5:00pm:  Q&A
5:00pm – 5:30pm: Reception

NEW MEETING LOCATION
Data Science Institute
5460 S University Ave
Room 105

Title: Thinking about high-dimensional biological data in the age of AI

Abstract: The molecular biology revolution has transformed our view of living systems. Scientific explanations of biological phenomena are now synonymous with the identification of genes and proteins. The preeminence of the molecular paradigm has only become more pronounced as new technologies allow us to make measurements at scale. Combining this wealth of data with new artificial intelligence (AI) techniques is widely viewed as the future of biology. Here, I will discuss the promise and perils of this approach. I will focus on two recent projects: (i) transformer-based models for understanding genotype-to-phenotype maps, and (ii) LLM-based foundational models for cellular identity, such as TranscriptFormer, trained on single-cell RNA sequencing (scRNAseq) data. I will argue that while LLMs excel at capturing complex evolutionary and demographic structure in DNA sequence data, they are much less adept at elucidating the biology of cellular identity. In particular, we will show that simple parameter-free models inspired by methods from our group outperform TranscriptFormer on downstream tasks related to cellular identity, even though TranscriptFormer has nearly a billion parameters.

Bio: Pankaj Mehta, Professor, Physics, Boston University. I am interested in theoretical problems at the interface of statistical physics and biology. I want to understand how large-scale, collective behaviors observed in biological systems emerge from the interaction of many individual molecular elements, and how these interactions allow cells to perform complex computations in response to environmental cues. I am also a part of the BU Bioinformatics Program and the BUMC Center for Regenerative Medicine (CReM) , and the BU Biological Design Center.

For more information and complete list of publicaitons please visit my webpage.