Ben Raphael

‍Monday, November 3, 2025

4:00 - 5:00 pm (refreshments at 3:30 pm)

Broad Auditorium (Merkin building, 415 Main St.)

Or via YouTube Livestream: broad.io/ewsc

‍Ben Raphael

Graduate Class of 1991 Professor of Computer Science, Princeton University

Abstract:

The spatial organization of tissues is essential to their biological function. Recent spatialomics technologies measure mRNA, protein, metabolite, and other modalities atthousands of locations within tissue sections, revealing spatial patterns of cell types andmolecular activity. However, current datasets are often sparse and incomplete due totechnological and cost constraints. I will present machine learning approaches toovercome this sparsity by modeling the latent geometry of individual tissue slices and byintegrating measurements across multiple modalities over space and time. Theseapproaches utilize deep neural networks and novel formulations of low-rank optimaltransport. We apply the resulting methods to analyze spatial variation in cell types andgene expression in normal tissues, derive gene expression gradients within tumormicroenvironments, reconstruct three-dimensional tissue architecture across modalities,and describe spatiotemporal changes in expression during organismal development.

Questions? Email Amanda Ogden at aogden@broadinstitute.org.