SMBP Group Meeting: Geoffrey Woollard (UBC)

Thursday Apr 10, 2025, 2:00 PM → 3:00 PM America/New_York

3rd Floor Classroom (162 Fifth Avenue )

Speaker: Geoffrey Woollard (UBC)

Topic: Optimal Transport Auditions: Preparing for the Cryo-EM Mainstage

Abstract: Structural biologists communicate using atomic models—3D coordinates and atom types—while cryo-EM experiments yield data in a more pixelated, voxelized form. This incongruence presents challenges. Forward simulators, which render atomic coordinates into voxels and pixels, enable (1) simulation-based inference, and (2) likelihood-based validation metrics. However, it's less clear how to incorporate prior knowledge from the model in terms of symbolic solutions or bespoke optimization objectives. 

In this talk, I will show how optimal transport tools—borrowed from the graphics and applied mathematics communities—can be adapted for two cryo-EM challenges: (1) comparing ensembles of density maps from the Flatiron heterogeneity challenge, and (2) extending Hanson & Hanson’s work on the quaternion adjugate to fit atomic models to 2D cryo-EM classes. 

I’ll conclude with an outlook on using optimal transport for inverse problems in cryo-EM and beyond.