Topological Data Analytic Frameworks for Discovering Biophysical Signatures in 3D Shapes and Images

Seminar series

Applied Topology Seminar

Date

Fri, 28 Oct 2022

Time

15:00 - 16:00

Location

Speaker

Lorin Crawford

Organisation

Brown University

The recent curation of large-scale databases with 3D surface scans of shapes has motivated the development of tools that better detect global patterns in morphological variation. Studies which focus on identifying differences between shapes have been limited to simple pairwise comparisons and rely on pre-specified landmarks (that are often known). In this talk, we present SINATRA: a machine learning pipeline for analyzing collections of shapes without requiring any correspondences. Our method takes in two classes of shapes and highlights the physical features that best describe the variation between them. We develop a rigorous simulation framework to assess our approach, which themselves are a novel contribution to 3D image and shape analyses. Lastly, as case studies with real data, we use SINATRA to (1) analyze mandibular molars from four different suborders of primates and (2) facilitate the visual identification of structural signatures differentiating between the trajectories of two protein ensembles resulting from molecular dynamics simulations. Together, these results highlight a promising future for interpretable machine learning to facilitate the non-trivial task of pattern recognition in evolutionary and structural biology with substantially increased resolution.

Further Information

Lorin Crawford is the RGSS Assistant Professor of Biostatistics at Brown University. He is affiliated with the Center for Statistical Sciences, Center for Computational Molecular Biology, and the Robert J. and Nancy D. Carney Institute for Brain Science.