On the Continuum Between Models, Data-Driven Discovery and Machine Learning: Mapping the Continuum of Molecular Conformations Using Cryo-Electron Microscopy

Applied and Computational Mathematics Seminar
Monday, October 19, 2020 - 2:00pm for 1 hour (actually 50 minutes)
Roy Lederman – Yale University – roy.lederman@yale.eduhttp://roy.lederman.name/
Wenjing Liao

Cryo-Electron Microscopy (cryo-EM) is an imaging technology that is revolutionizing structural biology. Cryo-electron microscopes produce a large number of very noisy two-dimensional projection images of individual frozen molecules; unlike related methods, such as computed tomography (CT), the viewing direction of each particle image is unknown. The unknown directions, together with extreme levels of noise and additional technical factors, make the determination of the structure of molecules challenging. While other methods for structure determination, such as x-ray crystallography and nuclear magnetic resonance (NMR), measure ensembles of molecules, cryo-electron microscopes produce images of individual molecules. Therefore, cryo-EM could potentially be used to study mixtures of different conformations of molecules. Indeed, current algorithms have been very successful at analyzing homogeneous samples, and can recover some distinct conformations mixed in solutions, but, the determination of multiple conformations, and in particular, continuums of similar conformations (continuous heterogeneity), remains one of the open problems in cryo-EM. In practice, some of the key components in “molecular machines” are flexible and therefore appear as very blurry regions in 3-D reconstructions of macro-molecular structures that are otherwise stunning in resolution and detail.

We will discuss “hyper-molecules,” the mathematical formulation of heterogenous 3-D objects as higher dimensional objects, and the machinery that goes into recovering these “hyper-objects” from data. We will discuss some of the statistical and computational challenges, and how they are addressed by merging data-driven exploration, models and computational tools originally built for deep-learning.

This is joint work with Joakim Andén and Amit Singer.