Amortized Inference for Heterogeneous Reconstruction in Cryo-EM

NeurIPS 2022

Axel Levy, Gordon Wetzstein, Julien Martel, Frederic Poitevin, Ellen D. Zhong


Cryo-electron microscopy (cryo-EM) is an imaging modality that provides unique insights into the dynamics of proteins and other building blocks of life. The algorithmic challenge of jointly estimating the poses, 3D structure, and conformational heterogeneity of a biomolecule from millions of noisy and randomly oriented 2D projections in a computationally efficient manner, however, remains unsolved. Our method, cryoFIRE, performs ab initio heterogeneous reconstruction with unknown poses in an amortized framework, thereby avoiding the computationally expensive step of pose search while enabling the analysis of conformational heterogeneity. Poses and conformation are jointly estimated by an encoder while a physics-based decoder aggregates the images into an implicit neural representation of the conformational space. We show that our method can provide one order of magnitude speedup on datasets containing millions of images without any loss of accuracy. We validate that the joint estimation of poses and conformations can be amortized over the size of the dataset. For the first time, we prove that an amortized method can extract interpretable dynamic information from experimental datasets.

Related Projects

We describe cryoDRGN2, an ab initio reconstruction algorithm, which can jointly estimate image poses and learn a neural model of a distribution of 3D structures on real heterogeneous cryo-EM data.
We introduce cryoAI, an ab initio reconstruction algorithm for homogeneous conformations that uses direct gradient-based optimization of particle poses and the electron scattering potential from single-particle cryo-EM data.



@inproceedings{levy2022cryofire, author = {Levy, Axel, Wetzstein, Gordon, Martel, Julien, Poitevin, Frederic, and Zhong, Ellen D.}, title = {Amoritized Inference for Heterogeneous Reconstruction in Cryo-EM}, booktitle = {Proc. NeurIPS}, year={2022} }