CryoAI: Amortized Inference of Poses for Ab Initio Reconstruction of 3D Molecular Volumes from Real Cryo-EM Images

• URL: http://arxiv.org/abs/2203.08138v2
• Date: Wed, 16 Mar 2022 04:25:18 GMT
• Title: CryoAI: Amortized Inference of Poses for Ab Initio Reconstruction of 3D Molecular Volumes from Real Cryo-EM Images
• Authors: Axel Levy, Fr\'ed\'eric Poitevin, Julien Martel, Youssef Nashed, Ariana Peck, Nina Miolane, Daniel Ratner, Mike Dunne, Gordon Wetzstein
• Abstract summary: We introduce cryoAI, an ab initio reconstruction algorithm for homogeneous conformations that uses gradient-based optimization of particle poses and the electron scattering potential from single-particle cryo-EM data. CryoAI achieves results on par with state-of-the-art cryo-EM solvers for both simulated and experimental data, one order of magnitude faster for large datasets and with significantly lower memory requirements than existing methods.
• Score: 30.738209997049395
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Cryo-electron microscopy (cryo-EM) has become a tool of fundamental importance in structural biology, helping us understand the basic building blocks of life. The algorithmic challenge of cryo-EM is to jointly estimate the unknown 3D poses and the 3D electron scattering potential of a biomolecule from millions of extremely noisy 2D images. Existing reconstruction algorithms, however, cannot easily keep pace with the rapidly growing size of cryo-EM datasets due to their high computational and memory cost. 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. CryoAI combines a learned encoder that predicts the poses of each particle image with a physics-based decoder to aggregate each particle image into an implicit representation of the scattering potential volume. This volume is stored in the Fourier domain for computational efficiency and leverages a modern coordinate network architecture for memory efficiency. Combined with a symmetrized loss function, this framework achieves results of a quality on par with state-of-the-art cryo-EM solvers for both simulated and experimental data, one order of magnitude faster for large datasets and with significantly lower memory requirements than existing methods.

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