# Deep Generative Modeling for Volume Reconstruction in Cryo-Electron Microscopy

@article{Donnat2022DeepGM, title={Deep Generative Modeling for Volume Reconstruction in Cryo-Electron Microscopy}, author={Claire Donnat and Axel Levy and Fr{\'e}d{\'e}ric Poitevin and Nina Miolane}, journal={Journal of structural biology}, year={2022}, pages={ 107920 } }

## 11 Citations

### An Unsupervised Classification Algorithm for Heterogeneous Cryo-EM Projection Images Based on Autoencoders

- 2023

Computer Science

International journal of molecular sciences

An unsupervised heterogeneous cryo-EM projection image classification algorithm based on autoencoders is proposed, which only needs to know the number of heterogeneous 3D structures in the dataset and does not require any labeling information of the projection images or other a priori knowledge.

### Stability and Inference of the Euler Characteristic Transform

- 2023

Mathematics, Computer Science

A new metric on compact one-dimensional shapes is proposed and it is proved that the ECT is stable with respect to this metric, which uses curvature, rather than the size of a triangulation of an underlying shape, to control stability.

### Using VAEs to Learn Latent Variables: Observations on Applications in cryo-EM

- 2023

Computer Science

ArXiv

This case study qualitatively examines the amortization properties of a VAE used in biological applications and finds that in this application the encoder bears a qualitative resemblance to more traditional explicit representation of latent variables.

### A stochastic approximate expectation-maximization for structure determination directly from cryo-EM micrographs

- 2023

Engineering

A single-particle cryo-electron microscopy (cryo-EM) measurement, called a micrograph, consists of multiple two-dimensional tomographic projections of a three-dimensional molecular structure at…

### Boosted ab initio Cryo-EM 3D Reconstruction with ACE-EM

- 2023

Computer Science

ArXiv

An improved autoencoder architecture called ACE (Asymmetric Complementary autoEncoder), based on which the ACE-EM method is designed, which reached the Nyquist resolution for 3D reconstructions of both simulated and experimental cryo-EM datasets.

### Methods for Cryo-EM Single Particle Reconstruction of Macromolecules Having Continuous Heterogeneity.

- 2023

Chemistry

Journal of molecular biology

### Latent Space Diffusion Models of Cryo-EM Structures

- 2022

Computer Science

By learning an accurate model of the data distribution, the cryoDRGN method unlocks tools in generative modeling, sampling, and distribution analysis for heterogeneous cryo-EM ensembles.

### Amortized Inference for Heterogeneous Reconstruction in Cryo-EM

- 2022

Computer Science

NeurIPS

It is proved that an amortized method can extract interpretable dynamic information from experimental datasets for the first time, and can provide one order of magnitude speedup on datasets containing millions of images without any loss of accuracy.

### Heterogeneous reconstruction of deformable atomic models in Cryo-EM

- 2022

Biology

ArXiv

A heterogeneous reconstruction method based on an atomistic representation whose deformation is reduced to a handful of collective motions through normal mode analysis that is able to recapitulate the intermediate atomic models with atomic-level accuracy.

### Defining an action of SO(d)-rotations on images generated by projections of d-dimensional objects: Applications to pose inference with Geometric VAEs

- 2022

Computer Science

ArXiv

– Les r´ecents progr`es dans le domaine des autoencodeurs variationnels (VAEs) ont permis l’apprentissage de vari´et´es latentes sur des groupes de Lie compacts, tels que SO ( d ) . Une telle…

## 59 References

### Cryo-EM, XFELs and the structure conundrum in structural biology

- 2019

Biology

Nature Methods

Single-particle techniques offer an unprecedented opportunity to understand the role of structural variability in biological function. They also call into question the meaning of ‘a structure’ and…

### Molecular driving forces : statistical thermodynamics in biology, chemistry, physics, and nanoscience

- 2012

Physics, Chemistry

Molecular Driving Forces Statistical Thermodynamics Molecular Driving Forces, Second Edition is an introductory statistical thermodynamics text that describes the principles and forces that drive…

### Computational methods for analyzing conformational variability of macromolecular complexes from cryo-electron microscopy images.

- 2017

Chemistry

Current opinion in structural biology

### RELION: Implementation of a Bayesian approach to cryo-EM structure determination

- 2012

Computer Science

Journal of structural biology

### Effects of cryo-EM cooling on structural ensembles

- 2022

Chemistry

Nature Communications

This work combined continuum model calculations of the temperature drop, molecular dynamics simulations of a ribosome complex before and during cooling with kinetic models, and the quantification of the heterogeneity of room-temperature ensembles from cryo-EM structures to suggest three effects markedly contribute to the narrowing of the structural ensemble.

### Inferring a Continuous Distribution of Atom Coordinates from Cryo-EM Images using VAEs

- 2021

Computer Science

ArXiv

This work presents a fully deep-learning-based approach using variational auto-encoders (VAEs) to recover a continuous distribution of atomic protein structures and poses directly from picked particle images and demonstrates its efficacy on realistic simulated data.

### cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

- 2017

Computer Science

Nature Methods

It is shown that stochastic gradient descent (SGD) and branch-and-bound maximum likelihood optimization algorithms permit the major steps in cryo-EM structure determination to be performed in hours or minutes on an inexpensive desktop computer.

### Convex optimization (Cambridge university

- 2004

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

- 2022

Computer Science

ECCV

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, is introduced.

### Machine Learning for Structure Determination in Single-Particle Cryo-Electron Microscopy: A Systematic Review

- 2022

Computer Science

IEEE Transactions on Neural Networks and Learning Systems

A systematic review of the applications of machine learning in single-particle cryo-EM, focusing on the workflow of structure determination, describes relevant machine learning algorithms and applications at different steps, including particle picking, 2-D clustering, 3-D reconstruction, and other steps.