Method of moments for 3D single particle \textit{ab initio} modeling with non-uniform distribution of viewing angles

DOI10.1088/1361-6420/AB6139zbMATH Open1468.94024arXiv1907.05377OpenAlexW3105017158MaRDI QIDQ5000567FDOQ5000567

Nir Sharon, Boris Landa, Joe Kileel, A. Singer, Yuehaw Khoo

Publication date: 14 July 2021

Published in: Inverse Problems (Search for Journal in Brave)

Abstract: Single-particle reconstruction in cryo-electron microscopy (cryo-EM) is an increasingly popular technique for determining the 3-D structure of a molecule from several noisy 2-D projections images taken at unknown viewing angles. Most reconstruction algorithms require a low-resolution initialization for the 3-D structure, which is the goal of ab initio modeling. Suggested by Zvi Kam in 1980, the method of moments (MoM) offers one approach, wherein low-order statistics of the 2-D images are computed and a 3-D structure is estimated by solving a system of polynomial equations. Unfortunately, Kam's method suffers from restrictive assumptions, most notably that viewing angles should be distributed uniformly. Often unrealistic, uniformity entails the computation of higher-order correlations, as in this case first and second moments fail to determine the 3-D structure. In the present paper, we remove this hypothesis, by permitting an unknown, non-uniform distribution of viewing angles in MoM. Perhaps surprisingly, we show that this case is statistically easier than the uniform case, as now first and second moments generically suffice to determine low-resolution expansions of the molecule. In the idealized setting of a known, non-uniform distribution, we find an efficient provable algorithm inverting first and second moments. For unknown, non-uniform distributions, we use non-convex optimization methods to solve for both the molecule and distribution.

Full work available at URL: https://arxiv.org/abs/1907.05377

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zbMATH Keywords

method of momentsnon-convex optimizationspherical harmonicsWigner matricescryo-EMautocorrelation analysisab initio modeling

Mathematics Subject Classification ID

Nonconvex programming, global optimization (90C26) Image processing (compression, reconstruction, etc.) in information and communication theory (94A08) Computing methodologies for image processing (68U10) Numerical methods for inverse problems for integral equations (65R32)

Cites Work

• Ideals, Varieties, and Algorithms
• Generalized inverses. Theory and applications.
• Condition
• Title not available (Why is that?)
• Title not available (Why is that?)
• Characterizing generic global rigidity
• Prolate Spheroidal Wave Functions, Fourier Analysis and Uncertainty - IV: Extensions to Many Dimensions; Generalized Prolate Spheroidal Functions
• Prolate spheroidal wave functions on a disc -- integration and approximation of two-dimensional bandlimited functions
• A trust region algorithm for equality constrained optimization
• Optimal shrinkage of eigenvalues in the spiked covariance model
• Three-Dimensional Structure Determination from Common Lines in Cryo-EM by Eigenvectors and Semidefinite Programming
• The Numerical Solution of Systems of Polynomials Arising in Engineering and Science
• Uniqueness of Low-Rank Matrix Completion by Rigidity Theory
• Angular Momentum in Quantum Physics
• A Regularized Variable Projection Algorithm for Separable Nonlinear Least Squares Problems
• The finite Hankel transform operator: some explicit and local estimates of the eigenfunctions and eigenvalues decay rates
• Approximation scheme for essentially bandlimited and space-concentrated functions on a disk
• Bispectrum Inversion With Application to Multireference Alignment
• Multireference Alignment Is Easier With an Aperiodic Translation Distribution
• The Sample Complexity of Multireference Alignment
• Sampling and approximation of bandlimited volumetric data
• Structural Variability from Noisy Tomographic Projections
• Steerable Principal Components for Space-Frequency Localized Images
• Iterative phasing for fluctuation X-ray scattering
• Rapid Solution of the Cryo-EM Reconstruction Problem by Frequency Marching

Cited In (16)

• Deep neural-network prior for orbit recovery from method of moments
• Multi-Reference Alignment in High Dimensions: Sample Complexity and Phase Transition
• Motion detection in diffraction tomography by common circle methods
• Maximum likelihood for high-noise group orbit estimation and single-particle cryo-EM
• Complete \({\boldsymbol{SE(3)}}\) Invariants for a Comeagre Set of \({\boldsymbol{C^3}}\) Compact Orientable Surfaces in \(\mathbb{R}^{\boldsymbol{3}}\)
• Likelihood landscape and maximum likelihood estimation for the discrete orbit recovery model
• Power spectrum unbiasing for dilation-invariant multi-reference alignment
• Rates of estimation for high-dimensional multireference alignment
• Orthogonal Matrix Retrieval with Spatial Consensus for 3D Unknown View Tomography
• Regularizing Orientation Estimation in Cryogenic Electron Microscopy Three-Dimensional Map Refinement through Measure-Based Lifting over Riemannian Manifolds
• Toward Single Particle Reconstruction without Particle Picking: Breaking the Detection Limit
• Ab initio reconstruction and experimental design for cryo electron microscopy.
• Signal recovery from a few linear measurements of its high-order spectra
• The beltway problem over orthogonal groups
• The \(G\)-invariant graph Laplacian. I: Convergence rate and eigendecomposition.
• Multi-target detection with rotations

Uses Software

• CTFFIND
• FREALIGN
• RELION
• cryoSPARC

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