-SUP: a clustering algorithm for cryo-electron microscopy images of asymmetric particles

DOI10.1214/13-AOAS680MaRDI QIDQ2453670zbMATH OpenFDO

Authors Ting-Li Chen, Dai-Ni Hsieh, Hung Hung, Iping Tu, Peishien Wu, Yiming Wu, Wei-Hau Chang, Suyun Huang

Publication date 10 June 2014

Published in The Annals of Applied Statistics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1205.2034, https://projecteuclid.org/euclid.aoas/1396966286

zbMATH Keywords

\(\gamma\)-divergence\(k\)-means\(q\)-Gaussian distributionclustering algorithmcryo-EM imagesmeanshift algorithmmultilinear principal component analysisrobust statisticsself-updating process

Mathematics Subject Classification ID

Robustness and adaptive procedures (parametric inference) (62F35) Factor analysis and principal components; correspondence analysis (62H25) Classification and discrimination; cluster analysis (statistical aspects) (62H30) Applications of statistics to physics (62P35)

Abstract: Cryo-electron microscopy (cryo-EM) has recently emerged as a powerful tool for obtaining three-dimensional (3D) structures of biological macromolecules in native states. A minimum cryo-EM image data set for deriving a meaningful reconstruction is comprised of thousands of randomly orientated projections of identical particles photographed with a small number of electrons. The computation of 3D structure from 2D projections requires clustering, which aims to enhance the signal to noise ratio in each view by grouping similarly oriented images. Nevertheless, the prevailing clustering techniques are often compromised by three characteristics of cryo-EM data: high noise content, high dimensionality and large number of clusters. Moreover, since clustering requires registering images of similar orientation into the same pixel coordinates by 2D alignment, it is desired that the clustering algorithm can label misaligned images as outliers. Herein, we introduce a clustering algorithm $gamma$-SUP to model the data with a $q$-Gaussian mixture and adopt the minimum $gamma$-divergence for estimation, and then use a self-updating procedure to obtain the numerical solution. We apply $gamma$-SUP to the cryo-EM images of two benchmark macromolecules, RNA polymerase II and ribosome. In the former case, simulated images were chosen to decouple clustering from alignment to demonstrate $gamma$-SUP is more robust to misalignment outliers than the existing clustering methods used in the cryo-EM community. In the latter case, the clustering of real cryo-EM data by our $gamma$-SUP method eliminates noise in many views to reveal true structure features of ribosome at the projection level.

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Cited in

(12)

• On the asymptotic normality and efficiency of Kronecker envelope principal component analysis
• AdaReg: data adaptive robust estimation in linear regression with application in GTEx gene expressions
• On the convergence and consistency of the blurring mean-shift process
• The generalized degrees of freedom of multilinear principal component analysis
• A jackknife entropy-based clustering algorithm for probability density functions
• A robust automatic clustering algorithm for probability density functions with application to categorizing color images
• On the strengths of the self-updating process clustering algorithm
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• On the weak convergence and central limit theorem of blurring and nonblurring processes with application to robust location estimation

Describes a project that uses

Uses Software

• XMIPP

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