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Structural Heterogeneity from 3D Covariance Estimation in Cryo-EM Anden, Joakim
Description
Molecules imaged using cryo-electron microscopy (cryo-EM) often exhibit a significant amount of variability, be it in conformation or composition. The molecules are typically represented as 3D volume maps of the electric potential as a function of space. In order to characterize the variability of these maps, the authors propose a method for fast and accurate estimation of the 3D covariance matrix. The estimator is given by the least-squares solution to a linear inverse problem and is efficiently calculated by exploiting its 6D convolutional structure. Combining this with a circulant preconditioner, the solution is obtained using the conjugate gradient method. For $n$ images of size $N$-by-$N$, the computational complexity of the algorithm is $O(n N^4 + \sqrt{\kappa} N^6 \log N)$, where $\kappa$ is a condition number typically of the order $200$. The method is evaluated on simulated and experimental datasets, achieving results comparable to the state of the art at very short runtimes.
Item Metadata
Title |
Structural Heterogeneity from 3D Covariance Estimation in Cryo-EM
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Creator | |
Publisher |
Banff International Research Station for Mathematical Innovation and Discovery
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Date Issued |
2017-10-16T10:05
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Description |
Molecules imaged using cryo-electron microscopy (cryo-EM) often exhibit a significant amount of variability, be it in conformation or composition. The molecules are typically represented as 3D volume maps of the electric potential as a function of space. In order to characterize the variability of these maps, the authors propose a method for fast and accurate estimation of the 3D covariance matrix. The estimator is given by the least-squares solution to a linear inverse problem and is efficiently calculated by exploiting its 6D convolutional structure. Combining this with a circulant preconditioner, the solution is obtained using the conjugate gradient method. For $n$ images of size $N$-by-$N$, the computational complexity of the algorithm is $O(n N^4 + \sqrt{\kappa} N^6 \log N)$, where $\kappa$ is a condition number typically of the order $200$. The method is evaluated on simulated and experimental datasets, achieving results comparable to the state of the art at very short runtimes.
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Extent |
28 minutes
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Type | |
File Format |
video/mp4
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Language |
eng
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Notes |
Author affiliation: Flatiron Institute
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Series | |
Date Available |
2018-04-15
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Provider |
Vancouver : University of British Columbia Library
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Rights |
Attribution-NonCommercial-NoDerivatives 4.0 International
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DOI |
10.14288/1.0365626
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URI | |
Affiliation | |
Peer Review Status |
Unreviewed
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Scholarly Level |
Other
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Rights URI | |
Aggregated Source Repository |
DSpace
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Rights
Attribution-NonCommercial-NoDerivatives 4.0 International