Literature DB >> 22975245

Fast Forward Maximum entropy reconstruction of sparsely sampled data.

Nicholas M Balsgart1, Thomas Vosegaard.   

Abstract

We present an analytical algorithm using fast Fourier transformations (FTs) for deriving the gradient needed as part of the iterative reconstruction of sparsely sampled datasets using the forward maximum entropy reconstruction (FM) procedure by Hyberts and Wagner [J. Am. Chem. Soc. 129 (2007) 5108]. The major drawback of the original algorithm is that it required one FT and one evaluation of the entropy per missing datapoint to establish the gradient. In the present study, we demonstrate that the entire gradient may be obtained using only two FT's and one evaluation of the entropy derivative, thus achieving impressive time savings compared to the original procedure. An example: A 2D dataset with sparse sampling of the indirect dimension, with sampling of only 75 out of 512 complex points (15% sampling) would lack (512-75)×2=874 points per ν(2) slice. The original FM algorithm would require 874 FT's and entropy function evaluations to setup the gradient, while the present algorithm is ∼450 times faster in this case, since it requires only two FT's. This allows reduction of the computational time from several hours to less than a minute. Even more impressive time savings may be achieved with 2D reconstructions of 3D datasets, where the original algorithm required days of CPU time on high-performance computing clusters only require few minutes of calculation on regular laptop computers with the new algorithm.
Copyright © 2012 Elsevier Inc. All rights reserved.

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Year:  2012        PMID: 22975245     DOI: 10.1016/j.jmr.2012.07.002

Source DB:  PubMed          Journal:  J Magn Reson        ISSN: 1090-7807            Impact factor:   2.229


  10 in total

1.  Sensitivity gains, linearity, and spectral reproducibility in nonuniformly sampled multidimensional MAS NMR spectra of high dynamic range.

Authors:  Christopher L Suiter; Sivakumar Paramasivam; Guangjin Hou; Shangjin Sun; David Rice; Jeffrey C Hoch; David Rovnyak; Tatyana Polenova
Journal:  J Biomol NMR       Date:  2014-04-22       Impact factor: 2.835

2.  Importance of time-ordered non-uniform sampling of multi-dimensional NMR spectra of Aβ1-42 peptide under aggregating conditions.

Authors:  Jinfa Ying; C Ashley Barnes; John M Louis; Ad Bax
Journal:  J Biomol NMR       Date:  2019-08-12       Impact factor: 2.835

3.  Interpolating and extrapolating with hmsIST: seeking a tmax for optimal sensitivity, resolution and frequency accuracy.

Authors:  Sven G Hyberts; Scott A Robson; Gerhard Wagner
Journal:  J Biomol NMR       Date:  2017-03-22       Impact factor: 2.835

4.  Subrandom methods for multidimensional nonuniform sampling.

Authors:  Bradley Worley
Journal:  J Magn Reson       Date:  2016-06-09       Impact factor: 2.229

5.  Convex accelerated maximum entropy reconstruction.

Authors:  Bradley Worley
Journal:  J Magn Reson       Date:  2016-02-10       Impact factor: 2.229

6.  Sparse multidimensional iterative lineshape-enhanced (SMILE) reconstruction of both non-uniformly sampled and conventional NMR data.

Authors:  Jinfa Ying; Frank Delaglio; Dennis A Torchia; Ad Bax
Journal:  J Biomol NMR       Date:  2016-11-19       Impact factor: 2.835

Review 7.  Magic angle spinning NMR of viruses.

Authors:  Caitlin M Quinn; Manman Lu; Christopher L Suiter; Guangjin Hou; Huilan Zhang; Tatyana Polenova
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2015-02-16       Impact factor: 9.795

Review 8.  Perspectives in magnetic resonance: NMR in the post-FFT era.

Authors:  Sven G Hyberts; Haribabu Arthanari; Scott A Robson; Gerhard Wagner
Journal:  J Magn Reson       Date:  2014-04       Impact factor: 2.229

9.  Using Deep Neural Networks to Reconstruct Non-uniformly Sampled NMR Spectra.

Authors:  D Flemming Hansen
Journal:  J Biomol NMR       Date:  2019-07-10       Impact factor: 2.835

10.  Core Scientific Dataset Model: A lightweight and portable model and file format for multi-dimensional scientific data.

Authors:  Deepansh J Srivastava; Thomas Vosegaard; Dominique Massiot; Philip J Grandinetti
Journal:  PLoS One       Date:  2020-01-02       Impact factor: 3.240

  10 in total

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