Literature DB >> 26256110

A new approach to compressed sensing for NMR.

Alan S Stern1, Jeffrey C Hoch2.   

Abstract

Compressed sensing (CS) has attracted a great deal of recent interest as an approach for spectrum analysis of nonuniformly sampled NMR data. Although theoretical justification for the method is abundant, it suffers from several weaknesses, among them poor convergence of some algorithms, and it remains an open question whether NMR spectra satisfy the sparsity requirements of CS theorems. The versions of CS used in NMR involve minimizing the l1 norm of the spectrum. They bear similarity to maximum entropy (MaxEnt) reconstruction, but critical comparison of the methods can be difficult. Here we describe a formalism that places CS and MaxEnt reconstruction on equal footing, enabling critical comparison of the two methods. We also describe a new algorithm for CS that restricts the computation of the l1 norm to the real channel for complex spectra and ensures causality. Preliminary 1D results demonstrate that this approach ameliorates some artifacts that can occur when using the l1 norm of the complex spectrum.
Copyright © 2015 John Wiley & Sons, Ltd.

Entities:  

Keywords:  compressed sensing; non-Fourier; signal processing; spectrum analysis

Mesh:

Year:  2015        PMID: 26256110      PMCID: PMC5776145          DOI: 10.1002/mrc.4287

Source DB:  PubMed          Journal:  Magn Reson Chem        ISSN: 0749-1581            Impact factor:   2.447


  14 in total

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2.  NMR data processing using iterative thresholding and minimum l(1)-norm reconstruction.

Authors:  Alan S Stern; David L Donoho; Jeffrey C Hoch
Journal:  J Magn Reson       Date:  2007-08-03       Impact factor: 2.229

3.  Quantification of maximum-entropy spectrum reconstructions.

Authors:  P Schmieder; A S Stern; G Wagner; J C Hoch
Journal:  J Magn Reson       Date:  1997-04       Impact factor: 2.229

4.  Compressed sensing reconstruction of undersampled 3D NOESY spectra: application to large membrane proteins.

Authors:  Mark J Bostock; Daniel J Holland; Daniel Nietlispach
Journal:  J Biomol NMR       Date:  2012-07-26       Impact factor: 2.835

5.  The causality principle in the reconstruction of sparse NMR spectra.

Authors:  M Mayzel; K Kazimierczuk; V Yu Orekhov
Journal:  Chem Commun (Camb)       Date:  2014-08-18       Impact factor: 6.222

6.  Application of phase sensitive two-dimensional correlated spectroscopy (COSY) for measurements of 1H-1H spin-spin coupling constants in proteins.

Authors:  D Marion; K Wüthrich
Journal:  Biochem Biophys Res Commun       Date:  1983-06-29       Impact factor: 3.575

Review 7.  Nonuniform sampling and non-Fourier signal processing methods in multidimensional NMR.

Authors:  Mehdi Mobli; Jeffrey C Hoch
Journal:  Prog Nucl Magn Reson Spectrosc       Date:  2014-10-13       Impact factor: 9.795

8.  Ultrahigh-resolution (1)H-(13)C HSQC spectra of metabolite mixtures using nonlinear sampling and forward maximum entropy reconstruction.

Authors:  Sven G Hyberts; Gregory J Heffron; Nestor G Tarragona; Kirty Solanky; Katherine A Edmonds; Harry Luithardt; Jasna Fejzo; Michael Chorev; Huseyin Aktas; Kimberly Colson; Kenneth H Falchuk; Jose A Halperin; Gerhard Wagner
Journal:  J Am Chem Soc       Date:  2007-03-28       Impact factor: 15.419

9.  Compressed sensing and the reconstruction of ultrafast 2D NMR data: Principles and biomolecular applications.

Authors:  Yoav Shrot; Lucio Frydman
Journal:  J Magn Reson       Date:  2011-01-21       Impact factor: 2.229

10.  Critical assessment of methods of protein structure prediction (CASP)--round x.

Authors:  John Moult; Krzysztof Fidelis; Andriy Kryshtafovych; Torsten Schwede; Anna Tramontano
Journal:  Proteins       Date:  2013-12-17
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  10 in total

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2.  Subrandom methods for multidimensional nonuniform sampling.

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

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

Review 4.  Non-Uniform and Absolute Minimal Sampling for High-Throughput Multidimensional NMR Applications.

Authors:  Dawei Li; Alexandar L Hansen; Lei Bruschweiler-Li; Rafael Brüschweiler
Journal:  Chemistry       Date:  2018-06-19       Impact factor: 5.236

5.  Pitfalls in compressed sensing reconstruction and how to avoid them.

Authors:  Alexandra Shchukina; Paweł Kasprzak; Rupashree Dass; Michał Nowakowski; Krzysztof Kazimierczuk
Journal:  J Biomol NMR       Date:  2016-11-11       Impact factor: 2.835

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

7.  Non-Uniform Sampling for All: More NMR Spectral Quality, Less Measurement Time.

Authors:  Frank Delaglio; Gregory S Walker; Kathleen A Farley; Raman Sharma; Jeffrey C Hoch; Luke W Arbogast; Robert G Brinson; John P Marino
Journal:  Am Pharm Rev       Date:  2017-06-30

8.  Reducing the measurement time of exact NOEs by non-uniform sampling.

Authors:  Parker J Nichols; Alexandra Born; Morkos A Henen; Dean Strotz; David N Jones; Frank Delaglio; Beat Vögeli
Journal:  J Biomol NMR       Date:  2020-09-03       Impact factor: 2.582

9.  NMRFx Processor: a cross-platform NMR data processing program.

Authors:  Michael Norris; Bayard Fetler; Jan Marchant; Bruce A Johnson
Journal:  J Biomol NMR       Date:  2016-07-25       Impact factor: 2.835

10.  Unbiased measurements of reconstruction fidelity of sparsely sampled magnetic resonance spectra.

Authors:  Qinglin Wu; Brian E Coggins; Pei Zhou
Journal:  Nat Commun       Date:  2016-07-27       Impact factor: 14.919

  10 in total

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