Literature DB >> 10053145

A new method for spectral decomposition using a bilinear Bayesian approach.

M F Ochs1, R S Stoyanova, F Arias-Mendoza, T R Brown.   

Abstract

A frequent problem in analysis is the need to find two matrices, closely related to the underlying measurement process, which when multiplied together reproduce the matrix of data points. Such problems arise throughout science, for example, in imaging where both the calibration of the sensor and the true scene may be unknown and in localized spectroscopy where multiple components may be present in varying amounts in any spectrum. Since both matrices are unknown, such a decomposition is a bilinear problem. We report here a solution to this problem for the case in which the decomposition results in matrices with elements drawn from positive additive distributions. We demonstrate the power of the methodology on chemical shift images (CSI). The new method, Bayesian spectral decomposition (BSD), reduces the CSI data to a small number of basis spectra together with their localized amplitudes. We apply this new algorithm to a 19F nonlocalized study of the catabolism of 5-fluorouracil in human liver, 31P CSI studies of a human head and calf muscle, and simulations which show its strengths and limitations. In all cases, the dataset, viewed as a matrix with rows containing the individual NMR spectra, results from the multiplication of a matrix of generally nonorthogonal basis spectra (the spectral matrix) by a matrix of the amplitudes of each basis spectrum in the the individual voxels (the amplitude matrix). The results show that BSD can simultaneously determine both the basis spectra and their distribution. In principle, BSD should solve this bilinear problem for any dataset which results from multiplication of matrices representing positive additive distributions if the data overdetermine the solutions. Copyright 1999 Academic Press.

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Year:  1999        PMID: 10053145     DOI: 10.1006/jmre.1998.1639

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


  16 in total

1.  Matrix Factorization for Transcriptional Regulatory Network Inference.

Authors:  Michael F Ochs; Elana J Fertig
Journal:  IEEE Symp Comput Intell Bioinforma Comput Biol Proc       Date:  2012-05

2.  CoGAPS: an R/C++ package to identify patterns and biological process activity in transcriptomic data.

Authors:  Elana J Fertig; Jie Ding; Alexander V Favorov; Giovanni Parmigiani; Michael F Ochs
Journal:  Bioinformatics       Date:  2010-09-01       Impact factor: 6.937

3.  MUNIN: a new approach to multi-dimensional NMR spectra interpretation.

Authors:  V Y Orekhov; I V Ibraghimov; M Billeter
Journal:  J Biomol NMR       Date:  2001-05       Impact factor: 2.835

4.  Identification and quantification of metabolites in (1)H NMR spectra by Bayesian model selection.

Authors:  Cheng Zheng; Shucha Zhang; Susanne Ragg; Daniel Raftery; Olga Vitek
Journal:  Bioinformatics       Date:  2011-03-12       Impact factor: 6.937

Review 5.  Matrix factorisation methods applied in microarray data analysis.

Authors:  Andrew V Kossenkov; Michael F Ochs
Journal:  Int J Data Min Bioinform       Date:  2010       Impact factor: 0.667

6.  Detection of treatment-induced changes in signaling pathways in gastrointestinal stromal tumors using transcriptomic data.

Authors:  Michael F Ochs; Lori Rink; Chi Tarn; Sarah Mburu; Takahiro Taguchi; Burton Eisenberg; Andrew K Godwin
Journal:  Cancer Res       Date:  2009-11-10       Impact factor: 12.701

7.  Matrix factorization for recovery of biological processes from microarray data.

Authors:  Andrew V Kossenkov; Michael F Ochs
Journal:  Methods Enzymol       Date:  2009       Impact factor: 1.600

8.  Knowledge-based data analysis comes of age.

Authors:  Michael F Ochs
Journal:  Brief Bioinform       Date:  2009-10-23       Impact factor: 11.622

9.  MetaboHunter: an automatic approach for identification of metabolites from 1H-NMR spectra of complex mixtures.

Authors:  Dan Tulpan; Serge Léger; Luc Belliveau; Adrian Culf; Miroslava Cuperlović-Culf
Journal:  BMC Bioinformatics       Date:  2011-10-14       Impact factor: 3.169

10.  Determination of strongly overlapping signaling activity from microarray data.

Authors:  Ghislain Bidaut; Karsten Suhre; Jean-Michel Claverie; Michael F Ochs
Journal:  BMC Bioinformatics       Date:  2006-02-28       Impact factor: 3.169

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