Journal Article

Bag of Peaks: interpretation of NMR spectrometry

Gavin Brelstaff, Manuele Bicego, Nicola Culeddu and Matilde Chessa

in Bioinformatics

Volume 25, issue 2, pages 258-264
Published in print January 2009 | ISSN: 1367-4803
Published online November 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn599
Bag of Peaks: interpretation of NMR spectrometry

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Motivation: The analysis of high-resolution proton nuclear magnetic resonance (NMR) spectrometry can assist human experts to implicate metabolites expressed by diseased biofluids. Here, we explore an intermediate representation, between spectral trace and classifier, able to furnish a communicative interface between expert and machine. This representation permits equivalent, or better, classification accuracies than either principal component analysis (PCA) or multi-dimensional scaling (MDS). In the training phase, the peaks in each trace are detected and clustered in order to compile a common dictionary, which could be visualized and adjusted by an expert. The dictionary is used to characterize each trace with a fixed-length feature vector, termed Bag of Peaks, ready to be classified with classical supervised methods.

Results: Our small-scale study, concerning Type I diabetes in Sardinian children, provides a preliminary indication of the effectiveness of the Bag of Peaks approach over standard PCA and MDS. Consistently, higher classification accuracies are obtained once a sufficient number of peaks (>10) are included in the dictionary. A large-scale simulation of noisy spectra further confirms this advantage. Finally, suggestions for metabolite-peak loci that may be implicated in the disease are obtained by applying standard feature selection techniques.

Availability: Matlab code to compute the Bag of Peaks representation may be found at http://economia.uniss.it/docenti/bicego/BagOfPeaks/BagOfPeaks.zip

Contact: gjb@crs4.it

Journal Article.  5588 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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