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Briefings in Bioinformatics Advance Access originally published online on March 11, 2008
Briefings in Bioinformatics 2008 9(2):129-143; doi:10.1093/bib/bbn009
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© The Author 2008. Published by Oxford University Press. For Permissions, please email: journals.permissions@oxfordjournals.org

Classification of mass-spectrometric data in clinical proteomics using learning vector quantization methods

Thomas Villmann, Frank-Michael Schleif, Markus Kostrzewa, Axel Walch and Barbara Hammer

Corresponding author. Thomas Villmann, Medical Department, University Leipzig Germany. Tel: +49 (0)341 9718868; E-mail: thomas.villmann{at}medizin.uni-leipzig.de

In the present contribution we propose two recently developed classification algorithms for the analysis of mass-spectrometric data—the supervised neural gas and the fuzzy-labeled self-organizing map. The algorithms are inherently regularizing, which is recommended, for these spectral data because of its high dimensionality and the sparseness for specific problems. The algorithms are both prototype-based such that the principle of characteristic representants is realized. This leads to an easy interpretation of the generated classifcation model. Further, the fuzzy-labeled self-organizing map is able to process uncertainty in data, and classification results can be obtained as fuzzy decisions. Moreover, this fuzzy classification together with the property of topographic mapping offers the possibility of class similarity detection, which can be used for class visualization. We demonstrate the power of both methods for two exemplary examples: the classification of bacteria (listeria types) and neoplastic and non-neoplastic cell populations in breast cancer tissue sections.

Keywords: classification, vector quantization, class visualization, machine learning, fuzzy-labeled self-organizing map, mass spectrometry

Submitted: August 15, 2007. Received (in revised form): January 25, 2008.


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