Advanced metric adaptation in Generalized LVQ for classification of mass spectrometry data

Abstract

Metric adaptation constitutes a powerful approach to improve the performance of prototype based classication schemes. We apply extensions of Generalized LVQ based on different adaptive distance measures in the domain of clinical proteomics. The Euclidean distance in GLVQ is extended by adaptive relevance vectors and matrices of global or local influence where training follows a stochastic gradient descent on an appropriate error function. We compare the performance of the resulting learning algorithms for the classification of high dimensional mass spectrometry data from cancer research. High prediction accuracies can be obtained by adapting full matrices of relevance factors in the distance measure in order to adjust the metric to the underlying data structure. The easy interpretability of the resulting models after training of relevance vectors allows to identify discriminative features in the original spectra.