Protein expression molecular pattern discovery by nonnegative principal component analysis

Abstract

Identifying cancer molecular patterns robustly from large dimensional protein expression data not only has significant impacts on clinical ontology, but also presents a challenge for statistical learning. Principal component analysis (PCA) is a widely used feature selection algorithm and generally integrated with classic classification algorithms to conduct cancer molecular pattern discovery. However, its holistic mechanism prevents local data characteristics capture in feature selection. This may lead to the increase of misclassification rates and affect robustness of cancer molecular diagnostics. In this study, we develop a nonnegative principal component analysis (NPCA) algorithm and propose a NPCA-based SVM algorithm with sparse coding in the cancer molecular pattern analysis of proteomics data. We report leading classification results from this novel algorithm in predicting cancer molecular patterns of three benchmark proteomics datasets, under 100 trials of 50% hold-out and leave one out cross validations, by directly comparing its performances with those of the PCA-SVM, NMF-SVM, SVM, k-NN and PCA-LDA classification algorithms with respect to classification rates, sensitivities and specificities. Our algorithm also overcomes the overfitting problem in the SVM and PCA-SVM classifications and provides exceptional sensitivities and specificities. © 2008 Springer Berlin Heidelberg.