Biomarker selection and sample prediction for multi-category disease on MALDI-TOF data

Abstract

Diseases normally progress through several stages. Therefore, biomarkers corresponding to each stage may exist. To deal with such a multi-category problem, including sample stage prediction and biomarker selection, we propose methods for classification and feature selection. The proposed classification method is based on two schemes: error-correcting output coding (ECOC) and pairwise coupling (PWC). The final decision for a test sample prediction is an integration of these two schemes. The biomarker pattern for distinguishing each disease category from another one is achieved by the development of an extended Markov blanket (EMB) feature selection method. In this study, a liver cancer matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) dataset was used, which comprises hepatocellular carcinoma (HCC), cirrhosis, and healthy spectra. Peak patterns were discovered for distinguishing pairwise categories among the three classes. Importance and reliability of individual peaks were presented by the measurements of certain weight values and frequencies. The classification capability of the proposed approach was compared with classical ECOC, random forest, Naive Bayes, and J48 methods. Supplementary materials are available at http://visionlab.uta.edu/biomarker/bioinfo.htm.