An ensemble predictive modeling framework for breast cancer classification

Abstract

Molecular changes often precede clinical presentation of diseases and can be useful surrogates with potential to assist in informed clinical decision making. Recent studies have demonstrated the usefulness of modeling approaches such as classification that can predict the clinical outcomes from molecular expression profiles. While useful, a majority of these approaches implicitly use all molecular markers as features in the classification process often resulting in sparse high-dimensional projection of the samples often comparable to that of the sample size. In this study, a variant of the recently proposed ensemble classification approach is used for predicting good and poor-prognosis breast cancer samples from their molecular expression profiles. In contrast to traditional single and ensemble classifiers, the proposed approach uses multiple base classifiers with varying feature sets obtained from two-dimensional projection of the samples in conjunction with a majority voting strategy for predicting the class labels. In contrast to our earlier implementation, base classifiers in the ensembles are chosen based on maximal sensitivity and minimal redundancy by choosing only those with low average cosine distance. The resulting ensemble sets are subsequently modeled as undirected graphs. Performance of four different classification algorithms is shown to be better within the proposed ensemble framework in contrast to using them as traditional single classifier systems. Significance of a subset of genes with high-degree centrality in the network abstractions across the poor-prognosis samples is also discussed.

Keywords: Ensemble classification; Molecular profiling; Predictive modeling.