Scientific Publications by FDA Staff

Brief Bioinform 2013 Jan;14(1):13-26

Class-imbalanced classifiers for high-dimensional data.

Lin WJ, Chen JJ

A class-imbalanced classifier is a decision rule to predict the class membership of new samples from an available data set where the class sizes differ considerably. When the class sizes are very different, most standard classification algorithms may favor the larger (majority) class resulting in poor accuracy in the minority class prediction. A class-imbalanced classifier typically modifies a standard classifier by a correction strategy or by incorporating a new strategy in the training phase to account for differential class sizes. This article reviews and evaluates some most important methods for class prediction of high-dimensional imbalanced data. The evaluation addresses the fundamental issues of the class-imbalanced classification problem: imbalance ratio, small disjuncts and overlap complexity, lack of data and feature selection. Four class-imbalanced classifiers are considered. The four classifiers include three standard classification algorithms each coupled with an ensemble correction strategy and one support vector machines (SVM)-based correction classifier. The three algorithms are (i) diagonal linear discriminant analysis (DLDA), (ii) random forests (RFs) and (ii) SVMs. The SVM-based correction classifier is SVM threshold adjustment (SVM-THR). A Monte-Carlo simulation and five genomic data sets were used to illustrate the analysis and address the issues. The SVM-ensemble classifier appears to perform the best when the class imbalance is not too severe. The SVM-THR performs well if the imbalance is severe and predictors are highly correlated. The DLDA with a feature selection can perform well without using the ensemble correction.