A Robust Masked Painter Framework for Gene Selection in Binary Classification of High-Dimensional Functional Genomic Data

Abstract

High-dimensional gene expression datasets in chemometric and biomedical research present significant challenges for machine learning because the number of genes greatly exceeds the number of available samples, increasing the risk of overfitting and reducing classification reliability. Existing gene selection methods are often sensitive to noise and outliers, leading to unstable feature subsets and degraded classification performance. To address these limitations, this study proposes a Robust Masked Painter (RMP) framework that integrates robust measures of location and dispersion, namely the Median and the Rousseeuw & Croux statistic (Qn), for reliable gene selection. The proposed framework operates in two stages. First, we identify informative genes using a round-robin strategy with a greedy search algorithm and robust core intervals to reduce the influence of noise and outliers. Second, Dominant Class (DC) analysis and Overlapping Scores (OS) further refine the selected gene subset by minimizing class overlap. We evaluate the proposed method on four publicly available gene expression datasets and compare it with several established feature selection methods using Random Forest, K-Nearest Neighbors, and Support Vector Machine classifiers. We assess classification performance using the Classification Error Rate. Experimental results and simulation studies demonstrate that the proposed RMP framework consistently outperforms competing methods by selecting highly informative genes that improve classification accuracy, robustness, and generalization.