Genetic algorithms for multi-omic feature selection: a comparative study in cancer survival analysis

TL;DR

This study introduces Sweeping*, a multi-view, multi-objective genetic algorithm for multi-omic feature selection in cancer survival analysis, improving biomarker panel identification by capturing cross-modal signals.

Contribution

It presents Sweeping*, a novel algorithm that alternates between single- and multi-view optimization to enhance multi-omic feature selection in survival prediction.

Findings

Sweeping* improves accuracy-complexity trade-off with sufficient survival signal.

Integrating omic layers can enhance survival prediction beyond clinical models.

Different Sweeping* strategies show cohort-dependent benefits.

Abstract

Multi-omic datasets offer opportunities for improved biomarker discovery in cancer research, but their high dimensionality and limited sample sizes make identifying compact and effective biomarker panels challenging. Feature selection in large-scale omics can be efficiently addressed by combining machine learning with genetic algorithms, which naturally support multi-objective optimization of predictive accuracy and biomarker set size. However, genetic algorithms remain relatively underexplored for multi-omic feature selection, where most approaches concatenate all layers into a single feature space. To address this limitation, we introduce Sweeping*, a multi-view, multi-objective algorithm alternating between single- and multi-view optimization. It employs a nested single-view multi-objective optimizer, and for this study we use the genetic algorithm NSGA3-CHS. It first identifies informative biomarkers within each layer, then jointly evaluates cross-layer interactions; these multi-omic solutions guide the next single-view search. Through repeated sweeps, the algorithm progressively identifies compact biomarker panels capturing cross-modal complementary signals. We benchmark five Sweeping* strategies, including hierarchical and concatenation-based variants, using survival prediction on three TCGA cohorts. Each strategy jointly optimizes predictive accuracy and set size, measured via the concordance index and root-leanness. Overall performance and estimation error are assessed through cross hypervolume and Pareto delta under 5-fold cross-validation. Our results show that Sweeping* can improve the accuracy-complexity trade-off when sufficient survival signal is present and that integrating omic layers can enhance survival prediction beyond clinical-only models, although benefits remain cohort-dependent.