A Competitive Coevolution-Based Cancer Driver Pathway Identification Algorithm for Maximizing Coverage, Mutual...

Identifying cancer driver pathways is crucial for elucidating tumorigenesis and the progression of cancer. The vast accumulation of omics data now enables the use of computational approaches to infer these pathways. In the currently proposed identification methods, the gene set with "dominant" genes (mutating in most of the samples) may be captured. Although the "dominant" genes are usually driver genes, their absolute predominance of mutations in cancer samples may lead to the other genes within the set are not cancer driver genes at all. In this article, a parameter-free identification model MCMS (Maximizing Coverage, Mutual exclusivity, and Subnet importance) is proposed, which employs a novel mutual exclusivity metric to exclude the gene set with "dominant" genes (i.e., eliminating bias toward predominant mutations). A competitive coevolution algorithm CCA is devised to solve the model (CCA-MCMS), it implements an effective population fitness function that dynamically regulates inter-population competition to preserve population diversity. The gene sets derived from the proposed CCA-MCMS method demonstrate both superior enrichment in biological signaling pathways and increased connectivity in the HINT-HI2012 network, relative to sets identified by other prominent approaches. The demonstrated computational efficiency of CCA-MCMS further supports its use in practical biomarker discovery tasks.