Artificial bee colony algorithm based on self-adjusting random grouping for high-order epistasis detection

Abstract

In the genome-wide association studies (GWAS), epistasis detection is of great significance to study the pathogenesis of complex diseases. Epistasis refers to the effect of interactions between multiple single nucleotide polymorphisms (SNPs) on complex diseases. In this paper, an artificial bee colony algorithm based on self-adjusting random grouping (ABC-SRG) is proposed for high-order epistasis detection. ABC-SRG adopts a new self-adjusting random grouping strategy, which realizes the division of the original data according to the fitness value of each grouping. In addition, a variance-based adaptive iteration strategy is proposed, which implements the adaptive iteration through the variance of the fitness value of each iteration of the algorithm. To demonstrate the effectiveness of the algorithm, the experiments on simulated data and real data were conducted. In the simulation experiments, ABC-SRG was compared with the other five methods for second-order and third-order SNP interaction detection. Age-related macular degeneration (AMD) data were selected for the real data experiment, and most of the SNP interactions detected in the experiment have been confirmed to be related to the AMD disease. Therefore, ABC-SRG is an effective method to detect high-order epistasis.