A Particle Swarm Optimization Algorithm Based on Multi-Population Mutual Learning for SNP-SNP Interaction Detection

Single nucleotide polymorphism (SNPs) data have become abundant thanks to the quick advancement of high-throughput sequencing technology, which provides convenience for genome-wide association studies. Single SNPs have been proven to be the cause of some diseases, and the emergence of complex diseases is often thought to be the result of the interaction of multiple SNPs. However, the possible interaction of millions of SNPs imposes a heavy computational burden for uncovering complex disease mechanisms. The existing SNP-SNP interaction detection algorithms frequently have flaws including high computation complexity and poor optimization effectiveness. In this study, a particle swarm optimization algorithm based on multi-population mutual learning (PSOMPML) is proposed to detect SNP-SNP interactions. In this algorithm, the mutual learning strategy is introduced to deal with different particles in different sub-populations to facilitate knowledge exchange. In addition, the elite preservation mechanism is incorporated into PSOMPML, to better preserve the good SNPs in the elite particles. The promising region local search strategy searches the optimal solution along the target solution and its near space to increase the convergence speed of the proposed algorithm. Experiments on simulated data sets and real data also demonstrate the effectiveness of the proposed algorithm.