A Survey on Swarm Intelligence Search Methods Dedicated to Detection of High-Order SNP Interactions

Detecting high-order single-nucleotide polymorphism (SNP) interactions is of great importance for the discovery of pathogenic causes of human complex diseases. However, a considerable computing challenge exists in analyzing each SNP combination at a genome-wide scale. Swarm intelligence search (SIS) is an effective and efficient method for solving NP-hard problems and has been extensively researched for detecting high-order SNP interactions. In this review, we first analyze the strengths and limitations of existing methods such as exhaustive search using cluster computing and parallel computing, stochastic search and high-performance computing. Then, SIS algorithms for the detection of high-order SNP interactions are introduced in detail. The algorithms discussed are the genetic algorithm (GA), ant colony optimization (ACO), harmony search (HS), particle swarm optimization (PSO), differential evolution (DE), cuckoo search (CS), fish swarm (FS) and artificial bee colony (ABC). Finally, we discuss the characteristics and limitations of the involved methods and provide several suggestions for improving SIS algorithms to detect high-order SNP interactions.