SAMA: A Fast Self-Adaptive Memetic Algorithm for Detecting SNP-SNP Interactions Associated with Disease

• Published in: BioMed research international Vol. 2020; no. 2020; pp. 1 - 11
• Main Authors: Li, Yuan, Zhao, Yuhai, Guan, Boxin, Yin, Ying
• Format: Journal Article
• Language: English
• Published: Cairo, Egypt Hindawi Publishing Corporation 2020; Hindawi; John Wiley & Sons, Inc
• Subjects: Adaptive algorithms; Adaptive search techniques; Algorithms; Comparative studies; Computer applications; Computer Simulation; Datasets; Disease; Epistasis, Genetic - genetics; Evolutionary algorithms; Genetic algorithms; Genome-wide association studies; Genome-Wide Association Study - methods; Genomes; Genotype & phenotype; Humans; Mutation; Optimization algorithms; Polymorphism, Single Nucleotide - genetics; Search algorithms
• ISSN: 2314-6133; 2314-6141; 2314-6141
• DOI: 10.1155/2020/5610658

Detecting SNP-SNP interactions associated with disease is significant in genome-wide association study (GWAS). Owing to intensive computational burden and diversity of disease models, existing methods have drawbacks on low detection power and long running time. To tackle these drawbacks, a fast self-adaptive memetic algorithm (SAMA) is proposed in this paper. In this method, the crossover, mutation, and selection of standard memetic algorithm are improved to make SAMA adapt to the detection of SNP-SNP interactions associated with disease. Furthermore, a self-adaptive local search algorithm is introduced to enhance the detecting power of the proposed method. SAMA is evaluated on a variety of simulated datasets and a real-world biological dataset, and a comparative study between it and the other four methods (FHSA-SED, AntEpiSeeker, IEACO, and DESeeker) that have been developed recently based on evolutionary algorithms is performed. The results of extensive experiments show that SAMA outperforms the other four compared methods in terms of detection power and running time.