Niche Genetic Algorithm for Solving Multiplicity Problems in Genetic Association Studies

This paper proposes a novel genetic algorithm (GA) that embeds a niche competition strategy (NCS) in the evolutionary flow to solve the combinational optimization problems that involve multiple loci in the search space. Unlike other niche-information based algorithms, the proposed NCSGA does not need prior knowledge to design niche parameters in the niching phase. To verify the solution capability of the new method, benchmark studies on both the travelling salesman problem (TSP) and the airline recovery scheduling problem were first made. Then, the proposed method was used to solve single nucleotide polymorphism (SNP) barcodes generation problems in a genetic association study. Experiments showed that the proposed NCS-based solver substantially improves solution quality by maintaining multiple optima.