Two-Level ACO for Haplotype Inference Under Pure Parsimony

Abstract

Haplotype Inference is a challenging problem in bioinformatics that consists in inferring the basic genetic constitution of diploid organisms on the basis of their genotype. This information enables researchers to perform association studies for the genetic variants involved in diseases and the individual responses to therapeutic agents. A notable approach to the problem is to encode it as a combinatorial problem under certain hypotheses (such as the pure parsimony criterion) and to solve it using off-the-shelf combinatorial optimization techniques. At present, the main methods applied to Haplotype Inference are either simple greedy heuristic or exact methods, which are adequate only for moderate size instances. In this paper, we present an iterative constructive approach to Haplotype Inference based on ACO and we compare it against a state-of-the-art exact method.