Generic ILP vs Specialized 0-1 ILP for Haplotype Inference

Haplotype inference is an important and computationally challenging problem in genetics. A well-known approach to haplotype inference is pure parsimony (HIPP). Despite being based on a simple optimization criterion, HIPP is a computationally hard problem. Recent work has shown that approaches based on Boolean satisfiability namely pseudo-Boolean optimization (PBO), are very effective at tackling the HIPP problem. Extensive work on PBO-based HIPP approaches has been recently developed. Considering that the PBO problem, also known as 0-1 ILP problem, is a particular case of the integer linear programming (ILP) problem, generic ILP solvers can be considered. This paper compares the performance of PBO and ILP solvers on a variety of HIPP models. We conclude that specialized PBO solvers are more suitable than generic ILP solvers.