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AAAI
2008

Efficient Haplotype Inference with Answer Set Programming

10 years 28 days ago
Efficient Haplotype Inference with Answer Set Programming
Identifying maternal and paternal inheritance is essential to be able to find the set of genes responsible for a particular disease. Although we have access to genotype data (genetic makeup of an individual), determining haplotypes (genetic makeup of the parents) experimentally is a costly and time consuming procedure due to technological limitations. With these biological motivations, we study a computational problem, called Haplotype Inference with Pure Parsimony (HIPP), that asks for the minimal number of haplotypes that form a given set of genotypes. We introduce a novel approach to solving HIPP, using Answer Set Programming (ASP). According to our experiments with a large number of problem instances (some automatically generated and some real), our ASP-based approach solves the most number of problems compared to other approaches based on, e.g., integer linear programming, branch and bound algorithms, SAT-based algorithms, or pseudo-boolean optimization methods.
Esra Erdem, Ferhan Türe
Added 02 Oct 2010
Updated 02 Oct 2010
Type Conference
Year 2008
Where AAAI
Authors Esra Erdem, Ferhan Türe
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