Efficient Haplotype Inference with Combined CP and OR Techniques

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Efficient Haplotype Inference with Combined CP and OR Techniques
Abstract. Haplotype inference has relevant biological applications, and represents a challenging computational problem. Among others, pure parsimony provides a viable modeling approach for haplotype inference and provides a simple optimization criterion. Alternative approaches have been proposed for haplotype inference by pure parsimony (HIPP), including branch and bound, integer programming and, more recently, propositional satisfiability and pseudo-Boolean optimization (PBO). Among these, the currently best performing HIPP approach is based on PBO. This paper proposes a number of effective improvements to PBO-based HIPP, including the use of lower bounding and pruning techniques effective with other approaches. The new PBO-based HIPP approach reduces by 50% the number of instances that remain unsolvable by HIPP based approaches.
Ana Graça, João Marques-Silva, In&ec
Added 19 Oct 2010
Updated 19 Oct 2010
Type Conference
Year 2008
Authors Ana Graça, João Marques-Silva, Inês Lynce, Arlindo L. Oliveira
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