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CPAIOR
2008
Springer

Efficient Haplotype Inference with Combined CP and OR Techniques

13 years 11 months ago
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
Where CPAIOR
Authors Ana Graça, João Marques-Silva, Inês Lynce, Arlindo L. Oliveira
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