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.
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Graça, A., Marques-Silva, J., Lynce, I., Oliveira, A.L. (2008). Efficient Haplotype Inference with Combined CP and OR Techniques. In: Perron, L., Trick, M.A. (eds) Integration of AI and OR Techniques in Constraint Programming for Combinatorial Optimization Problems. CPAIOR 2008. Lecture Notes in Computer Science, vol 5015. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-68155-7_28
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DOI: https://doi.org/10.1007/978-3-540-68155-7_28
Publisher Name: Springer, Berlin, Heidelberg
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