Effective Lower Bounding Techniques for Pseudo-Boolean Optimization
Proceedings of the conference on Design, Automation and Test in Europe - Volume 2
Complexity and approximation of the minimum recombinant haplotype configuration problem
Theoretical Computer Science
Haplotyping Populations by Pure Parsimony: Complexity of Exact and Approximation Algorithms
INFORMS Journal on Computing
Boosting Haplotype Inference with Local Search
Constraints
How frugal is mother nature with haplotypes?
Bioinformatics
Haplotype Inference in Complex Pedigrees
RECOMB 2'09 Proceedings of the 13th Annual International Conference on Research in Computational Molecular Biology
Solving (Weighted) Partial MaxSAT through Satisfiability Testing
SAT '09 Proceedings of the 12th International Conference on Theory and Applications of Satisfiability Testing
Exploiting Cycle Structures in Max-SAT
SAT '09 Proceedings of the 12th International Conference on Theory and Applications of Satisfiability Testing
Within-problem learning for efficient lower bound computation in Max-SAT solving
AAAI'08 Proceedings of the 23rd national conference on Artificial intelligence - Volume 1
On solving Boolean multilevel optimization problems
IJCAI'09 Proceedings of the 21st international jont conference on Artifical intelligence
Haplotype inference by pure Parsimony
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Efficient haplotype inference with pseudo-boolean optimization
AB'07 Proceedings of the 2nd international conference on Algebraic biology
Constraint integer programming: a new approach to integrate CP and MIP
CPAIOR'08 Proceedings of the 5th international conference on Integration of AI and OR techniques in constraint programming for combinatorial optimization problems
Efficient haplotype inference with combined CP and OR techniques
CPAIOR'08 Proceedings of the 5th international conference on Integration of AI and OR techniques in constraint programming for combinatorial optimization problems
Boolean lexicographic optimization: algorithms & applications
Annals of Mathematics and Artificial Intelligence
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Existing genotyping technologies have enabled researchers to genotype hundreds of thousands of SNPs efficiently and inexpensively. Methods for the imputation of non-genotyped SNPs and the inference of haplotype information from genotypes, however, remain important, since they have the potential to increase the power of statistical association tests. In many cases, studies are conducted in sets of individuals where the pedigree information is relevant, and can be used to increase the power of tests and to decrease the impact of population structure on the obtained results. This paper proposes a new Boolean optimization model for haplotype inference combining two combinatorial approaches: the Minimum Recombinant Haplotyping Configuration (MRHC), which minimizes the number of recombinant events within a pedigree, and the Haplotype Inference by Pure Parsimony (HIPP), that aims at finding a solution with a minimum number of distinct haplotypes within a population. The paper also describes the use of well-known techniques, which yield significant performance gains. Concrete examples include symmetry breaking, identification of lower bounds, and the use of an appropriate constraint solver. Experimental results show that the new PedRPoly model is competitive both in terms of accuracy and efficiency.