Global Constraints for Lexicographic Orderings
CP '02 Proceedings of the 8th International Conference on Principles and Practice of Constraint Programming
Integer Programming Approaches to Haplotype Inference by Pure Parsimony
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Haplotyping Populations by Pure Parsimony: Complexity of Exact and Approximation Algorithms
INFORMS Journal on Computing
Efficient haplotype inference with boolean satisfiability
AAAI'06 Proceedings of the 21st national conference on Artificial intelligence - Volume 1
Haplotype inference by pure Parsimony
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
Boosting Haplotype Inference with Local Search
Constraints
Two-Level ACO for Haplotype Inference Under Pure Parsimony
ANTS '08 Proceedings of the 6th international conference on Ant Colony Optimization and Swarm Intelligence
A Set-Covering Approach with Column Generation for Parsimony Haplotyping
INFORMS Journal on Computing
Breaking symmetries in SAT matrix models
SAT'07 Proceedings of the 10th international conference on Theory and applications of satisfiability testing
Efficient haplotype inference with pseudo-boolean optimization
AB'07 Proceedings of the 2nd international conference on Algebraic biology
EPIA'07 Proceedings of the aritficial intelligence 13th Portuguese conference on Progress in artificial intelligence
CollHaps: A Heuristic Approach to Haplotype Inference by Parsimony
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Extending clause learning of SAT solvers with Boolean Gröbner bases
CASC'10 Proceedings of the 12th international conference on Computer algebra in scientific computing
Improving resource-unaware SAT solvers
LPAR'10 Proceedings of the 17th international conference on Logic for programming, artificial intelligence, and reasoning
SAT solving with reference points
SAT'10 Proceedings of the 13th international conference on Theory and Applications of Satisfiability Testing
Designing scalable parallel SAT solvers
SAT'12 Proceedings of the 15th international conference on Theory and Applications of Satisfiability Testing
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Mutation in DNA is the principal cause for differences among human beings, and Single Nucleotide Polymorphisms (SNPs) are the most common mutations. Hence, a fundamental task is to complete a map of haplotypes (which identify SNPs) in the human population. Associated with this effort, a key computational problem is the inference of haplotype data from genotype data, since in practice genotype data rather than haplotype data is usually obtained. Recent work has shown that a SAT-based approach is by far the most efficient solution to the problem of haplotype inference by pure parsimony (HIPP), being several orders of magnitude faster than existing integer linear programming and branch and bound solutions. This paper proposes a number of key optimizations to the the original SAT-based model. The new version of the model can be orders of magnitude faster than the original SAT-based HIPP model, particularly on biological test data.