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2011 Third International Conference on Knowledge and Systems Engineering
A Fast and Efficient Ant Colony Optimization for Haplotype Inference by Pure Parsimony
Hanoi, Vietnam
October 14-October 17
ISBN: 978-0-7695-4567-7
Haplotype inference is a challenging computational problem in population genetics. We introduce an approach using Ant Colony Optimization (ACO) metaheuristic, named ACOHAP, to infer haplotypes from unphased Single Polymorphism Nucleotide (SNP) marker data. Our method employs an efficient method for constructing the ACO graph through which ants flexibly traverse to build haplotypes. ACOHAP also uses a well-performed pheromone trail update strategy and a local search to improve the performance. Experiments showed that ACOHAP outperformed the state-of-the-art methods for haplotype inference in both simulated and biological data.
Index Terms:
Ant Colony Optimization, Haplotype inference, ACOHAP
Citation:
Dong Do Duc, Huan Hoang Xuan, "A Fast and Efficient Ant Colony Optimization for Haplotype Inference by Pure Parsimony," kse, pp.128-134, 2011 Third International Conference on Knowledge and Systems Engineering, 2011
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