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Mathematical programming strategies for solving the minimum common string partition problem

descriptionPublicationkeyboard_double_arrow_right Article , Preprint 01 May 2015Embargo end date: 01 Jan 2014Publisher:Elsevier BVJournal:European Journal of Operational Research, volume 242, pages 769-777 (issn: 0377-2217,

Authors: Christian Blum; Christian Blum; Pedro Pinacho Davidson; Pedro Pinacho Davidson; Jose A. Lozano;

doi: 10.1016/j.ejor.2014.10.049 , 10.48550/arxiv.1405.5646

arXiv: http://arxiv.org/abs/1405.5646

Mathematical programming strategies for solving the minimum common string partition problem

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Abstract

The minimum common string partition problem is an NP-hard combinatorial optimization problem with applications in computational biology. In this work we propose the first integer linear programming model for solving this problem. Moreover, on the basis of the integer linear programming model we develop a deterministic 2-phase heuristic which is applicable to larger problem instances. The results show that provenly optimal solutions can be obtained for problem instances of small and medium size from the literature by solving the proposed integer linear programming model with CPLEX. Furthermore, new best-known solutions are obtained for all considered problem instances from the literature. Concerning the heuristic, we were able to show that it outperforms heuristic competitors from the related literature.

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Keywords

FOS: Computer and information sciences, Artificial Intelligence (cs.AI), 90-08, Computer Science - Artificial Intelligence, Computer Science - Data Structures and Algorithms, Data Structures and Algorithms (cs.DS)

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