Title:
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Large neighborhood search for the most strings with few bad columns problem
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Author:
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Lizárraga Olivas, Evelia; Blesa Aguilera, Maria Josep; Blum, Christian; Raidl, Günther
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Other authors:
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Universitat Politècnica de Catalunya. Departament de Ciències de la Computació; Universitat Politècnica de Catalunya. ALBCOM - Algorismia, Bioinformàtica, Complexitat i Mètodes Formals |
Abstract:
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In this work, we consider the following NP-hard combinatorial optimization problem from computational biology. Given a set of input strings of equal length, the goal is to identify a maximum cardinality subset of strings that differ maximally in a pre-defined number of positions. First of all, we introduce an integer linear programming model for this problem. Second, two variants of a rather simple greedy strategy are proposed. Finally, a large neighborhood search algorithm is presented. A comprehensive experimental comparison among the proposed techniques shows, first, that larger neighborhood search generally outperforms both greedy strategies. Second, while large neighborhood search shows to be competitive with the stand-alone application of CPLEX for small- and medium-sized problem instances, it outperforms CPLEX in the context of larger instances. |
Abstract:
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Peer Reviewed |
Subject(s):
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-Àrees temàtiques de la UPC::Informàtica::Programació -Linear programming -Computational biology -Most strings with few bad columns -Integer linear programming -Large neighborhood search -Programació lineal -Biologia computacional |
Rights:
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Document type:
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Article - Submitted version Article |
Published by:
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Springer
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