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Título:
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Large neighborhood search for the most strings with few bad columns problem
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Autor/a:
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Lizárraga Olivas, Evelia; Blesa Aguilera, Maria Josep; Blum, Christian; Raidl, Günther
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Otros autores:
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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 |
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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. |
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Abstract:
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Peer Reviewed |
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Materia(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 |
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Derechos:
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Tipo de documento:
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Artículo - Versión presentada
Artículo |
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Editor:
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Springer
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Compartir:
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