|
Title:
|
Large neighborhood search for the most strings with few bad columns problem
|
|
Author:
|
Lizárraga Olivas, Evelia; Blesa Aguilera, Maria Josep; Blum, Christian; Raidl, Günther
|
|
Other authors:
|
Universitat Politècnica de Catalunya. Departament de Ciències de la Computació; Universitat Politècnica de Catalunya. ALBCOM - Algorismia, Bioinformàtica, Complexitat i Mètodes Formals |
|
Abstract:
|
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:
|
Peer Reviewed |
|
Subject(s):
|
-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:
|
|
|
Document type:
|
Article - Submitted version
Article |
|
Published by:
|
Springer
|
|
Share:
|
|
