Title | Large neighborhood search for the most strings with few bad columns problem |
Publication Type | Journal Article |
Year of Publication | 2017 |
Authors | Lizárraga E, Blesa MJ, Blum C, Raidl GR |
Journal | Soft Computing |
Volume | 21 |
Issue | 17 |
Pagination | 4901–4915 |
ISSN | 1432-7643 |
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. |
DOI | 10.1007/s00500-016-2379-4 |