TitleLarge neighborhood search for the most strings with few bad columns problem
Publication TypeJournal Article
Year of Publication2017
AuthorsLizárraga E, Blesa MJ, Blum C, Raidl GR
JournalSoft Computing

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.