Title | Large neighborhood search for the most strings with few bad columns problem |

Publication Type | Journal Article |

Year of Publication | 2017 |

Authors | Lizárraga E [1], Blesa MJ [2], Blum C [3], Raidl GR [4] |

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 [5] |