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New heuristics for the Bicluster Editing Problem

Author

Listed:
  • Gilberto F. Sousa Filho

    (Universidade Federal da Paraíba (UFPB))

  • Teobaldo L. Bulhões Júnior

    (Universidade Federal da Paraíba (UFPB))

  • Lucidio A. F. Cabral

    (Universidade Federal da Paraíba (UFPB))

  • Luiz Satoru Ochi

    (Universidade Federal Fluminense (UFF))

  • Fábio Protti

    (Universidade Federal Fluminense (UFF))

Abstract

The NP-hard Bicluster Editing Problem (BEP) consists of editing a minimum number of edges of an input bipartite graph G in order to transform it into a vertex-disjoint union of complete bipartite subgraphs. Editing an edge consists of either adding it to the graph or deleting it from the graph. Applications of the BEP include data mining and analysis of gene expression data. In this work, we generate and analyze random bipartite instances for the BEP to perform empirical tests. A new reduction rule for the problem is proposed, based on the concept of critical independent sets, providing an effective reduction in the size of the instances. We also propose a set of heuristics using concepts of the metaheuristics ILS, VNS, and GRASP, including a constructive heuristic based on analyzing vertex neighborhoods, three local search procedures, and an auxiliary data structure to speed up the local search. Computational experiments show that our heuristics outperform other methods from the literature with respect to both solution quality and computational time.

Suggested Citation

  • Gilberto F. Sousa Filho & Teobaldo L. Bulhões Júnior & Lucidio A. F. Cabral & Luiz Satoru Ochi & Fábio Protti, 2017. "New heuristics for the Bicluster Editing Problem," Annals of Operations Research, Springer, vol. 258(2), pages 781-814, November.
    • Handle: RePEc:spr:annopr:v:258:y:2017:i:2:d:10.1007_s10479-016-2261-x
    DOI: 10.1007/s10479-016-2261-x
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    References listed on IDEAS

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    1. Pierre Hansen & Nenad Mladenović & José Moreno Pérez, 2010. "Variable neighbourhood search: methods and applications," Annals of Operations Research, Springer, vol. 175(1), pages 367-407, March.
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