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Bi-MOCK: A Multi-objective Evolutionary Algorithm for Bi-clustering with Automatic Determination of the Number of Bi-clusters

  • Meriem Bousselmi
  • Slim Bechikh
  • Chih-Cheng Hung
  • Lamjed Ben Said
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10637)

Abstract

Bi-clustering is one of the main tasks in data mining with many possible applications in bioinformatics, pattern recognition, text mining, just to cite a few. It refers to simultaneously partitioning a data matrix based on both rows and columns. One of the main issues in bi-clustering is the difficulty to find the number of bi-clusters, which is usually pre-specified by the human user. During the last decade, a new algorithm, called MOCK, has appeared and shown its performance in data clustering where the number of clusters is determined automatically. Motivated by the interesting results of MOCK, we propose in this paper a new algorithm, called Bi-MOCK, which could be seen as an extension of MOCK for bi-clustering. Like MOCK, Bi-MOCK uses the concept of multi-objective optimization and is able to find automatically the number of bi-clusters thanks to a newly proposed variable string length encoding scheme. The performance of our proposed algorithm is assessed on a set of real gene expression datasets. The comparative experiments show the merits and the outperformance of Bi-MOCK with respect to some existing recent works.

Keywords

Bi-clustering Number of bi-clusters Multi-objective evolutionary algorithms Variable-size encoding 

References

  1. 1.
    Madeira, S.C., Oliveira, A.L.: Biclustering algorithms for biological data analysis: a survey. IEEE/ACM Trans. Comput. Biol. Bioinform. 1(1), 24–45 (2004)CrossRefGoogle Scholar
  2. 2.
    Kasim, A., Shkedy, Z., Kaiser, S., Hochreiter, S., Talloen, W.: Applied biclustering methods for big and high dimensional data using R (2016). ISBN 9781482208238Google Scholar
  3. 3.
    Freitas, A.V., Ayadi, W., Elloumi, M., Oliveira, J., Oliveira, J., Hao, J.-K.: A survey on biclustering of gene expression data. In: Elloumi, M., Zomaya, A.Y. (eds.) Biological Knowledge Discovery Handbook: Preprocessing, Mining, and Postprocessing of Biological Data. Wiley, Hoboken (2013). doi: 10.1002/9781118617151.ch25 Google Scholar
  4. 4.
    Handl, J., Knowles, J.D.: An evolutionary approach to multiobjective clustering. IEEE Trans. Evol. Comput. 11(1), 56–76 (2007)CrossRefGoogle Scholar
  5. 5.
    Mitra, S., Banka, H.: Multi-objective evolutionary biclustering of gene expression data. Pattern Recogn. 39(12), 2464–2477 (2006)CrossRefMATHGoogle Scholar
  6. 6.
    Handl, J., Knowles, J.: Exploiting the trade-off—the benefits of multiple objectives in data clustering. In: Coello Coello, C.A., Hernández Aguirre, A., Zitzler, E. (eds.) EMO 2005. LNCS, vol. 3410, pp. 547–560. Springer, Heidelberg (2005). doi: 10.1007/978-3-540-31880-4_38 CrossRefGoogle Scholar
  7. 7.
    Bechikh, S., Ben Said, L., Ghedira, K.: Negotiating decision makers’ reference points for group preference-based evolutionary multi-objective optimization. In: International Conference on Hybrid Intelligent Systems, pp. 377–382 (2011)Google Scholar
  8. 8.
    Cheng, Y., Church, G.M.: Biclustering of expression data. In: International Conference on Intelligent Systems for Molecular Biology, pp. 93–103 (2000)Google Scholar
  9. 9.
  10. 10.
  11. 11.
    Seridi, K., Jourdan, L., Talbi, E.G.: Using multiobjective optimization for biclustering microarray data. Appl. Soft Comput. 33(1), 239–249 (2015)CrossRefGoogle Scholar
  12. 12.
    Divina, F., Aguilar-Ruiz, J.S.: A multi-objective approach to discover biclusters in microarray data. In: International Conference on Genetic and Evolutionary Computation (GECCO 2007), pp. 385–392 (2007)Google Scholar

Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Meriem Bousselmi
    • 1
  • Slim Bechikh
    • 1
    • 2
  • Chih-Cheng Hung
    • 2
    • 3
  • Lamjed Ben Said
    • 1
  1. 1.SMART Lab, Computer Science DepartmentUniversity of TunisTunisTunisia
  2. 2.Kennesaw State UniversityMariettaUSA
  3. 3.Anyang Normal UniversityAnyangChina

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