Solving Biclustering with a GRASP-Like Metaheuristic: Two Case-Studies on Gene Expression Analysis

  • Angelo Facchiano
  • Paola Festa
  • Anna Marabotti
  • Luciano Milanesi
  • Francesco Musacchia
Conference paper

DOI: 10.1007/978-3-642-35686-5_21

Part of the Lecture Notes in Computer Science book series (LNCS, volume 7548)
Cite this paper as:
Facchiano A., Festa P., Marabotti A., Milanesi L., Musacchia F. (2012) Solving Biclustering with a GRASP-Like Metaheuristic: Two Case-Studies on Gene Expression Analysis. In: Biganzoli E., Vellido A., Ambrogi F., Tagliaferri R. (eds) Computational Intelligence Methods for Bioinformatics and Biostatistics. CIBB 2011. Lecture Notes in Computer Science, vol 7548. Springer, Berlin, Heidelberg

Abstract

The explosion of ‘‘omics’’ data over the past few decades has generated an increasing need of efficiently analyzing high-dimensional gene expression data in several different and heterogenous contexts, such as for example in information retrieval, knowledge discovery, and data mining. For this reason, biclustering, or simultaneous clustering of both genes and conditions has generated considerable interest over the past few decades. Unfortunately, the problem of locating the most significant bicluster has been shown to be NP-complete. We have designed and implemented a GRASP-like heuristic algorithm to efficiently find good solutions in reasonable running times, and to overcome the inner intractability of the problem from a computational point of view.

Experimental results on two datasets of expression data are promising indicating that this algorithm is able to find significant biclusters, especially from a biological point of view.

Keywords

Biclustering gene expression analysis GRASP combinatorial optimization approximate solutions 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Angelo Facchiano
    • 1
  • Paola Festa
    • 2
  • Anna Marabotti
    • 3
  • Luciano Milanesi
    • 3
  • Francesco Musacchia
    • 2
  1. 1.Istituto di Scienze dell’Alimentazione - CNRItaly
  2. 2.University of Napoli ‘‘Federico II’’Italy
  3. 3.Istituto di Tecnologie Biomediche - CNRItaly

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