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

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Computational Intelligence Methods for Bioinformatics and Biostatistics (CIBB 2011)

Part of the book series: Lecture Notes in Computer Science ((LNBI,volume 7548))

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.

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Author information

Authors and Affiliations

  1. Istituto di Scienze dell’Alimentazione - CNR, Italy

    Angelo Facchiano

  2. University of Napoli ‘‘Federico II’’, Italy

    Paola Festa & Francesco Musacchia

  3. Istituto di Tecnologie Biomediche - CNR, Italy

    Anna Marabotti & Luciano Milanesi

Authors
  1. Angelo Facchiano
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  2. Paola Festa
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  3. Anna Marabotti
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  4. Luciano Milanesi
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  5. Francesco Musacchia
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Editor information

Editors and Affiliations

  1. Department of Clinical Sciences and Community, University of Milan, via Vanzetti, 5, 20133, Milan, Italy

    Elia Biganzoli  & Federico Ambrogi  & 

  2. Dpto. de Lenguajes y Sistemas Informáticos (LSI), Universidad Politecnica de la Catalunya, C/Jordi Girona 1-3, Ed. Omega, 08034, Barcelona, Spain

    Alfredo Vellido

  3. Department of Mathematics and Information Sciences, University of Salerno, Via Ponte don Melillo, 84084, Fisciano, SA, Italy

    Roberto Tagliaferri

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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. https://doi.org/10.1007/978-3-642-35686-5_21

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  • DOI: https://doi.org/10.1007/978-3-642-35686-5_21

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-35685-8

  • Online ISBN: 978-3-642-35686-5

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