Clustering Nodes in Large-Scale Biological Networks Using External Memory Algorithms

  • Ahmed Shamsul Arefin
  • Mario Inostroza-Ponta
  • Luke Mathieson
  • Regina Berretta
  • Pablo Moscato
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7017)

Abstract

Novel analytical techniques have dramatically enhanced our understanding of many application domains including biological networks inferred from gene expression studies. However, there are clear computational challenges associated to the large datasets generated from these studies. The algorithmic solution of some NP-hard combinatorial optimization problems that naturally arise on the analysis of large networks is difficult without specialized computer facilities (i.e. supercomputers). In this work, we address the data clustering problem of large-scale biological networks with a polynomial-time algorithm that uses reasonable computing resources and is limited by the available memory. We have adapted and improved the MSTkNN graph partitioning algorithm and redesigned it to take advantage of external memory (EM) algorithms. We evaluate the scalability and performance of our proposed algorithm on a well-known breast cancer microarray study and its associated dataset.

Keywords

Data clustering external memory algorithms graph algorithms gene expression data analysis 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Ahmed Shamsul Arefin
    • 1
  • Mario Inostroza-Ponta
    • 2
  • Luke Mathieson
    • 3
  • Regina Berretta
    • 1
    • 4
  • Pablo Moscato
    • 1
    • 4
    • 5
  1. 1.Centre for Bioinformatics, Biomarker Discovery and Information-Based MedicineThe University of NewcastleCallaghanAustralia
  2. 2.Departamento de Ingeniería InformáticaUniversidad de Santiago de ChileChile
  3. 3.Department of Computing, Faculty of ScienceMacquarie UniversitySydneyAustralia
  4. 4.Hunter Medical Research InstituteInformation Based Medicine ProgramAustralia
  5. 5.ARC Centre of Excellence in BioinformaticsCallaghanAustralia

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