Title: A modified harmony search method for biclustering microarray gene expression data

Authors: R. Balamurugan; A.M. Natarajan; K. Premalatha

Addresses: Department of Computer Science and Engineering, Bannari Amman Institute of Technology, Sathyamangalam, Erode 638401, Tamil Nadu, India ' Department of Computer Science and Engineering, Bannari Amman Institute of Technology, Sathyamangalam, Erode 638401, Tamil Nadu, India ' Department of Computer Science and Engineering, Bannari Amman Institute of Technology, Sathyamangalam, Erode 638401, Tamil Nadu, India

Abstract: Microarray experiments generate vast amounts of data, leading to new requirements and challenges for bioinformatics. The crucial step in considering gene expression data is to discover a group of genes that have similar patterns. Biclustering is a two-dimensional clustering problem where the genes and samples are grouped simultaneously. Latest research showed that biclustering has a great potential in finding marker genes that are associated with certain tissues or diseases. Here, we present an efficient biclustering algorithm called Modified Harmony Search (MHS) method. The MHS algorithm includes a step for generating the new solution by using levy flight. Levy flight increases the diversity of the solutions of harmony search (HS) algorithm and the Pitch Adjusting Rate (PAR) is changed dynamically to escape from local optima. To know the performance of the MHS, it is applied on various benchmark optimisation functions and the benchmark gene expression data sets. The experimental results show that the MHS outperforms HS in optimisation functions and biclustering problems. Also, this work determines the biological relevance of the biclusters with Gene Ontology in terms of function, process and component.

Keywords: biclustering; gene expression data; gene ontology; harmony search; Levy flight; pitch adjusting rate; microarrays; bioinformatics.

DOI: 10.1504/IJDMB.2016.082205

International Journal of Data Mining and Bioinformatics, 2016 Vol.16 No.4, pp.269 - 289

Received: 05 May 2016
Accepted: 24 Nov 2016
Published online: 12 Feb 2017 *

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