Title: Assessing the quality of biclusters using fuzzy biclustering index

Authors: Nishchal Kumar Verma; Esha Dutta; Yan Cui

Addresses: Department of Electrical Engineering, Indian Institute of Technology Kanpur, Kanpur, India ' Department of Electronics and Telecommunication Engineering, Jadavpur University, Kolkata, India ' Department of Microbiology Immunology and Biochemistry, Center for Integrative and Translational Genomics, University of Tennessee Health Science Center, Memphis, TN 38163, USA

Abstract: Several algorithms are proposed in the literature for extracting local patterns from a large data matrix. This technique of data mining is known as biclustering. Each of the biclustering algorithms is specialised in extracting different kinds of biclusters. Some algorithms detect equal biclusters, whereas some identify scaled biclusters (Madeira et al., 2004). For any practical database, since we are not aware of the biclusters present in it, we are not sure of the biclustering algorithm to be used. In such a scenario, it is important to define metrics to compare the quality of the extracted biclusters and hence the quality of the biclustering algorithm. In this paper, we have defined novel measures of Hausdorff distance between biclusters and global silhouette index for estimating the quality of biclusters extracted by the existing algorithms. We have also combined these metrics with the proportion of enriched biclusters extracted and defined an overall index defined as the Fuzzy Biclustering Index (FBI) to compare the various algorithms. For a given data set, higher is the FBI, better is the biclustering algorithm.

Keywords: bicluster quality; biclusters; gene enrichment; gene expression data; global silhouette index; Hausdorff distance; Jaccard index; p-value; fuzzy biclustering index; fuzzy logic; data mining; bioinformatics.

DOI: 10.1504/IJDMB.2016.078145

International Journal of Data Mining and Bioinformatics, 2016 Vol.15 No.4, pp.291 - 311

Received: 17 Mar 2016
Accepted: 21 Mar 2016
Published online: 04 Aug 2016 *

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