A graph spectrum based geometric biclustering algorithm

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review

7 Scopus Citations
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Detail(s)

Original languageEnglish
Pages (from-to)200-211
Journal / PublicationJournal of Theoretical Biology
Volume317
Publication statusPublished - 1 Jan 2013

Abstract

Biclustering is capable of performing simultaneous clustering on two dimensions of a data matrix and has many applications in pattern classification. For example, in microarray experiments, a subset of genes is co-expressed in a subset of conditions, and biclustering algorithms can be used to detect the coherent patterns in the data for further analysis of function. In this paper, we present a graph spectrum based geometric biclustering (GSGBC) algorithm. In the geometrical view, biclusters can be seen as different linear geometrical patterns in high dimensional spaces. Based on this, the modified Hough transform is used to find the Hough vector (HV) corresponding to sub-bicluster patterns in 2D spaces. A graph can be built regarding each HV as a node. The graph spectrum is utilized to identify the eigengroups in which the sub-biclusters are grouped naturally to produce larger biclusters. Through a comparative study, we find that the GSGBC achieves as good a result as GBC and outperforms other kinds of biclustering algorithms. Also, compared with the original geometrical biclustering algorithm, it reduces the computing time complexity significantly. We also show that biologically meaningful biclusters can be identified by our method from real microarray gene expression data. © 2012 Elsevier Ltd.

Research Area(s)

  • Geometric biclustering, Graph spectra, Hough transform, Microarray data analysis