A Framework for Mining Coherent Patterns Using Particle Swarm Optimization based Biclustering

Abstract

Abstract-High-throughput microarray technologies have enabled development of robust biclustering algorithms which are capable of discovering relevant local patterns in gene expression datasets wherein subset of genes shows coherent expression patterns under subset of experimental conditions. In this work, we have proposed an algorithm that combines biclustering technique with Particle Swarm Optimization (PSO) structure in order to extract significant biological relevant patterns from such dataset. This algorithm comprises of two phases for extracting biclusters, one is the seed finding phase and another is the seed growing phase. In the seed finding phase, gene clustering and condition clustering is done separately on the gene expression data matrix and the result obtained from both the clustering is combined to form small tightly bound submatrices and those submatrices are used as seeds for the algorithm, which are having the Mean Squared Residue (MSR) value less than the defined threshold value. In the seed growing phase, the number of genes and the number of conditions are added in these seeds to enlarge it by using the PSO structure. It is observed that by using our technique in Yeast Saccharomyces Cerevisiae cell cycle expression dataset, significant biclusters are obtained which are having large volume and less MSR value in comparison to other biclustering algorithms.