Biclustering with Alternating K-Means

Biclustering is the task of simultaneously clustering the rows and columns of the data matrix into different subgroups such that the rows and columns within a subgroup exhibit similar patterns. In this paper, we consider the case of producing block-diagonal biclusters. We provide a new formulation of the biclustering problem based on the idea of minimizing the empirical clustering risk. We develop and prove a consistency result with respect to the empirical clustering risk. Since the optimization problem is combinatorial in nature, finding the global minimum is computationally intractable. In light of this fact, we propose a simple and novel algorithm that finds a local minimum by alternating the use of an adapted version of the k-means clustering algorithm between columns and rows. We evaluate and compare the performance of our algorithm to other related biclustering methods on both simulated data and real-world gene expression data sets. The results demonstrate that our algorithm is able to detect meaningful structures in the data and outperform other competing biclustering methods in various settings and situations.