Biclustering Gene Expressions Using Factor Graphs and the Max-Sum Algorithm

Abstract

Biclustering is an intrinsically challenging and highly complex problem, particularly studied in the biology field, where the goal is to simultaneously cluster genes and samples of an expression data matrix. In this paper we present a novel approach to gene expression biclustering by providing a binary Factor Graph formulation to such problem. In more detail, we reformulate biclustering as a sequential search for single biclusters and use an efficient optimization procedure based on the Max Sum algorithm. Such approach, drastically alleviates the scaling issues of previous approaches for biclustering based on Factor Graphs obtaining significantly more accurate results on synthetic datasets. A further analysis on two real-world datasets confirms the potentials of the proposed methodology when compared to alternative state of the art methods.