Fast convex optimization for connectivity enforcement in gene regulatory network inference

Abstract

With the advent of microarrays, arose the need to analyze gene expression data. Tools for building gene regulation networks are indeed of high interest for regulatory relationship sketching and gene interaction prediction. Given all pairwise gene regulation information available, we propose to determine the presence of edges in the final gene regulatory network by adopting a convex optimization formulation. Our energy minimization strategy includes a regularization term accounting for the difference of connectivity of particular genes (i.e. transcription factors), and we employ proximal methods to compute the optimal solution. The resulting algorithm, called “Brane relax”, outperforms state-of-the-art methods while keeping a reduced computational cost.