bLARS: An Algorithm to Infer Gene Regulatory Networks

TLDR: This work proposes a new regression based method named bLARS that permits a variety of regulatory interactions from a predefined but otherwise arbitrary family of functions and offers the best performance among currently available similar algorithms.

Abstract: Inferring gene regulatory networks (GRNs) from high-throughput gene-expression data is an important and challenging problem in systems biology. Several existing algorithms formulate GRN inference as a regression problem. The available regression based algorithms are based on the assumption that all regulatory interactions are linear. However, nonlinear transcription regulation mechanisms are common in biology. In this work, we propose a new regression based method named bLARS that permits a variety of regulatory interactions from a predefined but otherwise arbitrary family of functions. On three DREAM benchmark datasets, namely gene expression data from E. coli, Yeast, and a synthetic data set, bLARS outperforms state-of-the-art algorithms in the terms of the overall score . On the individual networks, bLARS offers the best performance among currently available similar algorithms, namely algorithms that do not use perturbation information and are not meta-algorithms. Moreover, the presented approach can also be utilized for general feature selection problems in domains other than biology, provided they are of a similar structure.