A Hybrid Methodology for the Reverse Engineering of Gene Regulatory Networks

Abstract

In this work, a computational approach has been proposed based on the hybridisation of two modelling formalisms, recurrent neural networks and half-systems, for the reconstruction of gene regulatory networks from time-series gene expression datasets. To the best of our knowledge, the proposed hybridisation has not been attempted previously in this domain. Here, recurrent neural networks and half-systems have been hybridised to capture the underlying dynamics present in the temporal gene expression profiles. The motivation behind this work is to integrate the advantages of both the techniques in the proposed model such that the problem of reverse engineering of gene regulatory networks can be resolved more efficiently. Artificial bee colony optimisation has been used for the estimation of the model parameters. We have implemented the proposed hybrid methodology on the real-world experimental datasets (in vivo) of the SOS DNA Repair network of Escherichia coli. The obtained results are comparable to or better than that of other reverse engineering methodologies present in contemporary literature.