Extreme learning machines for reverse engineering of gene regulatory networks from expression time series

• Published in: Bioinformatics 2018-04, Vol.34 (7), p.1253-1260
• Main Authors: Rubiolo, M, Milone, D H, Stegmayer, G
• Format: Article
• Language: English
• Subjects: Computational Biology - methods; Escherichia coli - genetics; Gene Expression Regulation; Gene Regulatory Networks; Models, Genetic; Saccharomyces cerevisiae - genetics; Software; Supervised Machine Learning
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btx730

Abstract Motivation The reconstruction of gene regulatory networks (GRNs) from genes profiles has a growing interest in bioinformatics for understanding the complex regulatory mechanisms in cellular systems. GRNs explicitly represent the cause-effect of regulation among a group of genes and its reconstruction is today a challenging computational problem. Several methods were proposed, but most of them require different input sources to provide an acceptable prediction. Thus, it is a great challenge to reconstruct a GRN only from temporal gene expression data. Results Extreme Learning Machine (ELM) is a new supervised neural model that has gained interest in the last years because of its higher learning rate and better performance than existing supervised models in terms of predictive power. This work proposes a novel approach for GRNs reconstruction in which ELMs are used for modeling the relationships between gene expression time series. Artificial datasets generated with the well-known benchmark tool used in DREAM competitions were used. Real datasets were used for validation of this novel proposal with well-known GRNs underlying the time series. The impact of increasing the size of GRNs was analyzed in detail for the compared methods. The results obtained confirm the superiority of the ELM approach against very recent state-of-the-art methods in the same experimental conditions. Availability and implementation The web demo can be found at http://sinc.unl.edu.ar/web-demo/elm-grnnminer/. The source code is available at https://sourceforge.net/projects/sourcesinc/files/elm-grnnminer. Supplementary information Supplementary data are available at Bioinformatics online.