Modeling of gene regulatory networks with hybrid differential evolution and particle swarm optimization.
In the last decade, recurrent neural networks (RNNs) have attracted more efforts in inferring genetic regulatory networks (GRNs), using time series gene expression data from microarray experiments. This is critically important for revealing fundamental cellular processes, investigating gene functions, and understanding their relations. However, RNNs are well known for training difficulty. Traditional gradient descent-based methods are easily stuck in local minima and the computation of the derivatives is also not always possible. Here, the performance of three evolutionary-swarm computation technology-based methods, known as differential evolution (DE), particle swarm optimization (PSO), and the hybrid of DE and PSO (DEPSO), in training RNNs is investigated. Furthermore, the gene networks are reconstructed via the identification of the gene interactions, which are explained through corresponding connection weight matrices. The experimental results on two data sets studied in this paper demonstrate that the DEPSO algorithm performs better in RNN training. Also, the RNN-based model can provide meaningful insight in capturing the nonlinear dynamics of genetic networks and revealing genetic regulatory interactions.
Xu
Rui
R
Applied Computational Intelligence Laboratory, Department of Electrical and Computer Engineering, University of Missouri-Rolla, MO 65409, USA. rxu@umr.edu
Venayagamoorthy
Ganesh K
GK
Wunsch
Donald C
DC
D000818:Animals; D001185:Artificial Intelligence; D002678:Chimera; D019295:Computational Biology; D003198:Computer Simulation; D019143:Evolution, Molecular; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation / Q000235:genetics*; D053263:Gene Regulatory Networks / Q000235:genetics*; D005796:Genes / Q000235:genetics*; D006801:Humans; D008954:Models, Biological; D008967:Molecular Biology / Q000379:methods*; D016571:Neural Networks, Computer; D017711:Nonlinear Dynamics; D020411:Oligonucleotide Array Sequence Analysis; D010363:Pattern Recognition, Automated