Journal ArticleDOI
Recurrent neural network-based modeling of gene regulatory network using elephant swarm water search algorithm
TLDR
A new metaheuristic namely Elephant Swarm Water Search Algorithm (ESWSA) to infer Gene Regulatory Network (GRN) is proposed, mainly based on the water search strategy of intelligent and social elephants during drought, utilizing the different types of communication techniques.Abstract:
Correct inference of genetic regulations inside a cell from the biological database like time series microarray data is one of the greatest challenges in post genomic era for biologists and researchers. Recurrent Neural Network (RNN) is one of the most popular and simple approach to model the dynamics as well as to infer correct dependencies among genes. Inspired by the behavior of social elephants, we propose a new metaheuristic namely Elephant Swarm Water Search Algorithm (ESWSA) to infer Gene Regulatory Network (GRN). This algorithm is mainly based on the water search strategy of intelligent and social elephants during drought, utilizing the different types of communication techniques. Initially, the algorithm is tested against benchmark small and medium scale artificial genetic networks without and with presence of different noise levels and the efficiency was observed in term of parametric error, minimum fitness value, execution time, accuracy of prediction of true regulation, etc. Next, the proposed algorithm is tested against the real time gene expression data of Escherichia Coli SOS Network and results were also compared with others state of the art optimization methods. The experimental results suggest that ESWSA is very efficient for GRN inference problem and performs better than other methods in many ways.read more
Citations
More filters
Journal ArticleDOI
Repository and Mutation based Particle Swarm Optimization (RMPSO): A new PSO variant applied to reconstruction of Gene Regulatory Network
TL;DR: RMPSO is applied to a practical scenario: the reconstruction of Gene Regulatory Networks (GRN) based on Recurrent Neural Network (RNN) model and the experimental results ensure that the RMPSO performs better than the state-of-the-art methods in the synthetic gene data set (gold standard) as well as real gene data data set.
Journal ArticleDOI
Modeling of photovoltaic systems using Modified Elephant Swarm Water Search Algorithm
TL;DR: Results show the efficiency of MESWSA algorithm for I-V characteristics of solar modules at different operating conditions can serve as a new alternative metaheuristic for parameter estimation of solar cells/PV modules.
Journal ArticleDOI
Modeling of liquid flow control process using improved versions of elephant swarm water search algorithm
TL;DR: In this work, three different improved versions of original elephant swarm water search algorithm (ESWSA) is proposed and tested against the present problem of liquid flow control and ESWSA is found to be best efficient algorithm with respect to success rate and computational time.
Journal ArticleDOI
Modified Half-System Based Method for Reverse Engineering of Gene Regulatory Networks
TL;DR: This work has proposed a novel methodology for reverse engineering of gene regulatory networks based on a new technique: half-system, which uses half the number of parameters compared to S-systems and thus significantly reduce the computational complexity.
Journal ArticleDOI
Metaheuristic Based Parametric Optimization of TIG Welded Joint
TL;DR: In this article, the authors identify the proper combination of input parameters in TIG welding of martensitic stainless steel AISI 420 and identify a critical operating region in terms of maximum UTS and Ductility.
References
More filters
Journal ArticleDOI
Neural network model of gene expression
TL;DR: Artificial neural networks are used as a model of the dynamics of gene expression and the significance of the regulatory effect of one gene product on the expression of other genes of the system is defined by a weight matrix.
Journal ArticleDOI
Inference of Genetic Regulatory Networks with Recurrent Neural Network Models Using Particle Swarm Optimization
TL;DR: Zhang et al. as mentioned in this paper proposed a particle swarm optimization (PSO) based approach to infer genetic regulatory networks from time series gene expression data, which can provide meaningful insights in understanding the nonlinear dynamics of the gene expression time series and revealing potential regulatory interactions between genes.
Journal ArticleDOI
Framework for a protein ontology.
Darren A. Natale,Cecilia N. Arighi,Winona C. Barker,Judith A. Blake,Ti-Cheng Chang,Zhang-Zhi Hu,Hongfang Liu,Barry Smith,Cathy H. Wu +8 more
TL;DR: The initial development of the PR otein O ntology (PRO) is described, illustrated using human and mouse proteins involved in the transforming growth factor-beta and bone morphogenetic protein signaling pathways.
Journal ArticleDOI
Elephant behaviour and conservation: social relationships, the effects of poaching, and genetic tools for management
TL;DR: By comparing studies from populations that have experienced a range of poaching intensities, it is found that human activities have a large effect on elephant behaviour and genetic structure, and genetic tools to census populations or gather forensic information are almost always more accurate than non‐genetic alternatives.
Journal ArticleDOI
A Swarm Intelligence Framework for Reconstructing Gene Networks: Searching for Biologically Plausible Architectures
TL;DR: Results demonstrate the relative advantage of utilizing problem-specific knowledge regarding biologically plausible structural properties of gene networks over conducting a problem-agnostic search in the vast space of network architectures.