Reconstructing Gene Regulatory Network with Enhanced Particle Swarm Optimization (original) (raw)
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Applied Soft Computing, 2019
Particle Swarm Optimization (PSO) is a meta-heuristic approach based on swarm intelligence, which is inspired by the social behaviour of bird flocking or fish schooling. The main disadvantage of the basic PSO is that it suffers from premature convergence. To prevent the process of search from premature convergence as well as to improve the exploration and exploitation capability as a whole, here, in this paper, a modified variant, named Repository and Mutation based PSO (RMPSO) is proposed. In RMPSO variant, apart from applying five-staged successive mutation strategies for improving the swarm best as referred in Enhanced Leader PSO (ELPSO), two extra repositories have been introduced and maintained to store personal best and global best solutions having same fitness values. In each step, the personal and global best solutions are chosen randomly from their respective repositories which enhance exploration capability further, retaining the exploitation capability. The computational experiment on benchmark problem instances shows that in most of the cases, RMPSO performs better than other algorithms in terms of the statistical metrics taken into account. Moreover, the performance of the proposed algorithm remains consistent in most of the cases when the dimension of the problem is scaled up. RMPSO is further applied to a practical scenario: the reconstruction of Gene Regulatory Networks (GRN) based on Recurrent Neural Network (RNN) model. 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 set.
Neural Networks, 2007
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.
Intelligent Framework With Controlled Behavior for Gene Regulatory Network Reconstruction
International Journal of Information Retrieval Research, 2022
Gene Regulatory Networks (GRNs) are the pioneering methodology for finding new gene interactions getting insights of the biological processes using time series gene expression data. It remains a challenge to study the temporal nature of gene expression data that mimic complex non-linear dynamics of the network. In this paper, an intelligent framework of recurrent neural network (RNN) and swarm intelligence (SI) based Particle Swarm Optimization (PSO) with controlled behaviour has been proposed for the reconstruction of GRN from time-series gene expression data. A novel PSO algorithm enhanced by human cognition influenced by the ideology of Bhagavad Gita is employed for improved learning of RNN. RNN guided by the proposed algorithm simulates the nonlinear and dynamic gene interactions to a greater extent. The proposed method shows superior performance over traditional SI algorithms in searching biologically plausible candidate networks. The strength of the method is verified by analy...
A Hybrid Methodology for the Reverse Engineering of Gene Regulatory Networks
2020 IEEE Congress on Evolutionary Computation (CEC), 2020
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 ar...
Gene Regulatory Network Inference Using Prominent Swarm Intelligence Methods
2017
Genes are the basic blue print of life in an organism containing the physiological and behavioral characteristics. A gene regulatory network (GRN) is a set of genes, or parts of genes, that interact with each other to control a specific cell function. GRN inference is the reverse engineering approach to predict the biological network from the gene expression data. Biochemical system theory based S-System is a popular model in GRN inference and the model is defined with its different parameters. The task of S-System based GRN inference is its parameter estimation which is an optimization problem. Several studies employed Particle Swarm Optimization (PSO) and other pioneer optimization techniques to estimate S-System model. In this paper several prominent swarm intelligence (SI) techniques have been studied and adapted for S-System parameter estimation. They are Group Search Optimizer, Grey Wolf Optimizer and PSO. Proficiency of optimization techniques are compared to infer GRN from S...
2006
We present a novel algorithm that combines a recurrent neural network (RNN) and two swarm intelligence (SI) methods to infer a gene regulatory network (GRN) from time course gene expression data. The algorithm uses ant colony optimization (ACO) to identify the optimal architecture of an RNN, while the weights of the RNN are optimized using particle swarm optimization (PSO). Our goal is to construct an RNN whose response mimics gene expression data generated by time course DNA microarray experiments. We observed promising results in applying the proposed hybrid SI-RNN algorithm to infer networks of interaction from simulated and real-world gene expression data
BMC Bioinformatics, 2008
Background: Inferring gene regulatory networks from data requires the development of algorithms devoted to structure extraction. When only static data are available, gene interactions may be modelled by a Bayesian Network (BN) that represents the presence of direct interactions from regulators to regulees by conditional probability distributions. We used enhanced evolutionary algorithms to stochastically evolve a set of candidate BN structures and found the model that best fits data without prior knowledge.
Gene regulatory network model identification using artificial bee colony and swarm intelligence
2012 IEEE Congress on Evolutionary Computation, 2012
Gene association/interaction networks have complex structures that provide a better understanding of mechanisms at the molecular level that govern essential processes inside the cell. The interaction mechanisms are conventionally modeled by nonlinear dynamic systems of coupled differential equations (Ssystems) adhering to the power-law formalism. Our implementation adopts an S-system that is rich enough in structure to capture the dynamics of the gene regulatory networks (GRN) of interest. A comparison of three widely used population-based techniques, namely evolutionary algorithms (EAs), local best particle swarm optimization (PSO) with random topology, and artificial bee colony (ABC) are performed in this study to rapidly identify a solution to inverse problem of GRN reconstruction for understanding the dynamics of the underlying system. A simple yet effective modification of the ABC algorithm, shortly ABC* is proposed as well and tested on the GRN problem. Simulation results on two small-size and a medium size hypothetical gene regulatory networks confirms that the proposed ABC* is superior to all other search schemes studied here.
Reverse Engineering Gene Regulatory Networks with Various Machine Learning Methods
Wiley-VCH Verlag GmbH & Co. KGaA eBooks, 2008
Background: To infer gene regulatory networks from time series gene profiles, two important tasks that are related to biological systems must be undertaken. One task is to determine a valid network structure that has topological properties that can influence the network dynamics profoundly. The other task is to optimize the network parameters to minimize the accumulated discrepancy between the gene expression data and the values produced by the inferred network model. Though the above two tasks must be conducted simultaneously, most existing work addresses only one of the tasks. Results: We propose an iterative approach that couples parameter identification and parameter optimization techniques, to address the two tasks simultaneously during network inference. This approach first identifies the most influential parameters against internal perturbations; this identification is based on sensitivity measurements. Then, a hybrid GA-PSO optimization method infers parameters in accordance with their criticalities. The proposed approach has been applied to several datasets, including subsets of the SOS DNA repair system in E. coli, the Rat central nervous system (CNS), and the protein glycosylation system of yeast S. cerevisiae. The result and analysis show that our approach can infer solutions to satisfy both the requirements of network structure and network behavior. Conclusions: Network structure is an important though challenging issue to address in inferring sophisticated networks with biological details. In need of prior structural knowledge, we turn to measure parameter sensitivity instead to account for the network structure in an indirect way. By developing an integrated approach for considering both the network structure and behavior in the inference process, we can successfully infer critical gene interactions as well as valid time expression profiles.