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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.
Abstract: In this paper, we investigate the problem of reverse engineering the topology of gene regulatory networks from temporal gene expression data. We adopt a computational intelligence approach comprising swarm intelligence techniques, namely particle swarm optimization (PSO) and ant colony optimization (ACO). In addition, the recurrent neural network (RNN) formalism is employed for modeling the dynamical behavior of gene regulatory systems. More specifically, ACO is used for searching the discrete space of network architectures and PSO for searching the corresponding continuous space of RNN model parameters. We propose a novel solution construction process in the context of ACO for generating biologically plausible candidate architectures. The objective is to concentrate the search effort into areas of the structure space that contain architectures which are feasible in terms of their topological resemblance to real-world networks. The proposed framework is initially applied to the reconstruction of a small artificial network that has previously been studied in the context of gene network reverse engineering. Subsequently, we consider an artificial data set with added noise for reconstructing a subnetwork of the genetic interaction network of S. cerevisiae (yeast). Finally, the framework is applied to a real-world data set for reverse engineering the SOS response system of the bacterium Escherichia coli. 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.

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Citations
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Journal ArticleDOI
TL;DR: This work presents coagSODA, a CUDA-powered computational tool that was purposely developed for the analysis of a large mechanistic model of the blood coagulation cascade, defined according to both mass-action kinetics and Hill functions, and shows that GPU-accelerated parallel simulations of this model can increase the computational performances up to a 181× speedup compared to the corresponding sequential simulations.
Abstract: The introduction of general-purpose Graphics Processing Units (GPUs) is boosting scientific applications in Bioinformatics, Systems Biology, and Computational Biology. In these fields, the use of high-performance computing solutions is motivated by the need of performing large numbers of in silico analysis to study the behavior of biological systems in different conditions, which necessitate a computing power that usually overtakes the capability of standard desktop computers. In this work we present coagSODA, a CUDA-powered computational tool that was purposely developed for the analysis of a large mechanistic model of the blood coagulation cascade (BCC), defined according to both mass-action kinetics and Hill functions. coagSODA allows the execution of parallel simulations of the dynamics of the BCC by automatically deriving the system of ordinary differential equations and then exploiting the numerical integration algorithm LSODA. We present the biological results achieved with a massive exploration of perturbed conditions of the BCC, carried out with one-dimensional and bi-dimensional parameter sweep analysis, and show that GPU-accelerated parallel simulations of this model can increase the computational performances up to a 181× speedup compared to the corresponding sequential simulations.

210 citations

Journal ArticleDOI
TL;DR: This paper formulates this gait generation task as a constrained multiobjective optimization problem and solves this problem through an AMO-CACO-based evolutionary learning approach.
Abstract: This paper proposes the optimization of a fully connected recurrent neural network (FCRNN) using advanced multiobjective continuous ant colony optimization (AMO-CACO) for the multiobjective gait generation of a biped robot (the NAO). The FCRNN functions as a central pattern generator and is optimized to generate angles of the hip roll and pitch, the knee pitch, and the ankle pitch and roll. The performance of the FCRNN-generated gait is evaluated according to the walking speed, trajectory straightness, oscillations of the body in the pitch and yaw directions, and walking posture, subject to the basic constraints that the robot cannot fall down and must walk forward. This paper formulates this gait generation task as a constrained multiobjective optimization problem and solves this problem through an AMO-CACO-based evolutionary learning approach. The AMO-CACO finds Pareto optimal solutions through ant-path selection and sampling operations by introducing an accumulated rank for the solutions in each single-objective function into solution sorting to improve learning performance. Simulations are conducted to verify the AMO-CACO-based FCRNN gait generation performance through comparisons with different multiobjective optimization algorithms. Selected software-designed Pareto optimal FCRNNs are then applied to control the gait of a real NAO robot.

58 citations


Cites methods from "A Swarm Intelligence Framework for ..."

  • ...The optimization of RNNs using genetic algorithms (GAs) [7], [12]–[15], particle swarm optimization (PSO) [8], [16], [17], or their hybrid [18] have been proposed....

    [...]

Journal ArticleDOI
TL;DR: The ability of the proposed algorithm to predict the presence of regulatory interactions between genes, their directionality and their states is demonstrated and high false positive values were discovered by the GRN prediction methods.

52 citations

Journal ArticleDOI
TL;DR: It is shown how CI techniques including neural networks, restricted Boltzmann machine, deep belief network, fuzzy logic, rough sets, evolutionary algorithms (EA), genetic algorithms (GA), swarm intelligence, artificial immune systems and support vector machines, could be successfully employed to tackle various problems such as gene expression clustering and classification.

49 citations

Journal ArticleDOI
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.

40 citations

References
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Proceedings ArticleDOI
06 Aug 2002
TL;DR: A concept for the optimization of nonlinear functions using particle swarm methodology is introduced, and the evolution of several paradigms is outlined, and an implementation of one of the paradigm is discussed.
Abstract: A concept for the optimization of nonlinear functions using particle swarm methodology is introduced. The evolution of several paradigms is outlined, and an implementation of one of the paradigms is discussed. Benchmark testing of the paradigm is described, and applications, including nonlinear function optimization and neural network training, are proposed. The relationships between particle swarm optimization and both artificial life and genetic algorithms are described.

35,104 citations

Journal ArticleDOI
15 Oct 1999-Science
TL;DR: A model based on these two ingredients reproduces the observed stationary scale-free distributions, which indicates that the development of large networks is governed by robust self-organizing phenomena that go beyond the particulars of the individual systems.
Abstract: Systems as diverse as genetic networks or the World Wide Web are best described as networks with complex topology. A common property of many large networks is that the vertex connectivities follow a scale-free power-law distribution. This feature was found to be a consequence of two generic mechanisms: (i) networks expand continuously by the addition of new vertices, and (ii) new vertices attach preferentially to sites that are already well connected. A model based on these two ingredients reproduces the observed stationary scale-free distributions, which indicates that the development of large networks is governed by robust self-organizing phenomena that go beyond the particulars of the individual systems.

33,771 citations

Journal ArticleDOI
TL;DR: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
Abstract: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is de- scribed that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression. The output is displayed graphically, conveying the clustering and the underlying expression data simultaneously in a form intuitive for biologists. We have found in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function, and we find a similar tendency in human data. Thus patterns seen in genome-wide expression experiments can be inter- preted as indications of the status of cellular processes. Also, coexpression of genes of known function with poorly charac- terized or novel genes may provide a simple means of gaining leads to the functions of many genes for which information is not available currently.

16,371 citations

Journal ArticleDOI
01 Feb 1996
TL;DR: It is shown how the ant system (AS) can be applied to other optimization problems like the asymmetric traveling salesman, the quadratic assignment and the job-shop scheduling, and the salient characteristics-global data structure revision, distributed communication and probabilistic transitions of the AS.
Abstract: An analogy with the way ant colonies function has suggested the definition of a new computational paradigm, which we call ant system (AS). We propose it as a viable new approach to stochastic combinatorial optimization. The main characteristics of this model are positive feedback, distributed computation, and the use of a constructive greedy heuristic. Positive feedback accounts for rapid discovery of good solutions, distributed computation avoids premature convergence, and the greedy heuristic helps find acceptable solutions in the early stages of the search process. We apply the proposed methodology to the classical traveling salesman problem (TSP), and report simulation results. We also discuss parameter selection and the early setups of the model, and compare it with tabu search and simulated annealing using TSP. To demonstrate the robustness of the approach, we show how the ant system (AS) can be applied to other optimization problems like the asymmetric traveling salesman, the quadratic assignment and the job-shop scheduling. Finally we discuss the salient characteristics-global data structure revision, distributed communication and probabilistic transitions of the AS.

11,224 citations

Journal ArticleDOI
TL;DR: This paper analyzes a particle's trajectory as it moves in discrete time, then progresses to the view of it in continuous time, leading to a generalized model of the algorithm, containing a set of coefficients to control the system's convergence tendencies.
Abstract: The particle swarm is an algorithm for finding optimal regions of complex search spaces through the interaction of individuals in a population of particles. This paper analyzes a particle's trajectory as it moves in discrete time (the algebraic view), then progresses to the view of it in continuous time (the analytical view). A five-dimensional depiction is developed, which describes the system completely. These analyses lead to a generalized model of the algorithm, containing a set of coefficients to control the system's convergence tendencies. Some results of the particle swarm optimizer, implementing modifications derived from the analysis, suggest methods for altering the original algorithm in ways that eliminate problems and increase the ability of the particle swarm to find optima of some well-studied test functions.

8,287 citations