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Proceedings ArticleDOI

A swarm intelligence based scheme for reduction of false positives in inferred gene regulatory networks

24 Jul 2016-pp 40-47

TL;DR: This work has proposed a novel scheme, based on different swarm intelligence algorithms, to reduce the number of inferred false regulations in gene regulatory networks, and the obtained results suggest that the proposed methodology can reduce theNumber of false predictions, significantly, without using any supplementary biological information for larger gene Regulatory networks.

AbstractA gene regulatory network reveals the regulatory relationships among genes at a cellular level. The accurate reconstruction of such networks using computational tools, from time series genetic expression data, is crucial to the understanding of the proper functioning of a living organism. Investigations in this domain focused mainly on the identification of as many true regulations as possible. This has somewhat overshadowed the reduction of false predictions in inferred networks. In the present investigation, we have proposed a novel scheme, based on different swarm intelligence algorithms, to reduce the number of inferred false regulations. We have first applied our proposed methodology on the much studied, benchmark experimental datasets of the DNA SOS repair network of Escherichia Coli. Subsequently, we have experimented upon a larger, in silico network extracted from the GeneNetWeaver database. The obtained results suggest that the proposed methodology can reduce the number of false predictions, significantly, without using any supplementary biological information for larger gene regulatory networks.

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Citations
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Journal ArticleDOI
TL;DR: A simple model is presented to infer GRNs, using RNA-seq based coexpression map provided by GeneFriends database, and a graph-based database tool is used to create regulatory network, showing that it is convenient to use graph database tools to work with regulatory networks instead of developing a new model from scratch.
Abstract: Gene expressions are controlled by a series of processes known as Gene Regulation, and their abstract mapping is represented by Gene Regulatory Network (GRN) which is a descriptive model of gene interactions. Reverse engineering GRNs can reveal the complexity of gene interactions whose comprehension can lead to several other details. RNA-seq data provides better measurement of gene expressions, however it is difficult to infer GRNs using it because of its discreteness. Multiple other methods have already been proposed to infer GRN using RNA-seq data, but these methodologies are difficult to grasp. In this paper, a simple model is presented to infer GRNs, using RNA-seq based coexpression map provided by GeneFriends database, and a graph-based database tool is used to create regulatory network. The obtained results show that it is convenient to use graph database tools to work with regulatory networks instead of developing a new model from scratch.

Cites background or methods from "A swarm intelligence based scheme f..."

  • ...The functional circuitry of all living organisms is formed by genes [1]and synergistic actions between inter related genes is the reason of all biological reactions inside a cell....

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  • ...Based on FA, PSO, BA-PSO which are swarm intelligence techniques, RNN formalism is used to investigate reverse engineering of GRNs from time series microarray datasets [1]....

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References
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Proceedings ArticleDOI
04 Oct 1995
TL;DR: The optimization of nonlinear functions using particle swarm methodology is described and implementations of two paradigms are discussed and compared, including a recently developed locally oriented paradigm.
Abstract: The optimization of nonlinear functions using particle swarm methodology is described. Implementations of two paradigms are discussed and compared, including a recently developed locally oriented paradigm. Benchmark testing of both paradigms is described, and applications, including neural network training and robot task learning, are proposed. Relationships between particle swarm optimization and both artificial life and evolutionary computation are reviewed.

13,173 citations


"A swarm intelligence based scheme f..." refers background or methods in this paper

  • ...PSO is one of the simplest, robust, effective, and easy-tocode swarm intelligence algorithms [3]....

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  • ...The proposed scheme is based on the amalgamation of three swarm intelligence algorithms: particle swarm optimization (PSO) algorithm [3], a bat algorithm (BA) [4] inspired version of the same, and firefly algorithm [5]....

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Journal ArticleDOI
TL;DR: A framework is developed to explore the connection between effective optimization algorithms and the problems they are solving and a number of "no free lunch" (NFL) theorems are presented which establish that for any algorithm, any elevated performance over one class of problems is offset by performance over another class.
Abstract: A framework is developed to explore the connection between effective optimization algorithms and the problems they are solving. A number of "no free lunch" (NFL) theorems are presented which establish that for any algorithm, any elevated performance over one class of problems is offset by performance over another class. These theorems result in a geometric interpretation of what it means for an algorithm to be well suited to an optimization problem. Applications of the NFL theorems to information-theoretic aspects of optimization and benchmark measures of performance are also presented. Other issues addressed include time-varying optimization problems and a priori "head-to-head" minimax distinctions between optimization algorithms, distinctions that result despite the NFL theorems' enforcing of a type of uniformity over all algorithms.

8,548 citations


"A swarm intelligence based scheme f..." refers background in this paper

  • ...The No Free Lunch (NFL) theorem [9] affirms that no particular metaheuristic is the best suited for all categories of optimization problems....

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Posted Content
Abstract: Metaheuristic algorithms such as particle swarm optimization, firefly algorithm and harmony search are now becoming powerful methods for solving many tough optimization problems. In this paper, we propose a new metaheuristic method, the Bat Algorithm, based on the echolocation behaviour of bats. We also intend to combine the advantages of existing algorithms into the new bat algorithm. After a detailed formulation and explanation of its implementation, we will then compare the proposed algorithm with other existing algorithms, including genetic algorithms and particle swarm optimization. Simulations show that the proposed algorithm seems much superior to other algorithms, and further studies are also discussed.

3,035 citations

Book ChapterDOI
23 Apr 2010
Abstract: Metaheuristic algorithms such as particle swarm optimization, firefly algorithm and harmony search are now becoming powerful methods for solving many tough optimization problems. In this paper, we propose a new metaheuristic method, the Bat Algorithm, based on the echolocation behaviour of bats. We also intend to combine the advantages of existing algorithms into the new bat algorithm. After a detailed formulation and explanation of its implementation, we will then compare the proposed algorithm with other existing algorithms, including genetic algorithms and particle swarm optimization. Simulations show that the proposed algorithm seems much superior to other algorithms, and further studies are also discussed.

2,669 citations

Journal ArticleDOI
Abstract: Reconstructing gene regulatory networks from high-throughput data is a long-standing challenge. Through the Dialogue on Reverse Engineering Assessment and Methods (DREAM) project, we performed a comprehensive blind assessment of over 30 network inference methods on Escherichia coli, Staphylococcus aureus, Saccharomyces cerevisiae and in silico microarray data. We characterize the performance, data requirements and inherent biases of different inference approaches, and we provide guidelines for algorithm application and development. We observed that no single inference method performs optimally across all data sets. In contrast, integration of predictions from multiple inference methods shows robust and high performance across diverse data sets. We thereby constructed high-confidence networks for E. coli and S. aureus, each comprising ~1,700 transcriptional interactions at a precision of ~50%. We experimentally tested 53 previously unobserved regulatory interactions in E. coli, of which 23 (43%) were supported. Our results establish community-based methods as a powerful and robust tool for the inference of transcriptional gene regulatory networks.

1,251 citations