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An Improved Opposition-Based Learning Particle Swarm Optimization for the Detection of SNP-SNP Interactions.

ABSTRACT: SNP-SNP interactions have been receiving increasing attention in understanding the mechanism underlying susceptibility to complex diseases. Though many works have been done for the detection of SNP-SNP interactions, the algorithmic development is still ongoing. In this study, an improved opposition-based learning particle swarm optimization (IOBLPSO) is proposed for the detection of SNP-SNP interactions. Highlights of IOBLPSO are the introduction of three strategies, namely, opposition-based learning, dynamic inertia weight, and a postprocedure. Opposition-based learning not only enhances the global explorative ability, but also avoids premature convergence. Dynamic inertia weight allows particles to cover a wider search space when the considered SNP is likely to be a random one and converges on promising regions of the search space while capturing a highly suspected SNP. The postprocedure is used to carry out a deep search in highly suspected SNP sets. Experiments of IOBLPSO are performed on both simulation data sets and a real data set of age-related macular degeneration, results of which demonstrate that IOBLPSO is promising in detecting SNP-SNP interactions. IOBLPSO might be an alternative to existing methods for detecting SNP-SNP interactions.

SUBMITTER: Shang J

PROVIDER: S-EPMC4509494 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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An Improved Opposition-Based Learning Particle Swarm Optimization for the Detection of SNP-SNP Interactions.

Shang Junliang J Sun Yan Y Li Shengjun S Liu Jin-Xing JX Zheng Chun-Hou CH Zhang Junying J

BioMed research international 20150705

SNP-SNP interactions have been receiving increasing attention in understanding the mechanism underlying susceptibility to complex diseases. Though many works have been done for the detection of SNP-SNP interactions, the algorithmic development is still ongoing. In this study, an improved opposition-based learning particle swarm optimization (IOBLPSO) is proposed for the detection of SNP-SNP interactions. Highlights of IOBLPSO are the introduction of three strategies, namely, opposition-based lea ...[more]

PMID: 26236727

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Project description:This research paper develops a novel hybrid approach, called hybrid particle swarm optimization-teaching-learning-based optimization (hPSO-TLBO), by combining two metaheuristic algorithms to solve optimization problems. The main idea in hPSO-TLBO design is to integrate the exploitation ability of PSO with the exploration ability of TLBO. The meaning of "exploitation capabilities of PSO" is the ability of PSO to manage local search with the aim of obtaining possible better solutions near the obtained solutions and promising areas of the problem-solving space. Also, "exploration abilities of TLBO" means the ability of TLBO to manage the global search with the aim of preventing the algorithm from getting stuck in inappropriate local optima. hPSO-TLBO design methodology is such that in the first step, the teacher phase in TLBO is combined with the speed equation in PSO. Then, in the second step, the learning phase of TLBO is improved based on each student learning from a selected better student that has a better value for the objective function against the corresponding student. The algorithm is presented in detail, accompanied by a comprehensive mathematical model. A group of benchmarks is used to evaluate the effectiveness of hPSO-TLBO, covering various types such as unimodal, high-dimensional multimodal, and fixed-dimensional multimodal. In addition, CEC 2017 benchmark problems are also utilized for evaluation purposes. The optimization results clearly demonstrate that hPSO-TLBO performs remarkably well in addressing the benchmark functions. It exhibits a remarkable ability to explore and exploit the search space while maintaining a balanced approach throughout the optimization process. Furthermore, a comparative analysis is conducted to evaluate the performance of hPSO-TLBO against twelve widely recognized metaheuristic algorithms. The evaluation of the experimental findings illustrates that hPSO-TLBO consistently outperforms the competing algorithms across various benchmark functions, showcasing its superior performance. The successful deployment of hPSO-TLBO in addressing four engineering challenges highlights its effectiveness in tackling real-world applications.

Dataset Information

An Improved Opposition-Based Learning Particle Swarm Optimization for the Detection of SNP-SNP Interactions.

Publications

An Improved Opposition-Based Learning Particle Swarm Optimization for the Detection of SNP-SNP Interactions.

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