Dataset Information

The Spherical Evolutionary Multi-Objective (SEMO) Algorithm for Identifying Disease Multi-Locus SNP Interactions.

ABSTRACT: Single-nucleotide polymorphisms (SNPs), as disease-related biogenetic markers, are crucial in elucidating complex disease susceptibility and pathogenesis. Due to computational inefficiency, it is difficult to identify high-dimensional SNP interactions efficiently using combinatorial search methods, so the spherical evolutionary multi-objective (SEMO) algorithm for detecting multi-locus SNP interactions was proposed. The algorithm uses a spherical search factor and a feedback mechanism of excellent individual history memory to enhance the balance between search and acquisition. Moreover, a multi-objective fitness function based on the decomposition idea was used to evaluate the associations by combining two functions, K2-Score and LR-Score, as an objective function for the algorithm's evolutionary iterations. The performance evaluation of SEMO was compared with six state-of-the-art algorithms on a simulated dataset. The results showed that SEMO outperforms the comparative methods by detecting SNP interactions quickly and accurately with a shorter average run time. The SEMO algorithm was applied to the Wellcome Trust Case Control Consortium (WTCCC) breast cancer dataset and detected two- and three-point SNP interactions that were significantly associated with breast cancer, confirming the effectiveness of the algorithm. New combinations of SNPs associated with breast cancer were also identified, which will provide a new way to detect SNP interactions quickly and accurately.

SUBMITTER: Ren F

PROVIDER: S-EPMC10815643 | biostudies-literature | 2023 Dec

REPOSITORIES: biostudies-literature

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Publications

The Spherical Evolutionary Multi-Objective (SEMO) Algorithm for Identifying Disease Multi-Locus SNP Interactions.

Ren Fuxiang F Li Shiyin S Wen Zihao Z Liu Yidi Y Tang Deyu D

Genes 20231220 1

Single-nucleotide polymorphisms (SNPs), as disease-related biogenetic markers, are crucial in elucidating complex disease susceptibility and pathogenesis. Due to computational inefficiency, it is difficult to identify high-dimensional SNP interactions efficiently using combinatorial search methods, so the spherical evolutionary multi-objective (SEMO) algorithm for detecting multi-locus SNP interactions was proposed. The algorithm uses a spherical search factor and a feedback mechanism of excelle ...[more]

PMID: 38275593

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Project description:BackgroundFor non-invasive brain-computer interface systems (BCIs) with multiple electroencephalogram (EEG) channels, the key factor limiting their convenient application in the real world is how to perform reasonable channel selection while ensuring task accuracy, which can be modeled as a multi-objective optimization problem. Therefore, this paper proposed a two-objective problem model for the channel selection problem and introduced a domain knowledge-assisted multi-objective optimization algorithm (DK-MOEA) to solve the aforementioned problem.MethodsThe multi-objective optimization problem model was designed based on the channel connectivity matrix and comprises two objectives: one is the task accuracy and the other one can sensitively indicate the removal status of channels in BCIs. The proposed DK-MOEA adopted a two-space framework, consisting of the population space and the knowledge space. Furthermore, a knowledge-assisted update operator was introduced to enhance the search efficiency of the population space by leveraging the domain knowledge stored in the knowledge space.ResultsThe proposed two-objective problem model and DK-MOEA were tested on a fatigue detection task and four state-of-the-art multi-objective evolutionary algorithms were used for comparison. The experimental results indicated that the proposed algorithm achieved the best results among all the comparative algorithms for most cases by the Wilcoxon rank sum test at a significance level of 0.05. DK-MOEA was also compared with a version without the utilization of domain knowledge and the experimental results validated the effectiveness of the knowledge-assisted mutation operator. Moreover, the comparison between DK-MOEA and a traditional classification algorithm using all channels demonstrated that DK-MOEA can strike the balance between task accuracy and the number of selected channels.ConclusionThe formulated two-objective optimization model enabled the selection of a minimal number of channels without compromising classification accuracy. The utilization of domain knowledge improved the performance of DK-MOEA. By adopting the proposed two-objective problem model and DK-MOEA, a balance can be achieved between the number of the selected channels and the accuracy of the fatigue detection task. The methods proposed in this paper can reduce the complexity of subsequent data processing and enhance the convenience of practical applications.

Dataset Information

The Spherical Evolutionary Multi-Objective (SEMO) Algorithm for Identifying Disease Multi-Locus SNP Interactions.

Publications

The Spherical Evolutionary Multi-Objective (SEMO) Algorithm for Identifying Disease Multi-Locus SNP Interactions.

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