A novel parallel feature rank aggregation algorithm for gene selection applied to microarray data classification

IF 2.6 4区 生物学 Q2 BIOLOGY Computational Biology and Chemistry Pub Date : 2024-08-24 DOI:10.1016/j.compbiolchem.2024.108182
Imtisenla Longkumer, Dilwar Hussain Mazumder
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Abstract

Microarray data often comprises numerous genes, yet not all genes are relevant for predicting cancer. Feature selection becomes a crucial step to reduce the high dimensionality in these kinds of data. While no single feature selection method consistently outperforms others across diverse domains, the combination of multiple feature selectors or rankers tends to produce more effective results compared to relying on a single ranker alone. However, this approach can be computationally expensive, particularly when handling a large quantity of features. Hence, this paper presents a parallel feature rank aggregation that utilizes borda count as the rank aggregator. The concept of vertically partitioning the data along feature space was adapted to ease the parallel execution of the aggregation task. Features were selected based on the final aggregated rank list, and their classification performances were evaluated. The model’s execution time was also observed across multiple worker nodes of the cluster. The experiment was conducted on six benchmark microarray datasets. The results show the capability of the proposed distributed framework compared to the sequential version in all the cases. It also illustrated the improved accuracy performance of the proposed method and its ability to select a minimal number of genes.

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应用于微阵列数据分类的新型基因选择并行特征等级聚合算法
微阵列数据通常包含大量基因,但并非所有基因都与癌症预测相关。特征选择成为降低这类数据高维度的关键步骤。虽然在不同领域中,没有一种特征选择方法能够始终优于其他方法,但与单独依赖一种排序器相比,多种特征选择器或排序器的组合往往能产生更有效的结果。然而,这种方法的计算成本很高,尤其是在处理大量特征时。因此,本文提出了一种并行特征排序聚合方法,利用波达计数作为排序聚合器。为了便于并行执行聚合任务,本文采用了沿特征空间垂直划分数据的概念。根据最终聚合的等级列表选择特征,并对其分类性能进行评估。此外,还观察了模型在集群多个工作节点上的执行时间。实验在六个基准微阵列数据集上进行。结果表明,在所有情况下,与顺序版本相比,所提出的分布式框架都具有很强的能力。它还说明了所提出的方法提高了准确性,并能选择最少数量的基因。
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来源期刊
Computational Biology and Chemistry
Computational Biology and Chemistry 生物-计算机:跨学科应用
CiteScore
6.10
自引率
3.20%
发文量
142
审稿时长
24 days
期刊介绍: Computational Biology and Chemistry publishes original research papers and review articles in all areas of computational life sciences. High quality research contributions with a major computational component in the areas of nucleic acid and protein sequence research, molecular evolution, molecular genetics (functional genomics and proteomics), theory and practice of either biology-specific or chemical-biology-specific modeling, and structural biology of nucleic acids and proteins are particularly welcome. Exceptionally high quality research work in bioinformatics, systems biology, ecology, computational pharmacology, metabolism, biomedical engineering, epidemiology, and statistical genetics will also be considered. Given their inherent uncertainty, protein modeling and molecular docking studies should be thoroughly validated. In the absence of experimental results for validation, the use of molecular dynamics simulations along with detailed free energy calculations, for example, should be used as complementary techniques to support the major conclusions. Submissions of premature modeling exercises without additional biological insights will not be considered. Review articles will generally be commissioned by the editors and should not be submitted to the journal without explicit invitation. However prospective authors are welcome to send a brief (one to three pages) synopsis, which will be evaluated by the editors.
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