Two-stage feature selection for classification of gene expression data based on an improved Salp Swarm Algorithm

Xiwen Qin; Shuang Zhang; Dongmei Yin; Dongxue Chen; Xiaogang Dong; Xiwen Qin; Shuang Zhang; Dongmei Yin; Dongxue Chen; Xiaogang Dong

doi:10.3934/mbe.2022641

Mathematical Biosciences and Engineering

2022, Volume 19, Issue 12: 13747-13781. doi: 10.3934/mbe.2022641

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Research article

Two-stage feature selection for classification of gene expression data based on an improved Salp Swarm Algorithm

School of Mathematics and Statistics, Changchun University of Technology, Changchun 130012, China

Academic Editor: Jinzhi Lei

Received: 31 July 2022 Revised: 03 September 2022 Accepted: 07 September 2022 Published: 19 September 2022

Microarray technology has developed rapidly in recent years, producing a large number of ultra-high dimensional gene expression data. However, due to the huge sample size and dimension proportion of gene expression data, it is very challenging work to screen important genes from gene expression data. For small samples of high-dimensional biomedical data, this paper proposes a two-stage feature selection framework combining Wrapper, embedding and filtering to avoid the curse of dimensionality. The proposed framework uses weighted gene co-expression network (WGCNA), random forest and minimal redundancy maximal relevance (mRMR) for first stage feature selection. In the second stage, a new gene selection method based on the improved binary Salp Swarm Algorithm is proposed, which combines machine learning methods to adaptively select feature subsets suitable for classification algorithms. Finally, the classification accuracy is evaluated using six methods: lightGBM, RF, SVM, XGBoost, MLP and KNN. To verify the performance of the framework and the effectiveness of the proposed algorithm, the number of genes selected and the classification accuracy was compared with the other five intelligent optimization algorithms. The results show that the proposed framework achieves an accuracy equal to or higher than other advanced intelligent algorithms on 10 datasets, and achieves an accuracy of over 97.6% on all 10 datasets. This shows that the method proposed in this paper can solve the feature selection problem related to high-dimensional data, and the proposed framework has no data set limitation, and it can be applied to other fields involving feature selection.
- high-dimensional data,
- feature selection,
- swarm intelligence optimization algorithm,
- gene expression data,
- cancer classification
Citation: Xiwen Qin, Shuang Zhang, Dongmei Yin, Dongxue Chen, Xiaogang Dong. Two-stage feature selection for classification of gene expression data based on an improved Salp Swarm Algorithm[J]. Mathematical Biosciences and Engineering, 2022, 19(12): 13747-13781. doi: 10.3934/mbe.2022641

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Abstract

Microarray technology has developed rapidly in recent years, producing a large number of ultra-high dimensional gene expression data. However, due to the huge sample size and dimension proportion of gene expression data, it is very challenging work to screen important genes from gene expression data. For small samples of high-dimensional biomedical data, this paper proposes a two-stage feature selection framework combining Wrapper, embedding and filtering to avoid the curse of dimensionality. The proposed framework uses weighted gene co-expression network (WGCNA), random forest and minimal redundancy maximal relevance (mRMR) for first stage feature selection. In the second stage, a new gene selection method based on the improved binary Salp Swarm Algorithm is proposed, which combines machine learning methods to adaptively select feature subsets suitable for classification algorithms. Finally, the classification accuracy is evaluated using six methods: lightGBM, RF, SVM, XGBoost, MLP and KNN. To verify the performance of the framework and the effectiveness of the proposed algorithm, the number of genes selected and the classification accuracy was compared with the other five intelligent optimization algorithms. The results show that the proposed framework achieves an accuracy equal to or higher than other advanced intelligent algorithms on 10 datasets, and achieves an accuracy of over 97.6% on all 10 datasets. This shows that the method proposed in this paper can solve the feature selection problem related to high-dimensional data, and the proposed framework has no data set limitation, and it can be applied to other fields involving feature selection.

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