Mining order-preserving submatrix based on charm for gene expression data

Zhijie Li; Xuhong Liao; Hua Jiang; Sha Liao; Qinglan Li; Li Liu

doi:10.1117/12.3009465

16 October 2023 Mining order-preserving submatrix based on charm for gene expression data

Zhijie Li, Xuhong Liao, Hua Jiang, Sha Liao, Qinglan Li, Li Liu

Proceedings Volume 12803, Fifth International Conference on Artificial Intelligence and Computer Science (AICS 2023); 128030E (2023) https://doi.org/10.1117/12.3009465
Event: 2023 5th International Conference on Artificial Intelligence and Computer Science (AICS 2023), 2023, Wuhan, China

Abstract

Order-preserving submatrix (OPSM) is an important qualitative biclustering method of gene expression data. OPSM first sorts the expression values of gene and replaces them with corresponding column labels, and then mines the local patterns of the column label sequence set, where some rows rise and fall together under some columns. This paper proposes an order-preserving subsequence mining method (Charm_Seq) based on the Charm algorithm, and Charm_Seq makes full use of Charm’s efficient Itemset-Tidset prefix search tree to mine frequent closed patterns of column label sequence set. Meanwhile, Charm_Cla can effectively improve classification performance by restoring frequent closed sequences to training samples. Experiments were conducted on actual gene expression datasets, and the experimental results verified the efficiency and effectiveness of this method.

(2023) Published by SPIE. Downloading of the abstract is permitted for personal use only.

Citation Download Citation

Zhijie Li, Xuhong Liao, Hua Jiang, Sha Liao, Qinglan Li, and Li Liu "Mining order-preserving submatrix based on charm for gene expression data", Proc. SPIE 12803, Fifth International Conference on Artificial Intelligence and Computer Science (AICS 2023), 128030E (16 October 2023); https://doi.org/10.1117/12.3009465

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KEYWORDS

Mining

Biological samples

Education and training

Image classification

Matrices

Genetic algorithms

Leukemia

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