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J Biomed Inform. 2017 Mar;67:59-68. doi: 10.1016/j.jbi.2017.02.007. Epub 2017 Feb 13.

Gene selection for tumor classification using neighborhood rough sets and entropy measures.

Author information

1
College of Computer & Information Engineering, Xiamen University of Technology, Xiamen 361024, China.
2
Department of Urinary Surgery, The Third Xiamen Hospital of Fujian University of Traditional Chinese Medicine, Xiamen 316000, China. Electronic address: zunjun998@163.com.
3
Department of Urinary Surgery, The Third Xiamen Hospital of Fujian University of Traditional Chinese Medicine, Xiamen 316000, China.
4
School of Computer & Software, Nanjing University of Information Science & Technology, Nanjing 210044, China.

Abstract

With the development of bioinformatics, tumor classification from gene expression data becomes an important useful technology for cancer diagnosis. Since a gene expression data often contains thousands of genes and a small number of samples, gene selection from gene expression data becomes a key step for tumor classification. Attribute reduction of rough sets has been successfully applied to gene selection field, as it has the characters of data driving and requiring no additional information. However, traditional rough set method deals with discrete data only. As for the gene expression data containing real-value or noisy data, they are usually employed by a discrete preprocessing, which may result in poor classification accuracy. In this paper, we propose a novel gene selection method based on the neighborhood rough set model, which has the ability of dealing with real-value data whilst maintaining the original gene classification information. Moreover, this paper addresses an entropy measure under the frame of neighborhood rough sets for tackling the uncertainty and noisy of gene expression data. The utilization of this measure can bring about a discovery of compact gene subsets. Finally, a gene selection algorithm is designed based on neighborhood granules and the entropy measure. Some experiments on two gene expression data show that the proposed gene selection is an effective method for improving the accuracy of tumor classification.

KEYWORDS:

Entropy measure; Gene expression data; Gene selection; Neighborhood rough sets; Tumor classification

PMID:
28215562
DOI:
10.1016/j.jbi.2017.02.007
[Indexed for MEDLINE]
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