Non-negative matrix factorization by maximizing correntropy for cancer clustering

被引:97
作者
Wang, Jim Jing-Yan [1 ]
Wang, Xiaolei [1 ]
Gao, Xin [1 ,2 ]
机构
[1] King Abdullah Univ Sci & Technol, Comp Elect & Math Sci & Engn Div, Thuwal 239556900, Saudi Arabia
[2] King Abdullah Univ Sci & Technol, Computat Biosci Res Ctr, Thuwal 239556900, Saudi Arabia
来源
BMC BIOINFORMATICS | 2013年 / 14卷
关键词
GENE-EXPRESSION DATA; COMPREHENSIVE EVALUATION; CLASS DISCOVERY; CLASSIFICATION; PREDICTION; MODEL;
D O I
10.1186/1471-2105-14-107
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Background: Non-negative matrix factorization (NMF) has been shown to be a powerful tool for clustering gene expression data, which are widely used to classify cancers. NMF aims to find two non-negative matrices whose product closely approximates the original matrix. Traditional NMF methods minimize either the l(2) norm or the Kullback-Leibler distance between the product of the two matrices and the original matrix. Correntropy was recently shown to be an effective similarity measurement due to its stability to outliers or noise. Results: We propose a maximum correntropy criterion (MCC)-based NMF method (NMF-MCC) for gene expression data-based cancer clustering. Instead of minimizing the l(2) norm or the Kullback-Leibler distance, NMF-MCC maximizes the correntropy between the product of the two matrices and the original matrix. The optimization problem can be solved by an expectation conditional maximization algorithm. Conclusions: Extensive experiments on six cancer benchmark sets demonstrate that the
引用
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页数:11
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