Please use this identifier to cite or link to this item: http://hdl.handle.net/10397/30015
Title: Tumor clustering using nonnegative matrix factorization with gene selection
Authors: Zheng, CH
Huang, DS
Zhang, L 
Kong, XZ
Keywords: Clustering
Gene expression data
Independent component analysis (ICA)
Nonnegative matrix factorization (NMF)
Tumor
Issue Date: 2009
Publisher: Institute of Electrical and Electronics Engineers
Source: IEEE transactions on information technology in biomedicine, 2009, v. 13, no. 4, p. 599-607 How to cite?
Journal: IEEE transactions on information technology in biomedicine 
Abstract: Tumor clustering is becoming a powerful method in cancer class discovery. Nonnegative matrix factorization (NMF) has shown advantages over other conventional clustering techniques. Nonetheless, there is still considerable room for improving the performance of NMF. To this end, in this paper, gene selection and explicitly enforcing sparseness are introduced into the factorization process. Particularly, independent component analysis is employed to select a subset of genes so that the effect of irrelevant or noisy genes can be reduced. The NMF and its extensions, sparse NMF and NMF with sparseness constraint, are then used for tumor clustering on the selected genes. A series of elaborate experiments are performed by varying the number of clusters and the number of selected genes to evaluate the cooperation between different gene selection settings and NMF-based clustering. Finally, the experiments on three representative gene expression datasets demonstrated that the proposed scheme can achieve better clustering results.
URI: http://hdl.handle.net/10397/30015
ISSN: 1089-7771
DOI: 10.1109/TITB.2009.2018115
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