title: Regularized Non-Negative Matrix Factorization for Identifying Differentially Expressed Genes and Clustering Samples: A Survey.
abstract: Non-negative Matrix Factorization (NMF), a classical method for dimensionality reduction, has been applied in many fields. It is based on the idea that negative numbers are physically meaningless in various data-processing tasks. Apart from its contribution to conventional data analysis, the recent overwhelming interest in NMF is due to its newly discovered ability to solve challenging data mining and machine learning problems, especially in relation to gene expression data. This survey paper mainly focuses on research examining the application of NMF to identify differentially expressed genes and to cluster samples, and the main NMF models, properties, principles, and algorithms with its various generalizations, extensions, and modifications are summarized. The experimental results demonstrate the performance of the various NMF algorithms in identifying differentially expressed genes and clustering samples.
authors.forename: Jin-Xing
authors.initials: JX
authors.lastname: Liu
authors.forename: Dong
authors.initials: D
authors.lastname: Wang
authors.forename: Ying-Lian
authors.initials: YL
authors.lastname: Gao
authors.forename: Chun-Hou
authors.initials: CH
authors.lastname: Zheng
authors.forename: Yong
authors.initials: Y
authors.lastname: Xu
authors.forename: Jiguo
authors.initials: J
authors.lastname: Yu
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D006801:Humans; D000069550:Machine Learning; D015999:Multivariate Analysis; D009369:Neoplasms / Q000235:genetics / Q000378:metabolism