Literature DB >> 25821345

A unified statistical approach to non-negative matrix factorization and probabilistic latent semantic indexing.

Karthik Devarajan1, Guoli Wang2, Nader Ebrahimi3.   

Abstract

Non-negative matrix factorization (NMF) is a powerful machine learning method for decomposing a high-dimensional nonnegative matrix V into the product of two nonnegative matrices, W and H, such that V ∼ W H. It has been shown to have a parts-based, sparse representation of the data. NMF has been successfully applied in a variety of areas such as natural language processing, neuroscience, information retrieval, image processing, speech recognition and computational biology for the analysis and interpretation of large-scale data. There has also been simultaneous development of a related statistical latent class modeling approach, namely, probabilistic latent semantic indexing (PLSI), for analyzing and interpreting co-occurrence count data arising in natural language processing. In this paper, we present a generalized statistical approach to NMF and PLSI based on Renyi's divergence between two non-negative matrices, stemming from the Poisson likelihood. Our approach unifies various competing models and provides a unique theoretical framework for these methods. We propose a unified algorithm for NMF and provide a rigorous proof of monotonicity of multiplicative updates for W and H. In addition, we generalize the relationship between NMF and PLSI within this framework. We demonstrate the applicability and utility of our approach as well as its superior performance relative to existing methods using real-life and simulated document clustering data.

Entities:  

Keywords:  Biomedical informatics; EM algorithm; Nonnegative matrix factorization; Probabilistic latent semantic indexing; Renyi's divergence; λ-log-likelihood

Year:  2015        PMID: 25821345      PMCID: PMC4371760          DOI: 10.1007/s10994-014-5470-z

Source DB:  PubMed          Journal:  Mach Learn        ISSN: 0885-6125            Impact factor:   2.940


  13 in total

1.  Learning the parts of objects by non-negative matrix factorization.

Authors:  D D Lee; H S Seung
Journal:  Nature       Date:  1999-10-21       Impact factor: 49.962

2.  Metagenes and molecular pattern discovery using matrix factorization.

Authors:  Jean-Philippe Brunet; Pablo Tamayo; Todd R Golub; Jill P Mesirov
Journal:  Proc Natl Acad Sci U S A       Date:  2004-03-11       Impact factor: 11.205

3.  Accelerated multiplicative updates and hierarchical ALS algorithms for nonnegative matrix factorization.

Authors:  Nicolas Gillis; François Glineur
Journal:  Neural Comput       Date:  2011-12-14       Impact factor: 2.026

4.  A generalized divergence measure for nonnegative matrix factorization.

Authors:  Raul Kompass
Journal:  Neural Comput       Date:  2007-03       Impact factor: 2.026

5.  Non-negative matrix factorization algorithms modeling noise distributions within the exponential family.

Authors:  Vincent C K Cheung; Matthew C Tresch
Journal:  Conf Proc IEEE Eng Med Biol Soc       Date:  2005

6.  Projected gradient methods for nonnegative matrix factorization.

Authors:  Chih-Jen Lin
Journal:  Neural Comput       Date:  2007-10       Impact factor: 2.026

7.  Non-negative matrix factorization of gene expression profiles: a plug-in for BRB-ArrayTools.

Authors:  Qihao Qi; Yingdong Zhao; MingChung Li; Richard Simon
Journal:  Bioinformatics       Date:  2009-01-08       Impact factor: 6.937

8.  A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules.

Authors:  Shihua Zhang; Qingjiao Li; Juan Liu; Xianghong Jasmine Zhou
Journal:  Bioinformatics       Date:  2011-07-01       Impact factor: 6.937

9.  LS-NMF: a modified non-negative matrix factorization algorithm utilizing uncertainty estimates.

Authors:  Guoli Wang; Andrew V Kossenkov; Michael F Ochs
Journal:  BMC Bioinformatics       Date:  2006-03-28       Impact factor: 3.169

Review 10.  Nonnegative matrix factorization: an analytical and interpretive tool in computational biology.

Authors:  Karthik Devarajan
Journal:  PLoS Comput Biol       Date:  2008-07-25       Impact factor: 4.475

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  3 in total

1.  A Hybrid Algorithm for Non-negative Matrix Factorization Based on Symmetric Information Divergence.

Authors:  Karthik Devarajan; Nader Ebrahimi; Ehsan Soofi
Journal:  Proceedings (IEEE Int Conf Bioinformatics Biomed)       Date:  2015-12-17

2.  A Quasi-Likelihood Approach to Nonnegative Matrix Factorization.

Authors:  Karthik Devarajan; Vincent C K Cheung
Journal:  Neural Comput       Date:  2016-06-27       Impact factor: 2.026

3.  Using Dynamic Multi-Task Non-Negative Matrix Factorization to Detect the Evolution of User Preferences in Collaborative Filtering.

Authors:  Bin Ju; Yuntao Qian; Minchao Ye; Rong Ni; Chenxi Zhu
Journal:  PLoS One       Date:  2015-08-13       Impact factor: 3.240

  3 in total

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