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Convex and SemiNonnegative Matrix Factorizations
, 2008
"... We present several new variations on the theme of nonnegative matrix factorization (NMF). Considering factorizations of the form X = F GT, we focus on algorithms in which G is restricted to contain nonnegative entries, but allow the data matrix X to have mixed signs, thus extending the applicable ra ..."
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Cited by 112 (10 self)
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We present several new variations on the theme of nonnegative matrix factorization (NMF). Considering factorizations of the form X = F GT, we focus on algorithms in which G is restricted to contain nonnegative entries, but allow the data matrix X to have mixed signs, thus extending the applicable range of NMF methods. We also consider algorithms in which the basis vectors of F are constrained to be convex combinations of the data points. This is used for a kernel extension of NMF. We provide algorithms for computing these new factorizations and we provide supporting theoretical analysis. We also analyze the relationships between our algorithms and clustering algorithms, and consider the implications for sparseness of solutions. Finally, we present experimental results that explore the properties of these new methods.
Sparse nonnegative matrix factorizations via alternating nonnegativityconstrained least squares for microarray data analysis
 VOL. 23 NO. 12 2007, PAGES 1495–1502 BIOINFORMATICS
, 2007
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NONNEGATIVE MATRIX FACTORIZATION BASED ON ALTERNATING NONNEGATIVITY CONSTRAINED LEAST SQUARES AND ACTIVE SET METHOD
"... The nonnegative matrix factorization (NMF) determines a lower rank approximation of a ¢¤£¦¥¨§�©���� �� � matrix where an ������������������ � interger is given and nonnegativity is imposed on all components of the factors applied to numerous data analysis problems. In applications where the compone ..."
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Cited by 86 (7 self)
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The nonnegative matrix factorization (NMF) determines a lower rank approximation of a ¢¤£¦¥¨§�©���� �� � matrix where an ������������������ � interger is given and nonnegativity is imposed on all components of the factors applied to numerous data analysis problems. In applications where the components of the data are necessarily nonnegative such as chemical concentrations in experimental results or pixels in digital images, the NMF provides a more relevant interpretation of the results since it gives nonsubtractive combinations of nonnegative basis vectors. In this paper, we introduce an algorithm for the NMF based on alternating nonnegativity constrained least squares (NMF/ANLS) and the active set based fast algorithm for nonnegativity constrained least squares with multiple right hand side vectors, and discuss its convergence properties and a rigorous convergence criterion based on the KarushKuhnTucker (KKT) conditions. In addition, we also describe algorithms for sparse NMFs and regularized NMF. We show how we impose a sparsity constraint on one of the factors by �� �norm minimization and discuss its convergence properties. Our algorithms are compared to other commonly used NMF algorithms in the literature on several test data sets in terms of their convergence behavior. £�¥�§�©� � and � £�¥���©� �. The NMF has attracted much attention for over a decade and has been successfully
SVD based initialization: A head start for nonnegative matrix factorization
 PATTERN RECOGNITION
, 2007
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Fast Local Algorithms for Large Scale Nonnegative Matrix and Tensor Factorizations
, 2008
"... Nonnegative matrix factorization (NMF) and its extensions such as Nonnegative Tensor Factorization (NTF) have become prominent techniques for blind sources separation (BSS), analysis of image databases, data mining and other information retrieval and clustering applications. In this paper we propose ..."
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Cited by 49 (13 self)
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Nonnegative matrix factorization (NMF) and its extensions such as Nonnegative Tensor Factorization (NTF) have become prominent techniques for blind sources separation (BSS), analysis of image databases, data mining and other information retrieval and clustering applications. In this paper we propose a family of efficient algorithms for NMF/NTF, as well as sparse nonnegative coding and representation, that has many potential applications in computational neuroscience, multisensory processing, compressed sensing and multidimensional data analysis. We have developed a class of optimized local algorithms which are referred to as Hierarchical Alternating Least Squares (HALS) algorithms. For these purposes, we have performed sequential constrained minimization on a set of squared Euclidean distances. We then extend this approach to robust cost functions using the Alpha and Beta divergences and derive flexible update rules. Our algorithms are locally stable and work well for NMFbased blind source separation (BSS) not only for the overdetermined case but also for an underdetermined (overcomplete) case (i.e., for a system which has less sensors than sources) if data are sufficiently sparse. The NMF learning rules are extended and generalized for Nth order nonnegative tensor factorization (NTF). Moreover, these algorithms can be tuned to different noise statistics by adjusting a single parameter. Extensive experimental results confirm the accuracy and computational performance of the developed algorithms, especially, with usage of multilayer hierarchical NMF approach [3].
The relationships among various nonnegative matrix factorization methods for clustering
 In ICDM
, 2006
"... The nonnegative matrix factorization (NMF) has been shown recently to be useful for clustering. Various extensions of NMF have also been proposed. In this paper we present an overview and theoretically analyze the relationships among them. In addition, we clarify previously unaddressed issues, such ..."
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Cited by 48 (10 self)
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The nonnegative matrix factorization (NMF) has been shown recently to be useful for clustering. Various extensions of NMF have also been proposed. In this paper we present an overview and theoretically analyze the relationships among them. In addition, we clarify previously unaddressed issues, such as NMF normalization, cluster posterior probabilty, and NMF algoritm convergence rate. Experiments are also conducted to empirically evaluate and compare various factorization methods.
Fast newtontype methods for the least squares nonnegative matrix approximation problem
 Statistical Analysis and Data Mining
, 2008
"... Nonnegative Matrix Approximation is an effective matrix decomposition technique that has proven to be useful for a wide variety of applications ranging from document analysis and image processing to bioinformatics. There exist a few algorithms for nonnegative matrix approximation (NNMA), for example ..."
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Cited by 45 (6 self)
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Nonnegative Matrix Approximation is an effective matrix decomposition technique that has proven to be useful for a wide variety of applications ranging from document analysis and image processing to bioinformatics. There exist a few algorithms for nonnegative matrix approximation (NNMA), for example, Lee & Seung’s multiplicative updates, alternating least squares, and certain gradient descent based procedures. All of these procedures suffer from either slow convergence, numerical instabilities, or at worst, theoretical unsoundness. In this paper we present new and improved algorithms for the leastsquares NNMA problem, which are not only theoretically wellfounded, but also overcome many of the deficiencies of other methods. In particular, we use nondiagonal gradient scaling to obtain rapid convergence. Our methods provide numerical results superior to both Lee & Seung’s method as well to the alternating least squares (ALS) heuristic, which is known to work well in some situations but has no theoretical guarantees (Berry et al. 2006). Our approach extends naturally to include regularization and boxconstraints, without sacrificing convergence guarantees. We present experimental results on both synthetic and realworld datasets to demonstrate the superiority of our methods, in terms of better approximations as well as efficiency.
Hierarchical ALS Algorithms for Nonnegative Matrix and 3D Tensor Factorization
 In: Independent Component Analysis, ICA07
"... Abstract. In the paper we present new Alternating Least Squares (ALS) algorithms for Nonnegative Matrix Factorization (NMF) and their extensions to 3D Nonnegative Tensor Factorization (NTF) that are robust in the presence of noise and have many potential applications, including multiway Blind Sourc ..."
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Cited by 43 (7 self)
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Abstract. In the paper we present new Alternating Least Squares (ALS) algorithms for Nonnegative Matrix Factorization (NMF) and their extensions to 3D Nonnegative Tensor Factorization (NTF) that are robust in the presence of noise and have many potential applications, including multiway Blind Source Separation (BSS), multisensory or multidimensional data analysis, and nonnegative neural sparse coding. We propose to use local cost functions whose simultaneous or sequential (one by one) minimization leads to a very simple ALS algorithm which works under some sparsity constraints both for an underdetermined (a system which has less sensors than sources) and overdetermined model. The extensive experimental results confirm the validity and high performance of the developed algorithms, especially with usage of the multilayer hierarchical NMF. Extension of the proposed algorithm to
The discrete basis problem
, 2005
"... We consider the Discrete Basis Problem, which can be described as follows: given a collection of Boolean vectors find a collection of k Boolean basis vectors such that the original vectors can be represented using disjunctions of these basis vectors. We show that the decision version of this problem ..."
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Cited by 41 (13 self)
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We consider the Discrete Basis Problem, which can be described as follows: given a collection of Boolean vectors find a collection of k Boolean basis vectors such that the original vectors can be represented using disjunctions of these basis vectors. We show that the decision version of this problem is NPcomplete and that the optimization version cannot be approximated within any finite ratio. We also study two variations of this problem, where the Boolean basis vectors must be mutually otrhogonal. We show that the other variation is closely related with the wellknown Metric kmedian Problem in Boolean space. To solve these problems, two algorithms will be presented. One is designed for the variations mentioned above, and it is solely based on solving the kmedian problem, while another is a heuristic intended to solve the general Discrete Basis Problem. We will also study the results of extensive experiments made with these two algorithms with both synthetic and realworld data. The results are twofold: with the synthetic data, the algorithms did rather well, but with the realworld data the results were not as good.