Nonnegative Matrix and Tensor Factorization T
This book provides a broad survey of models and efficient algorithms for Nonnegative Matrix Factorization (NMF). This includes NMFs various extensions and modifications, especially Nonnegative Tensor Factorizations (NTF) and Nonnegative Tucker Decompositions (NTD). NMF/NTF and their extensions are increasingly used as tools in signal and image processing, and data analysis, having garnered interest due to their capability to provide new insights and relevant information about the complex latent relationships in experimental data sets. It is suggested that NMF can provide meaningful components with physical interpretations; for example, in bioinformatics, NMF and its extensions have been successfully applied to gene expression, sequence analysis, the functional characterization of genes, clustering and text mining. As such, the authors focus on the algorithms that are most useful in practice, looking at the fastest, most robust, and suitable for large-scale models. Key features: Acts as a single source reference guide to NMF, collating information that is widely dispersed in current literature, including the authors own recently developed techniques in the subject area. Uses generalized cost functions such as Bregman, Alpha and Beta divergences, to present practical implementations of several types of robust algorithms, in particular Multiplicative, Alternating Least Squares, Projected Gradient and Quasi Newton algorithms. Provides a comparative analysis of the different methods in order to identify approximation error and complexity. Includes pseudo codes and optimized MATLAB source codes for almost all algorithms presented in the book. The increasing interest in nonnegative matrix and tensor factorizations, as well as decompositions and sparse representation of data, will ensure that this book is essential reading for engineers, scientists, researchers, industry practitioners and graduate students across signal and image processing; neuroscience; data mining and data analysis; computer science; bioinformatics; speech processing; biomedical engineering; and multimedia.
Projected Gradient Methods for Nonnegative Matrix Factorization
Nonnegative matrix factorization (NMF) can be formulated as a minimization problem with bound constraints. Although bound-constrained optimization has been studied extensively in both theory and practice, so far no study has formally applied its techniques to NMF. In this letter, we propose two projected gradient methods for NMF, both of which exhibit strong optimization properties. We discuss efficient implementations and demonstrate that one of the proposed methods converges faster than the popular multiplicative update approach. A simple Matlab code is also provided.
Nonnegative Matrix and Tensor Factorizations - Applications to Exploratory Multi-way Data Analysis and Blind Source Separation
This book provides a broad survey of models and efficient algorithms for Nonnegative Matrix Factorization (NMF). This includes NMFs various extensions and modifications, especially Nonnegative Tensor Factorizations (NTF) and Nonnegative Tucker Decompositions (NTD). NMF/NTF and their extensions are increasingly used as tools in signal and image processing, and data analysis, having garnered interest due to their capability to provide new insights and relevant information about the complex latent relationships in experimental data sets. It is suggested that NMF can provide meaningful components with physical interpretations; for example, in bioinformatics, NMF and its extensions have been successfully applied to gene expression, sequence analysis, the functional characterization of genes, clustering and text mining. As such, the authors focus on the algorithms that are most useful in practice, looking at the fastest, most robust, and suitable for large-scale models. Key features: Acts as a single source reference guide to NMF, collating information that is widely dispersed in current literature, including the authors own recently developed techniques in the subject area. Uses generalized cost functions such as Bregman, Alpha and Beta divergences, to present practical implementations of several types of robust algorithms, in particular Multiplicative, Alternating Least Squares, Projected Gradient and Quasi Newton algorithms. Provides a comparative analysis of the different methods in order to identify approximation error and complexity. Includes pseudo codes and optimized MATLAB source codes for almost all algorithms presented in the book. The increasing interest in nonnegative matrix and tensor factorizations, as well as decompositions and sparse representation of data, will ensure that this book is essential reading for engineers, scientists, researchers, industry practitioners and graduate students across signal and image processing; neuroscience; data mining and data analysis; computer science; bioinformatics; speech processing; biomedical engineering; and multimedia.
Nonnegative Matrix Factorization with the Itakura-Saito Divergence: With Application to Music Analysis
This letter presents theoretical, algorithmic, and experimental results about nonnegative matrix factorization (NMF) with the Itakura-Saito (IS) divergence. We describe how IS-NMF is underlaid by a well-defined statistical model of superimposed gaussian components and is equivalent to maximum likelihood estimation of variance parameters. This setting can accommodate regularization constraints on the factors through Bayesian priors. In particular, inverse-gamma and gamma Markov chain priors are considered in this work. Estimation can be carried out using a space-alternating generalized expectation-maximization (SAGE) algorithm; this leads to a novel type of NMF algorithm, whose convergence to a stationary point of the IS cost function is guaranteed. We also discuss the links between the IS divergence and other cost functions used in NMF, in particular, the Euclidean distance and the generalized Kullback-Leibler (KL) divergence. As such, we describe how IS-NMF can also be performed using a gradient multiplicative algorithm (a standard algorithm structure in NMF) whose convergence is observed in practice, though not proven. Finally, we report a furnished experimental comparative study of Euclidean-NMF, KL-NMF, and IS-NMF algorithms applied to the power spectrogram of a short piano sequence recorded in real conditions, with various initializations and model orders. Then we show how IS-NMF can successfully be employed for denoising and upmix (mono to stereo conversion) of an original piece of early jazz music. These experiments indicate that IS-NMF correctly captures the semantics of audio and is better suited to the representation of music signals than NMF with the usual Euclidean and KL costs.
Graph Regularized Nonnegative Matrix Factorization for Data Representation
Matrix factorization techniques have been frequently applied in information retrieval, computer vision, and pattern recognition. Among them, Nonnegative Matrix Factorization (NMF) has received considerable attention due to its psychological and physiological interpretation of naturally occurring data whose representation may be parts based in the human brain. On the other hand, from the geometric perspective, the data is usually sampled from a low-dimensional manifold embedded in a high-dimensional ambient space. One then hopes to find a compact representation,which uncovers the hidden semantics and simultaneously respects the intrinsic geometric structure. In this paper, we propose a novel algorithm, called Graph Regularized Nonnegative Matrix Factorization (GNMF), for this purpose. In GNMF, an affinity graph is constructed to encode the geometrical information and we seek a matrix factorization, which respects the graph structure. Our empirical study shows encouraging results of the proposed algorithm in comparison to the state-of-the-art algorithms on real-world problems.
Graph Regularized Nonnegative Matrix Factorization for Data Representation.
Matrix factorization techniques have been frequently applied in information retrieval, computer vision, and pattern recognition. Among them, Nonnegative Matrix Factorization (NMF) has received considerable attention due to its psychological and physiological interpretation of naturally occurring data whose representation may be parts based in the human brain. On the other hand, from the geometric perspective, the data is usually sampled from a low-dimensional manifold embedded in a high-dimensional ambient space. One then hopes to find a compact representation,which uncovers the hidden semantics and simultaneously respects the intrinsic geometric structure. In this paper, we propose a novel algorithm, called Graph Regularized Nonnegative Matrix Factorization (GNMF), for this purpose. In GNMF, an affinity graph is constructed to encode the geometrical information and we seek a matrix factorization, which respects the graph structure. Our empirical study shows encouraging results of the proposed algorithm in comparison to the state-of-the-art algorithms on real-world problems.
A flexible R package for nonnegative matrix factorization
BackgroundNonnegative Matrix Factorization (NMF) is an unsupervised learning technique that has been applied successfully in several fields, including signal processing, face recognition and text mining. Recent applications of NMF in bioinformatics have demonstrated its ability to extract meaningful information from high-dimensional data such as gene expression microarrays. Developments in NMF theory and applications have resulted in a variety of algorithms and methods. However, most NMF implementations have been on commercial platforms, while those that are freely available typically require programming skills. This limits their use by the wider research community.ResultsOur objective is to provide the bioinformatics community with an open-source, easy-to-use and unified interface to standard NMF algorithms, as well as with a simple framework to help implement and test new NMF methods. For that purpose, we have developed a package for the R/BioConductor platform. The package ports public code to R, and is structured to enable users to easily modify and/or add algorithms. It includes a number of published NMF algorithms and initialization methods and facilitates the combination of these to produce new NMF strategies. Commonly used benchmark data and visualization methods are provided to help in the comparison and interpretation of the results.ConclusionsThe NMF package helps realize the potential of Nonnegative Matrix Factorization, especially in bioinformatics, providing easy access to methods that have already yielded new insights in many applications. Documentation, source code and sample data are available from CRAN.
Overlapping community detection at scale: a nonnegative matrix factorization approach
Network communities represent basic structures for understanding the organization of real-world networks. A community (also referred to as a module or a cluster) is typically thought of as a group of nodes with more connections amongst its members than between its members and the remainder of the network. Communities in networks also overlap as nodes belong to multiple clusters at once. Due to the difficulties in evaluating the detected communities and the lack of scalable algorithms, the task of overlapping community detection in large networks largely remains an open problem. In this paper we present BIGCLAM (Cluster Affiliation Model for Big Networks), an overlapping community detection method that scales to large networks of millions of nodes and edges. We build on a novel observation that overlaps between communities are densely connected. This is in sharp contrast with present community detection methods which implicitly assume that overlaps between communities are sparsely connected and thus cannot properly extract overlapping communities in networks. In this paper, we develop a model-based community detection algorithm that can detect densely overlapping, hierarchically nested as well as non-overlapping communities in massive networks. We evaluate our algorithm on 6 large social, collaboration and information networks with ground-truth community information. Experiments show state of the art performance both in terms of the quality of detected communities as well as in speed and scalability of our algorithm.
On the Equivalence of Nonnegative Matrix Factorization and Spectral Clustering
Current nonnegative matrix factorization (NMF) deals with X = FG type. We provide a systematic analysis and extensions of NMF to the symmetric W = HH , and the weighted W = HSH . We show that (1) W = HH is equivalent to Kernel K-means clustering and the Laplacian-based spectral clustering. (2) X = FG is equivalent to simultaneous clustering of rows and columns of a bipartite graph. Algorithms are given for computing these symmetric NMFs.
Multichannel Nonnegative Matrix Factorization in Convolutive Mixtures for Audio Source Separation
We consider inference in a general data-driven object-based model of multichannel audio data, assumed generated as a possibly underdetermined convolutive mixture of source signals. We work in the short-time Fourier transform (STFT) domain, where convolution is routinely approximated as linear instantaneous mixing in each frequency band. Each source STFT is given a model inspired from nonnegative matrix factorization (NMF) with the Itakura-Saito divergence, which underlies a statistical model of superimposed Gaussian components. We address estimation of the mixing and source parameters using two methods. The first one consists of maximizing the exact joint likelihood of the multichannel data using an expectation-maximization (EM) algorithm. The second method consists of maximizing the sum of individual likelihoods of all channels using a multiplicative update algorithm inspired from NMF methodology. Our decomposition algorithms are applied to stereo audio source separation in various settings, covering blind and supervised separation, music and speech sources, synthetic instantaneous and convolutive mixtures, as well as professionally produced music recordings. Our EM method produces competitive results with respect to state-of-the-art as illustrated on two tasks from the international Signal Separation Evaluation Campaign (SiSEC 2008).
Multi-View Clustering via Joint Nonnegative Matrix Factorization
Many real-world datasets are comprised of different representations or views which often provide information complementary to each other. To integrate information from multiple views in the unsupervised setting, multiview clustering algorithms have been developed to cluster multiple views simultaneously to derive a solution which uncovers the common latent structure shared by multiple views. In this paper, we propose a novel NMFbased multi-view clustering algorithm by searching for a factorization that gives compatible clustering solutions across multiple views. The key idea is to formulate a joint matrix factorization process with the constraint that pushes clustering solution of each view towards a common consensus instead of fixing it directly. The main challenge is how to keep clustering solutions across different views meaningful and comparable. To tackle this challenge, we design a novel and effective normalization strategy inspired by the connection between NMF and PLSA. Experimental results on synthetic and several real datasets demonstrate the effectiveness of our approach.
Nonnegative Matrix Factorization Based on Alternating Nonnegativity Constrained Least Squares and Active Set Method
Nonnegative matrix factorization (NMF) determines a lower rank approximation of a matrix $A \in \mathbb{R}^{m \times n} \approx WH$ where an integer $k \ll \min(m,n)$ is given and nonnegativity is imposed on all components of the factors $W \in \mathbb{R}^{m \times k}$ and $H \in \mathbb{R}^{k \times n}$. NMF has attracted much attention for over a decade and has been successfully 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, 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 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 we discuss its convergence properties and a rigorous convergence criterion based on the Karush-Kuhn-Tucker (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 $L_1$-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.
Coupled Nonnegative Matrix Factorization Unmixing for Hyperspectral and Multispectral Data Fusion
Coupled nonnegative matrix factorization (CNMF) unmixing is proposed for the fusion of low-spatial-resolution hyperspectral and high-spatial-resolution multispectral data to produce fused data with high spatial and spectral resolutions. Both hyperspectral and multispectral data are alternately unmixed into end member and abundance matrices by the CNMF algorithm based on a linear spectral mixture model. Sensor observation models that relate the two data are built into the initialization matrix of each NMF unmixing procedure. This algorithm is physically straightforward and easy to implement owing to its simple update rules. Simulations with various image data sets demonstrate that the CNMF algorithm can produce high-quality fused data both in terms of spatial and spectral domains, which contributes to the accurate identification and classification of materials observed at a high spatial resolution.
On the Complexity of Nonnegative Matrix Factorization
Nonnegative matrix factorization (NMF) has become a prominent technique for the analysis of image databases, text databases, and other information retrieval and clustering applications. The problem is most naturally posed as continuous optimization. In this report, we define an exact version of NMF. Then we establish several results about exact NMF: (i) that it is equivalent to a problem in polyhedral combinatorics; (ii) that it is NP-hard; and (iii) that a polynomial-time local search heuristic exists.
Nonnegative Matrix Factorization: A Comprehensive Review
Nonnegative Matrix Factorization (NMF), a relatively novel paradigm for dimensionality reduction, has been in the ascendant since its inception. It incorporates the nonnegativity constraint and thus obtains the parts-based representation as well as enhancing the interpretability of the issue correspondingly. This survey paper mainly focuses on the theoretical research into NMF over the last 5 years, where the principles, basic models, properties, and algorithms of NMF along with its various modifications, extensions, and generalizations are summarized systematically. The existing NMF algorithms are divided into four categories: Basic NMF (BNMF), Constrained NMF (CNMF), Structured NMF (SNMF), and Generalized NMF (GNMF), upon which the design principles, characteristics, problems, relationships, and evolution of these algorithms are presented and analyzed comprehensively. Some related work not on NMF that NMF should learn from or has connections with is involved too. Moreover, some open issues remained to be solved are discussed. Several relevant application areas of NMF are also briefly described. This survey aims to construct an integrated, state-of-the-art framework for NMF concept, from which the follow-up research may benefit.
Fast Local Algorithms for Large Scale Nonnegative Matrix and Tensor Factorizations
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, multi-sensory 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 NMF-based blind source separation (BSS) not only for the over-determined case but also for an under-determined (over-complete) 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 N-th 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 multi-layer hierarchical NMF approach [3].
NeNMF: An Optimal Gradient Method for Nonnegative Matrix Factorization
Nonnegative matrix factorization (NMF) is a powerful matrix decomposition technique that approximates a nonnegative matrix by the product of two low-rank nonnegative matrix factors. It has been widely applied to signal processing, computer vision, and data mining. Traditional NMF solvers include the multiplicative update rule (MUR), the projected gradient method (PG), the projected nonnegative least squares (PNLS), and the active set method (AS). However, they suffer from one or some of the following three problems: slow convergence rate, numerical instability and nonconvergence. In this paper, we present a new efficient NeNMF solver to simultaneously overcome the aforementioned problems. It applies Nesterov's optimal gradient method to alternatively optimize one factor with another fixed. In particular, at each iteration round, the matrix factor is updated by using the PG method performed on a smartly chosen search point, where the step size is determined by the Lipschitz constant. Since NeNMF does not use the time consuming line search and converges optimally at rate in optimizing each matrix factor, it is superior to MUR and PG in terms of efficiency as well as approximation accuracy. Compared to PNLS and AS that suffer from numerical instability problem in the worst case, NeNMF overcomes this deficiency. In addition, NeNMF can be used to solve -norm, -norm and manifold regularized NMF with the optimal convergence rate. Numerical experiments on both synthetic and real-world datasets show the efficiency of NeNMF for NMF and its variants comparing to representative NMF solvers. Extensive experiments on document clustering suggest the effectiveness of NeNMF.
On the Convergence of Multiplicative Update Algorithms for Nonnegative Matrix Factorization
Nonnegative matrix factorization (NMF) is useful to find basis information of nonnegative data. Currently, multiplicative updates are a simple and popular way to find the factorization. However, for the common NMF approach of minimizing the Euclidean distance between approximate and true values, no proof has shown that multiplicative updates converge to a stationary point of the NMF optimization problem. Stationarity is important as it is a necessary condition of a local minimum. This paper discusses the difficulty of proving the convergence. We propose slight modifications of existing updates and prove their convergence. Techniques invented in this paper may be applied to prove the convergence for other bound-constrained optimization problems.
Nonsmooth nonnegative matrix factorization (nsNMF)
We propose a novel nonnegative matrix factorization model that aims at finding localized, part-based, representations of nonnegative multivariate data items. Unlike the classical nonnegative matrix factorization (NMF) technique, this new model, denoted "nonsmooth nonnegative matrix factorization" (nsNMF), corresponds to the optimization of an unambiguous cost function designed to explicitly represent sparseness, in the form of nonsmoothness, which is controlled by a single parameter. In general, this method produces a set of basis and encoding vectors that are not only capable of representing the original data, but they also extract highly focalized patterns, which generally lend themselves to improved interpretability. The properties of this new method are illustrated with several data sets. Comparisons to previously published methods show that the new nsNMF method has some advantages in keeping faithfulness to the data in the achieving a high degree of sparseness for both the estimated basis and the encoding vectors and in better interpretability of the factors.
Hyperspectral Unmixing via $L_{1/2}$ Sparsity-Constrained Nonnegative Matrix Factorization
Hyperspectral unmixing is a crucial preprocessing step for material classification and recognition. In the last decade, nonnegative matrix factorization (NMF) and its extensions have been intensively studied to unmix hyperspectral imagery and recover the material end-members. As an important constraint for NMF, sparsity has been modeled making use of the <i>L</i><sub>1</sub> regularizer. Unfortunately, the <i>L</i><sub>1</sub> regularizer cannot enforce further sparsity when the full additivity constraint of material abundances is used, hence limiting the practical efficacy of NMF methods in hyperspectral unmixing. In this paper, we extend the NMF method by incorporating the <i>L</i><sub>1/2</sub> sparsity constraint, which we name <i>L</i><sub>1/2</sub> -NMF. The <i>L</i><sub>1/2</sub> regularizer not only induces sparsity but is also a better choice among <i>Lq</i>(0 <; <i>q</i> <; 1) regularizers. We propose an iterative estimation algorithm for <i>L</i><sub>1/2</sub>-NMF, which provides sparser and more accurate results than those delivered using the <i>L</i><sub>1</sub> norm. We illustrate the utility of our method on synthetic and real hyperspectral data and compare our results to those yielded by other state-of-the-art methods.
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