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Nicolas Gillis

Nicolas Gillis appears in the imported research catalog. Authorship, coauthor and topic links are available while profile ownership is still unclaimed.

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math.OCMachine LearningNumerical Analysismath.NAeess.SPComputer VisionInformation RetrievalComputational Engineering, Finance, and Scienceeess.ASeess.IVmath.COSoundSystems and Control

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Published work

33 published item(s)

preprint2026arXiv

Supervised Deep Multimodal Matrix Factorization for Interpretable Brain Network Analysis

We present Supervised Deep Multimodal Matrix Factorization (SD3MF), an interpretable framework for integrative brain network analysis that generalizes Symmetric Nonnegative Matrix Tri-Factorization (SNMTF) from unsupervised single-graph clustering to supervised prediction over populations of multimodal graphs. SD3MF learns deep hierarchical factorizations for each modality together with a shared latent representation that aligns subjects across views. An encoder-decoder formulation jointly optimizes graph reconstruction and supervised prediction, while adaptive weights enable data-driven multimodal fusion. By representing each subject through community-level interaction matrices, the model yields interpretable and discriminative features. Experiments on multimodal connectome datasets show that SD3MF consistently outperforms strong deep learning baselines such as CNNs and GNNs, while enabling biologically interpretable insights. Code for reproducibility is available at: https://github.com/amjadseyedi/SD3MF.

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preprint2022arXiv

Multiplicative Updates for NMF with $β$-Divergences under Disjoint Equality Constraints

Nonnegative matrix factorization (NMF) is the problem of approximating an input nonnegative matrix, $V$, as the product of two smaller nonnegative matrices, $W$ and $H$. In this paper, we introduce a general framework to design multiplicative updates (MU) for NMF based on $β$-divergences ($β$-NMF) with disjoint equality constraints, and with penalty terms in the objective function. By disjoint, we mean that each variable appears in at most one equality constraint. Our MU satisfy the set of constraints after each update of the variables during the optimization process, while guaranteeing that the objective function decreases monotonically. We showcase this framework on three NMF models, and show that it competes favorably the state of the art: (1)~$β$-NMF with sum-to-one constraints on the columns of $H$, (2) minimum-volume $β$-NMF with sum-to-one constraints on the columns of $W$, and (3) sparse $β$-NMF with $\ell_2$-norm constraints on the columns of $W$.

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preprint2022arXiv

Solving matrix nearness problems via Hamiltonian systems, matrix factorization, and optimization

In these lectures notes, we review our recent works addressing various problems of finding the nearest stable system to an unstable one. After the introduction, we provide some preliminary background, namely, defining Port-Hamiltonian systems and dissipative Hamiltonian systems and their properties, briefly discussing matrix factorizations, and describing the optimization methods that we will use in these notes. In the third chapter, we present our approach to tackle the distance to stability for standard continuous linear time invariant (LTI) systems. The main idea is to rely on the characterization of stable systems as dissipative Hamiltonian systems. We show how this idea can be generalized to compute the nearest $Ω$-stable matrix, where the eigenvalues of the sought system matrix $A$ are required to belong a rather general set $Ω$. We also show how these ideas can be used to compute minimal-norm static feedbacks, that is, stabilize a system by choosing a proper input $u(t)$ that linearly depends on $x(t)$ (static-state feedback), or on $y(t)$ (static-output feedback). In the fourth chapter, we present our approach to tackle the distance to passivity. The main idea is to rely on the characterization of stable systems as port-Hamiltonian systems. We also discuss in more details the special case of computing the nearest stable matrix pairs. In the last chapter, we focus on discrete-time LTI systems. Similarly as for the continuous case, we propose a parametrization that allows efficiently compute the nearest stable system (for matrices and matrix pairs), allowing to compute the distance to stability. We show how this idea can be used in data-driven system identification, that is, given a set of input-output pairs, identify the system $A$.

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preprint2021arXiv

Block Alternating Bregman Majorization Minimization with Extrapolation

In this paper, we consider a class of nonsmooth nonconvex optimization problems whose objective is the sum of a block relative smooth function and a proper and lower semicontinuous block separable function. Although the analysis of block proximal gradient (BPG) methods for the class of block $L$-smooth functions have been successfully extended to Bregman BPG methods that deal with the class of block relative smooth functions, accelerated Bregman BPG methods are scarce and challenging to design. Taking our inspiration from Nesterov-type acceleration and the majorization-minimization scheme, we propose a block alternating Bregman Majorization-Minimization framework with Extrapolation (BMME). We prove subsequential convergence of BMME to a first-order stationary point under mild assumptions, and study its global convergence under stronger conditions. We illustrate the effectiveness of BMME on the penalized orthogonal nonnegative matrix factorization problem.

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preprint2021arXiv

Distributionally Robust and Multi-Objective Nonnegative Matrix Factorization

Nonnegative matrix factorization (NMF) is a linear dimensionality reduction technique for analyzing nonnegative data. A key aspect of NMF is the choice of the objective function that depends on the noise model (or statistics of the noise) assumed on the data. In many applications, the noise model is unknown and difficult to estimate. In this paper, we define a multi-objective NMF (MO-NMF) problem, where several objectives are combined within the same NMF model. We propose to use Lagrange duality to judiciously optimize for a set of weights to be used within the framework of the weighted-sum approach, that is, we minimize a single objective function which is a weighted sum of the all objective functions. We design a simple algorithm based on multiplicative updates to minimize this weighted sum. We show how this can be used to find distributionally robust NMF (DR-NMF) solutions, that is, solutions that minimize the largest error among all objectives, using a dual approach solved via a heuristic inspired from the Frank-Wolfe algorithm. We illustrate the effectiveness of this approach on synthetic, document and audio data sets. The results show that DR-NMF is robust to our incognizance of the noise model of the NMF problem.

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preprint2021arXiv

On the non-symmetric semidefinite Procrustes problem

In this paper, we consider the non-symmetric positive semidefinite Procrustes (NSPSDP) problem: Given two matrices $X,Y \in \mathbb{R}^{n,m}$, find the matrix $A \in \mathbb{R}^{n,n}$ that minimizes the Frobenius norm of $AX-Y$ and which is such that $A+A^T$ is positive semidefinite. We generalize the semi-analytical approach for the symmetric positive semidefinite Procrustes problem, where $A$ is required to be positive semidefinite, that was proposed by Gillis and Sharma (A semi-analytical approach for the positive semidefinite Procrustes problem, Linear Algebra Appl. 540, 112-137, 2018). As for the symmetric case, we first show that the NSPSDP problem can be reduced to a smaller NSPSDP problem that always has a unique solution and where the matrix $X$ is diagonal and has full rank. Then, an efficient semi-analytical algorithm to solve the NSPSDP problem is proposed, solving the smaller and well-posed problem with a fast gradient method which guarantees a linear rate of convergence. This algorithm is also applicable to solve the complex NSPSDP problem, where $X,Y \in \mathbb{C}^{n,m}$, as we show the complex NSPSDP problem can be written as an overparametrized real NSPSDP problem. The efficiency of the proposed algorithm is illustrated on several numerical examples.

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preprint2020arXiv

A block inertial Bregman proximal algorithm for nonsmooth nonconvex problems with application to symmetric nonnegative matrix tri-factorization

We propose BIBPA, a block inertial Bregman proximal algorithm for minimizing the sum of a block relatively smooth function (that is, relatively smooth concerning each block) and block separable nonsmooth nonconvex functions. We prove that the sequence generated by BIBPA subsequentially converges to critical points of the objective under standard assumptions, and globally converges when the objective function is additionally assumed to satisfy the Kurdyka-Łojasiewicz (KŁ) property. We also provide the convergence rate when the objective satisfies the Łojasiewicz inequality. We apply BIBPA to the symmetric nonnegative matrix tri-factorization (SymTriNMF) problem, where we propose kernel functions for SymTriNMF and provide closed-form solutions for subproblems of BIBPA.

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preprint2020arXiv

Blind Audio Source Separation with Minimum-Volume Beta-Divergence NMF

Considering a mixed signal composed of various audio sources and recorded with a single microphone, we consider on this paper the blind audio source separation problem which consists in isolating and extracting each of the sources. To perform this task, nonnegative matrix factorization (NMF) based on the Kullback-Leibler and Itakura-Saito $β$-divergences is a standard and state-of-the-art technique that uses the time-frequency representation of the signal. We present a new NMF model better suited for this task. It is based on the minimization of $β$-divergences along with a penalty term that promotes the columns of the dictionary matrix to have a small volume. Under some mild assumptions and in noiseless conditions, we prove that this model is provably able to identify the sources. In order to solve this problem, we propose multiplicative updates whose derivations are based on the standard majorization-minimization framework. We show on several numerical experiments that our new model is able to obtain more interpretable results than standard NMF models. Moreover, we show that it is able to recover the sources even when the number of sources present into the mixed signal is overestimated. In fact, our model automatically sets sources to zero in this situation, hence performs model order selection automatically.

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preprint2020arXiv

Inertial Block Proximal Methods for Non-Convex Non-Smooth Optimization

We propose inertial versions of block coordinate descent methods for solving non-convex non-smooth composite optimization problems. Our methods possess three main advantages compared to current state-of-the-art accelerated first-order methods: (1) they allow using two different extrapolation points to evaluate the gradients and to add the inertial force (we will empirically show that it is more efficient than using a single extrapolation point), (2) they allow to randomly picking the block of variables to update, and (3) they do not require a restarting step. We prove the subsequential convergence of the generated sequence under mild assumptions, prove the global convergence under some additional assumptions, and provide convergence rates. We deploy the proposed methods to solve non-negative matrix factorization (NMF) and show that they compete favorably with the state-of-the-art NMF algorithms. Additional experiments on non-negative approximate canonical polyadic decomposition, also known as non-negative tensor factorization, are also provided.

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preprint2020arXiv

Off-diagonal Symmetric Nonnegative Matrix Factorization

Symmetric nonnegative matrix factorization (symNMF) is a variant of nonnegative matrix factorization (NMF) that allows to handle symmetric input matrices and has been shown to be particularly well suited for clustering tasks. In this paper, we present a new model, dubbed off-diagonal symNMF (ODsymNMF), that does not take into account the diagonal entries of the input matrix in the objective function. ODsymNMF has three key advantages compared to symNMF. First, ODsymNMF is theoretically much more sound as there always exists an exact factorization of size at most $\nicefrac{n(n-1)}{2}$ where $n$ is the dimension of the input matrix. Second, it makes more sense in practice as diagonal entries of the input matrix typically correspond to the similarity between an item and itself, not bringing much information. Third, it makes the optimization problem much easier to solve. In particular, it will allow us to design an algorithm based on coordinate descent that minimizes the component-wise $\ell_1$ norm between the input matrix and its approximation. We prove that this norm is much better suited for binary input matrices often encountered in practice. We also derive a coordinate descent method for the component-wise $\ell_2$ norm, and compare the two approaches with symNMF on synthetic and document data sets.

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preprint2020arXiv

On a minimum enclosing ball of a collection of linear subspaces

This paper concerns the minimax center of a collection of linear subspaces. When the subspaces are $k$-dimensional subspaces of $\mathbb{R}^n$, this can be cast as finding the center of a minimum enclosing ball on a Grassmann manifold, Gr$(k,n)$. For subspaces of different dimension, the setting becomes a disjoint union of Grassmannians rather than a single manifold, and the problem is no longer well-defined. However, natural geometric maps exist between these manifolds with a well-defined notion of distance for the images of the subspaces under the mappings. Solving the initial problem in this context leads to a candidate minimax center on each of the constituent manifolds, but does not inherently provide intuition about which candidate is the best representation of the data. Additionally, the solutions of different rank are generally not nested so a deflationary approach will not suffice, and the problem must be solved independently on each manifold. We propose and solve an optimization problem parametrized by the rank of the minimax center. The solution is computed using a subgradient algorithm on the dual. By scaling the objective and penalizing the information lost by the rank-$k$ minimax center, we jointly recover an optimal dimension, $k^*$, and a central subspace, $U^* \in$ Gr$(k^*,n)$ at the center of the minimum enclosing ball, that best represents the data.

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preprint2020arXiv

Sparse Separable Nonnegative Matrix Factorization

We propose a new variant of nonnegative matrix factorization (NMF), combining separability and sparsity assumptions. Separability requires that the columns of the first NMF factor are equal to columns of the input matrix, while sparsity requires that the columns of the second NMF factor are sparse. We call this variant sparse separable NMF (SSNMF), which we prove to be NP-complete, as opposed to separable NMF which can be solved in polynomial time. The main motivation to consider this new model is to handle underdetermined blind source separation problems, such as multispectral image unmixing. We introduce an algorithm to solve SSNMF, based on the successive nonnegative projection algorithm (SNPA, an effective algorithm for separable NMF), and an exact sparse nonnegative least squares solver. We prove that, in noiseless settings and under mild assumptions, our algorithm recovers the true underlying sources. This is illustrated by experiments on synthetic data sets and the unmixing of a multispectral image.

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preprint2019arXiv

Algorithms and Comparisons of Non-negative Matrix Factorization with Volume Regularization for Hyperspectral Unmixing

In this work, we consider nonnegative matrix factorization (NMF) with a regularization that promotes small volume of the convex hull spanned by the basis matrix. We present highly efficient algorithms for three different volume regularizers, and compare them on endmember recovery in hyperspectral unmixing. The NMF algorithms developed in this work are shown to outperform the state-of-the-art volume-regularized NMF methods, and produce meaningful decompositions on real-world hyperspectral images in situations where endmembers are highly mixed (no pure pixels). Furthermore, our extensive numerical experiments show that when the data is highly separable, meaning that there are data points close to the true endmembers, and there are a few endmembers, the regularizer based on the determinant of the Gramian produces the best results in most cases. For data that is less separable and/or contains more endmembers, the regularizer based on the logarithm of the determinant of the Gramian performs best in general.

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preprint2019arXiv

Near-Convex Archetypal Analysis

Nonnegative matrix factorization (NMF) is a widely used linear dimensionality reduction technique for nonnegative data. NMF requires that each data point is approximated by a convex combination of basis elements. Archetypal analysis (AA), also referred to as convex NMF, is a well-known NMF variant imposing that the basis elements are themselves convex combinations of the data points. AA has the advantage to be more interpretable than NMF because the basis elements are directly constructed from the data points. However, it usually suffers from a high data fitting error because the basis elements are constrained to be contained in the convex cone of the data points. In this letter, we introduce near-convex archetypal analysis (NCAA) which combines the advantages of both AA and NMF. As for AA, the basis vectors are required to be linear combinations of the data points and hence are easily interpretable. As for NMF, the additional flexibility in choosing the basis elements allows NCAA to have a low data fitting error. We show that NCAA compares favorably with a state-of-the-art minimum-volume NMF method on synthetic datasets and on a real-world hyperspectral image.

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preprint2018arXiv

Accelerating Nonnegative Matrix Factorization Algorithms using Extrapolation

In this paper, we propose a general framework to accelerate significantly the algorithms for nonnegative matrix factorization (NMF). This framework is inspired from the extrapolation scheme used to accelerate gradient methods in convex optimization and from the method of parallel tangents. However, the use of extrapolation in the context of the two-block exact coordinate descent algorithms tackling the non-convex NMF problems is novel. We illustrate the performance of this approach on two state-of-the-art NMF algorithms, namely, accelerated hierarchical alternating least squares (A-HALS) and alternating nonnegative least squares (ANLS), using synthetic, image and document data sets.

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preprint2016arXiv

Coordinate Descent Methods for Symmetric Nonnegative Matrix Factorization

Given a symmetric nonnegative matrix $A$, symmetric nonnegative matrix factorization (symNMF) is the problem of finding a nonnegative matrix $H$, usually with much fewer columns than $A$, such that $A \approx HH^T$. SymNMF can be used for data analysis and in particular for various clustering tasks. In this paper, we propose simple and very efficient coordinate descent schemes to solve this problem, and that can handle large and sparse input matrices. The effectiveness of our methods is illustrated on synthetic and real-world data sets, and we show that they perform favorably compared to recent state-of-the-art methods.

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preprint2016arXiv

Sequential Dimensionality Reduction for Extracting Localized Features

Linear dimensionality reduction techniques are powerful tools for image analysis as they allow the identification of important features in a data set. In particular, nonnegative matrix factorization (NMF) has become very popular as it is able to extract sparse, localized and easily interpretable features by imposing an additive combination of nonnegative basis elements. Nonnegative matrix underapproximation (NMU) is a closely related technique that has the advantage to identify features sequentially. In this paper, we propose a variant of NMU that is particularly well suited for image analysis as it incorporates the spatial information, that is, it takes into account the fact that neighboring pixels are more likely to be contained in the same features, and favors the extraction of localized features by looking for sparse basis elements. We show that our new approach competes favorably with comparable state-of-the-art techniques on synthetic, facial and hyperspectral image data sets.

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preprint2015arXiv

Exact and Heuristic Algorithms for Semi-Nonnegative Matrix Factorization

Given a matrix $M$ (not necessarily nonnegative) and a factorization rank $r$, semi-nonnegative matrix factorization (semi-NMF) looks for a matrix $U$ with $r$ columns and a nonnegative matrix $V$ with $r$ rows such that $UV$ is the best possible approximation of $M$ according to some metric. In this paper, we study the properties of semi-NMF from which we develop exact and heuristic algorithms. Our contribution is threefold. First, we prove that the error of a semi-NMF of rank $r$ has to be smaller than the best unconstrained approximation of rank $r-1$. This leads us to a new initialization procedure based on the singular value decomposition (SVD) with a guarantee on the quality of the approximation. Second, we propose an exact algorithm (that is, an algorithm that finds an optimal solution), also based on the SVD, for a certain class of matrices (including nonnegative irreducible matrices) from which we derive an initialization for matrices not belonging to that class. Numerical experiments illustrate that this second approach performs extremely well, and allows us to compute optimal semi-NMF decompositions in many situations. Finally, we analyze the computational complexity of semi-NMF proving its NP-hardness, already in the rank-one case (that is, for $r = 1$), and we show that semi-NMF is sometimes ill-posed (that is, an optimal solution does not exist).

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preprint2014arXiv

Enhancing Pure-Pixel Identification Performance via Preconditioning

In this paper, we analyze different preconditionings designed to enhance robustness of pure-pixel search algorithms, which are used for blind hyperspectral unmixing and which are equivalent to near-separable nonnegative matrix factorization algorithms. Our analysis focuses on the successive projection algorithm (SPA), a simple, efficient and provably robust algorithm in the pure-pixel algorithm class. Recently, a provably robust preconditioning was proposed by Gillis and Vavasis (arXiv:1310.2273) which requires the resolution of a semidefinite program (SDP) to find a data points-enclosing minimum volume ellipsoid. Since solving the SDP in high precisions can be time consuming, we generalize the robustness analysis to approximate solutions of the SDP, that is, solutions whose objective function values are some multiplicative factors away from the optimal value. It is shown that a high accuracy solution is not crucial for robustness, which paves the way for faster preconditionings (e.g., based on first-order optimization methods). This first contribution also allows us to provide a robustness analysis for two other preconditionings. The first one is pre-whitening, which can be interpreted as an optimal solution of the same SDP with additional constraints. We analyze robustness of pre-whitening which allows us to characterize situations in which it performs competitively with the SDP-based preconditioning. The second one is based on SPA itself and can be interpreted as an optimal solution of a relaxation of the SDP. It is extremely fast while competing with the SDP-based preconditioning on several synthetic data sets.

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preprint2014arXiv

Heuristics for Exact Nonnegative Matrix Factorization

The exact nonnegative matrix factorization (exact NMF) problem is the following: given an $m$-by-$n$ nonnegative matrix $X$ and a factorization rank $r$, find, if possible, an $m$-by-$r$ nonnegative matrix $W$ and an $r$-by-$n$ nonnegative matrix $H$ such that $X = WH$. In this paper, we propose two heuristics for exact NMF, one inspired from simulated annealing and the other from the greedy randomized adaptive search procedure. We show that these two heuristics are able to compute exact nonnegative factorizations for several classes of nonnegative matrices (namely, linear Euclidean distance matrices, slack matrices, unique-disjointness matrices, and randomly generated matrices) and as such demonstrate their superiority over standard multi-start strategies. We also consider a hybridization between these two heuristics that allows us to combine the advantages of both methods. Finally, we discuss the use of these heuristics to gain insight on the behavior of the nonnegative rank, i.e., the minimum factorization rank such that an exact NMF exists. In particular, we disprove a conjecture on the nonnegative rank of a Kronecker product, propose a new upper bound on the extension complexity of generic $n$-gons and conjecture the exact value of (i) the extension complexity of regular $n$-gons and (ii) the nonnegative rank of a submatrix of the slack matrix of the correlation polytope.

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preprint2014arXiv

Semidefinite Programming Based Preconditioning for More Robust Near-Separable Nonnegative Matrix Factorization

Nonnegative matrix factorization (NMF) under the separability assumption can provably be solved efficiently, even in the presence of noise, and has been shown to be a powerful technique in document classification and hyperspectral unmixing. This problem is referred to as near-separable NMF and requires that there exists a cone spanned by a small subset of the columns of the input nonnegative matrix approximately containing all columns. In this paper, we propose a preconditioning based on semidefinite programming making the input matrix well-conditioned. This in turn can improve significantly the performance of near-separable NMF algorithms which is illustrated on the popular successive projection algorithm (SPA). The new preconditioned SPA is provably more robust to noise, and outperforms SPA on several synthetic data sets. We also show how an active-set method allow us to apply the preconditioning on large-scale real-world hyperspectral images.

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preprint2014arXiv

Successive Nonnegative Projection Algorithm for Robust Nonnegative Blind Source Separation

In this paper, we propose a new fast and robust recursive algorithm for near-separable nonnegative matrix factorization, a particular nonnegative blind source separation problem. This algorithm, which we refer to as the successive nonnegative projection algorithm (SNPA), is closely related to the popular successive projection algorithm (SPA), but takes advantage of the nonnegativity constraint in the decomposition. We prove that SNPA is more robust than SPA and can be applied to a broader class of nonnegative matrices. This is illustrated on some synthetic data sets, and on a real-world hyperspectral image.

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preprint2014arXiv

The Why and How of Nonnegative Matrix Factorization

Nonnegative matrix factorization (NMF) has become a widely used tool for the analysis of high-dimensional data as it automatically extracts sparse and meaningful features from a set of nonnegative data vectors. We first illustrate this property of NMF on three applications, in image processing, text mining and hyperspectral imaging --this is the why. Then we address the problem of solving NMF, which is NP-hard in general. We review some standard NMF algorithms, and also present a recent subclass of NMF problems, referred to as near-separable NMF, that can be solved efficiently (that is, in polynomial time), even in the presence of noise --this is the how. Finally, we briefly describe some problems in mathematics and computer science closely related to NMF via the nonnegative rank.

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preprint2014arXiv

Two Algorithms for Orthogonal Nonnegative Matrix Factorization with Application to Clustering

Approximate matrix factorization techniques with both nonnegativity and orthogonality constraints, referred to as orthogonal nonnegative matrix factorization (ONMF), have been recently introduced and shown to work remarkably well for clustering tasks such as document classification. In this paper, we introduce two new methods to solve ONMF. First, we show athematical equivalence between ONMF and a weighted variant of spherical k-means, from which we derive our first method, a simple EM-like algorithm. This also allows us to determine when ONMF should be preferred to k-means and spherical k-means. Our second method is based on an augmented Lagrangian approach. Standard ONMF algorithms typically enforce nonnegativity for their iterates while trying to achieve orthogonality at the limit (e.g., using a proper penalization term or a suitably chosen search direction). Our method works the opposite way: orthogonality is strictly imposed at each step while nonnegativity is asymptotically obtained, using a quadratic penalty. Finally, we show that the two proposed approaches compare favorably with standard ONMF algorithms on synthetic, text and image data sets.

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preprint2013arXiv

Fast and Robust Recursive Algorithms for Separable Nonnegative Matrix Factorization

In this paper, we study the nonnegative matrix factorization problem under the separability assumption (that is, there exists a cone spanned by a small subset of the columns of the input nonnegative data matrix containing all columns), which is equivalent to the hyperspectral unmixing problem under the linear mixing model and the pure-pixel assumption. We present a family of fast recursive algorithms, and prove they are robust under any small perturbations of the input data matrix. This family generalizes several existing hyperspectral unmixing algorithms and hence provides for the first time a theoretical justification of their better practical performance.

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preprint2013arXiv

Robust Near-Separable Nonnegative Matrix Factorization Using Linear Optimization

Nonnegative matrix factorization (NMF) has been shown recently to be tractable under the separability assumption, under which all the columns of the input data matrix belong to the convex cone generated by only a few of these columns. Bittorf, Recht, Ré and Tropp (`Factoring nonnegative matrices with linear programs', NIPS 2012) proposed a linear programming (LP) model, referred to as Hottopixx, which is robust under any small perturbation of the input matrix. However, Hottopixx has two important drawbacks: (i) the input matrix has to be normalized, and (ii) the factorization rank has to be known in advance. In this paper, we generalize Hottopixx in order to resolve these two drawbacks, that is, we propose a new LP model which does not require normalization and detects the factorization rank automatically. Moreover, the new LP model is more flexible, significantly more tolerant to noise, and can easily be adapted to handle outliers and other noise models. Finally, we show on several synthetic datasets that it outperforms Hottopixx while competing favorably with two state-of-the-art methods.

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preprint2013arXiv

Robustness Analysis of Hottopixx, a Linear Programming Model for Factoring Nonnegative Matrices

Although nonnegative matrix factorization (NMF) is NP-hard in general, it has been shown very recently that it is tractable under the assumption that the input nonnegative data matrix is close to being separable (separability requires that all columns of the input matrix belongs to the cone spanned by a small subset of these columns). Since then, several algorithms have been designed to handle this subclass of NMF problems. In particular, Bittorf, Recht, Ré and Tropp (`Factoring nonnegative matrices with linear programs', NIPS 2012) proposed a linear programming model, referred to as Hottopixx. In this paper, we provide a new and more general robustness analysis of their method. In particular, we design a provably more robust variant using a post-processing strategy which allows us to deal with duplicates and near duplicates in the dataset.

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preprint2012arXiv

Sparse and Unique Nonnegative Matrix Factorization Through Data Preprocessing

Nonnegative matrix factorization (NMF) has become a very popular technique in machine learning because it automatically extracts meaningful features through a sparse and part-based representation. However, NMF has the drawback of being highly ill-posed, that is, there typically exist many different but equivalent factorizations. In this paper, we introduce a completely new way to obtaining more well-posed NMF problems whose solutions are sparser. Our technique is based on the preprocessing of the nonnegative input data matrix, and relies on the theory of M-matrices and the geometric interpretation of NMF. This approach provably leads to optimal and sparse solutions under the separability assumption of Donoho and Stodden (NIPS, 2003), and, for rank-three matrices, makes the number of exact factorizations finite. We illustrate the effectiveness of our technique on several image datasets.

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preprint2011arXiv

A Multilevel Approach For Nonnegative Matrix Factorization

Nonnegative Matrix Factorization (NMF) is the problem of approximating a nonnegative matrix with the product of two low-rank nonnegative matrices and has been shown to be particularly useful in many applications, e.g., in text mining, image processing, computational biology, etc. In this paper, we explain how algorithms for NMF can be embedded into the framework of multilevel methods in order to accelerate their convergence. This technique can be applied in situations where data admit a good approximate representation in a lower dimensional space through linear transformations preserving nonnegativity. A simple multilevel strategy is described and is experimentally shown to speed up significantly three popular NMF algorithms (alternating nonnegative least squares, multiplicative updates and hierarchical alternating least squares) on several standard image datasets.

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preprint2011arXiv

Accelerated Multiplicative Updates and Hierarchical ALS Algorithms for Nonnegative Matrix Factorization

Nonnegative matrix factorization (NMF) is a data analysis technique used in a great variety of applications such as text mining, image processing, hyperspectral data analysis, computational biology, and clustering. In this paper, we consider two well-known algorithms designed to solve NMF problems, namely the multiplicative updates of Lee and Seung and the hierarchical alternating least squares of Cichocki et al. We propose a simple way to significantly accelerate these schemes, based on a careful analysis of the computational cost needed at each iteration, while preserving their convergence properties. This acceleration technique can also be applied to other algorithms, which we illustrate on the projected gradient method of Lin. The efficiency of the accelerated algorithms is empirically demonstrated on image and text datasets, and compares favorably with a state-of-the-art alternating nonnegative least squares algorithm.

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preprint2011arXiv

Low-Rank Matrix Approximation with Weights or Missing Data is NP-hard

Weighted low-rank approximation (WLRA), a dimensionality reduction technique for data analysis, has been successfully used in several applications, such as in collaborative filtering to design recommender systems or in computer vision to recover structure from motion. In this paper, we study the computational complexity of WLRA and prove that it is NP-hard to find an approximate solution, even when a rank-one approximation is sought. Our proofs are based on a reduction from the maximum-edge biclique problem, and apply to strictly positive weights as well as binary weights (the latter corresponding to low-rank matrix approximation with missing data).

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preprint2010arXiv

On the Geometric Interpretation of the Nonnegative Rank

The nonnegative rank of a nonnegative matrix is the minimum number of nonnegative rank-one factors needed to reconstruct it exactly. The problem of determining this rank and computing the corresponding nonnegative factors is difficult; however it has many potential applications, e.g., in data mining, graph theory and computational geometry. In particular, it can be used to characterize the minimal size of any extended reformulation of a given combinatorial optimization program. In this paper, we introduce and study a related quantity, called the restricted nonnegative rank. We show that computing this quantity is equivalent to a problem in polyhedral combinatorics, and fully characterize its computational complexity. This in turn sheds new light on the nonnegative rank problem, and in particular allows us to provide new improved lower bounds based on its geometric interpretation. We apply these results to slack matrices and linear Euclidean distance matrices and obtain counter-examples to two conjectures of Beasly and Laffey, namely we show that the nonnegative rank of linear Euclidean distance matrices is not necessarily equal to their dimension, and that the rank of a matrix is not always greater than the nonnegative rank of its square.

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preprint2009arXiv

Using Underapproximations for Sparse Nonnegative Matrix Factorization

Nonnegative Matrix Factorization consists in (approximately) factorizing a nonnegative data matrix by the product of two low-rank nonnegative matrices. It has been successfully applied as a data analysis technique in numerous domains, e.g., text mining, image processing, microarray data analysis, collaborative filtering, etc. We introduce a novel approach to solve NMF problems, based on the use of an underapproximation technique, and show its effectiveness to obtain sparse solutions. This approach, based on Lagrangian relaxation, allows the resolution of NMF problems in a recursive fashion. We also prove that the underapproximation problem is NP-hard for any fixed factorization rank, using a reduction of the maximum edge biclique problem in bipartite graphs. We test two variants of our underapproximation approach on several standard image datasets and show that they provide sparse part-based representations with low reconstruction error. Our results are comparable and sometimes superior to those obtained by two standard Sparse Nonnegative Matrix Factorization techniques.

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