Tensors can be viewed as multilinear arrays or generalizations of the notion of matrices. Tensor decompositions have applications in various fields such as psychometrics, signal processing, numerical linear algebra and data mining. When the data are nonnegative, the nonnegative tensor factorization (NTF) better reflects the underlying structure. With NTF it is possible to extract information from a given dataset and construct lower-dimensional bases that capture the main features of the set and concisely describe the original data. Nonnegative tensor factorizations are commonly computed as the solution of a nonlinear bound-constrained optimization problem. Some inherent difficulties must be taken into consideration in order to achieve good solutions. Many existing methods for computing NTF optimize over each of the factors separately; the resulting algorithms are often slow to converge and difficult to control. We propose an all-at-once approach to computing NTF. Our method optimizes over all factors simultaneously and combines two regularization strategies to ensure that the factors in the decomposition remain bounded and equilibrated in norm. We present numerical experiments that illustrate the effectiveness of our approach. We also give an example of digital-inpainting, where our algorithm is employed to construct a basis that can be used to restore digital images.

Tensors can be viewed as multilinear arrays or generalizations of the notion of matrices. Tensor decompositions have applications in various fields such as psychometrics, signal processing, numerical linear algebra and data mining. When the data are nonnegative, the nonnegative tensor factorization (NTF) better reflects the underlying structure. With NTF it is possible to extract information from a given dataset and construct lower-dimensional bases that capture the main features of the set and concisely describe the original data. Nonnegative tensor factorizations are commonly computed as the solution of a nonlinear bound-constrained optimization problem. Some inherent difficulties must be taken into consideration in order to achieve good solutions. Many existing methods for computing NTF optimize over each of the factors separately; the resulting algorithms are often slow to converge and difficult to control. We propose an all-at-once approach to computing NTF. Our method optimizes over all factors simultaneously and combines two regularization strategies to ensure that the factors in the decomposition remain bounded and equilibrated in norm. We present numerical experiments that illustrate the effectiveness of our approach. We also give an example of digital-inpainting, where our algorithm is employed to construct a basis that can be used to restore digital images.

Tensors can be viewed as multilinear arrays or generalizations of the notion of matrices. Tensor decompositions have applications in various fields such as psychometrics, signal processing, numerical linear algebra and data mining. When the data are nonnegative, the nonnegative tensor factorization (NTF) better reflects the underlying structure. With NTF it is possible to extract information from a given dataset and construct lower-dimensional bases that capture the main features of the set and concisely describe the original data. Nonnegative tensor factorizations are commonly computed as the solution of a nonlinear bound-constrained optimization problem. Some inherent difficulties must be taken into consideration in order to achieve good solutions. Many existing methods for computing NTF optimize over each of the factors separately; the resulting algorithms are often slow to converge and difficult to control. We propose an all-at-once approach to computing NTF. Our method optimizes over all factors simultaneously and combines two regularization strategies to ensure that the factors in the decomposition remain bounded and equilibrated in norm. We present numerical experiments that illustrate the effectiveness of our approach. We also give an example of digital-inpainting, where our algorithm is employed to construct a basis that can be used to restore digital images. / Science, Faculty of / Computer Science, Department of / Graduate

The results presented here are concerned with questions of decomposability of multiplicative semigroups of matrices with nonnegative entries. Chapter 1 covers some preliminary results which become useful in the remainder of the exposition. Chapters 2 and 3 constitute an exposition of some recent known results on special semigroups. Chapter 2 explores conditions for decomposability of semigroups in terms of conditions derived from linear functionals and in Chapter 3, we give a complete proof of an extension of the celebrated Perron-Frobenius Theorem. No originality is claimed for the results in Chapters 2 and 3. In Chapter 4, we present some new results on sufficient conditions for finiteness of semigroups of matrices.

The results presented here are concerned with questions of decomposability of multiplicative semigroups of matrices with nonnegative entries. Chapter 1 covers some preliminary results which become useful in the remainder of the exposition. Chapters 2 and 3 constitute an exposition of some recent known results on special semigroups. Chapter 2 explores conditions for decomposability of semigroups in terms of conditions derived from linear functionals and in Chapter 3, we give a complete proof of an extension of the celebrated Perron-Frobenius Theorem. No originality is claimed for the results in Chapters 2 and 3. In Chapter 4, we present some new results on sufficient conditions for finiteness of semigroups of matrices.

Fluorescence microscopy is an important tool for biological research. However, the resolution of a standard fluorescence microscope is limited by diffraction, which makes it difficult to observe small details of a specimen’s structure. We have developed two fluorescence microscopy methods that achieve resolution beyond the classical diffraction limit. The first method represents an extension of localisation microscopy. We used nonnegative matrix factorisation (NMF) to model a noisy dataset of highly overlapping fluorophores with intermittent intensities. We can recover images of individual sources from the optimised model, despite their high mutual overlap in the original dataset. This allows us to consider blinking quantum dots as bright and stable fluorophores for localisation microscopy. Moreover, NMF allows recovery of sources each having a unique shape. Such a situation can arise, for example, when the sources are located in different focal planes, and NMF can potentially be used for three dimensional superresolution imaging. We discuss the practical aspects of applying NMF to real datasets, and show super-resolution images of biological samples labelled with quantum dots. It should be noted that this technique can be performed on any wide-field epifluorescence microscope equipped with a camera, which makes this super-resolution method very accessible to a wide scientific community. The second optical microscopy method we discuss in this thesis is a member of the growing family of structured illumination techniques. Our main goal is to apply structured illumination to thick fluorescent samples generating a large out-of-focus background. The out-of-focus fluorescence background degrades the illumination pattern, and the reconstructed images suffer from the influence of noise. We present a combination of structured illumination microscopy and line scanning. This technique reduces the out-of-focus fluorescence background, which improves the quality of the illumination pattern and therefore facilitates reconstruction. We present super-resolution, optically sectioned images of a thick fluorescent sample, revealing details of the specimen’s inner structure. In addition, in this thesis we also discuss a theoretical resolution limit for noisy and pixelated data. We correct a previously published expression for the so-called fundamental resolution measure (FREM) and derive FREM for two fluorophores with intermittent intensity. We show that the intensity intermittency of the sources (observed for quantum dots, for example) can increase the “resolution” defined in terms of FREM.

Data-mining has become a hot topic in recent years. It consists of extracting relevant information or structures from data such as: pictures, textual material, networks, etc. Such information or structures are usually not trivial to obtain and many techniques have been proposed to address this problem, including Independent Component Analysis, Latent Sematic Analysis, etc. Nonnegative Matrix Factorization is yet another technique that relies on the nonnegativity of the data and the nonnegativity assumption of the underlying model. The main advantage of this technique is that nonnegative objects are modeled by a combination of some basic nonnegative parts, which provides a physical interpretation of the construction of the objects. This is an exclusive feature that is known to be useful in many areas such as Computer Vision, Information Retrieval, etc. In this thesis, we look at several aspects of Nonnegative Matrix Factorization, focusing on numerical algorithms and their applications to different kinds of data and constraints. This includes Tensor Nonnegative Factorization, Weighted Nonnegative Matrix Factorization, Symmetric Nonnegative Matrix Factorization, Stochastic Matrix Approximation, etc. The recently proposed Rank-one Residue Iteration (RRI) is the common thread in all of these factorizations. It is shown to be a fast method with good convergence properties which adapts well to many situations.

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L'objectif de cette thèse est l'investigation de nouvelles méthodes de surface de réponse afin de réaliser l'analyse de sensibilité de modèles numériques complexes et coûteux en temps de calcul. Pour ce faire, nous nous sommes intéressés aux méthodes basées sur la décomposition ANOVA. Nous avons proposé l'utilisation d'une méthode basée sur les splines de lissage de type ANOVA, alliant procédures d'estimation et de sélection de variables. L'étape de sélection de variable peut devenir très coûteuse en temps de calcul, particulièrement dans le cas d'un grand nombre de paramètre d'entrée. Pour cela nous avons développé un algorithme de seuillage itératif dont l'originalité réside dans sa simplicité d'implémentation et son efficacité. Nous avons ensuite proposé une méthode directe pour estimer les indices de sensibilité. En s'inspirant de cette méthode de surface de réponse, nous avons développé par la suite une méthode adaptée à l'approximation de modèles très irréguliers et discontinus, qui utilise une base d'ondelettes. Ce type de méthode a pour propriété une approche multi-résolution permettant ainsi une meilleure approximation des fonctions à forte irrégularité ou ayant des discontinuités. Enfin, nous nous sommes penchés sur le cas où les sorties du simulateur sont des séries temporelles. Pour ce faire, nous avons développé une méthodologie alliant la méthode de surface de réponse à base de spline de lissage avec une décomposition en ondelettes. Afin d'apprécier l'efficacité des méthodes proposées, des résultats sur des fonctions analytiques ainsi que sur des cas d'ingénierie de réservoir sont présentées. / The purpose of this thesis is to investigate innovative response surface methods to address the problem of sensitivity analysis of complex and computationally demanding computer codes. To this end, we have focused our research work on methods based on ANOVA decomposition. We proposed to use a smoothing spline nonparametric regression method, which is an ANOVA based method that is performed using an iterative algorithm, combining an estimation procedure and a variable selection procedure. The latter can become computationally demanding when dealing with high dimensional problems. To deal with this, we developed a new iterative shrinkage algorithm, which is conceptually simple and efficient. Using the fact that this method is an ANOVA based method, it allows us to introduce a new method for computing sensitivity indices. Inspiring by this response surface method, we developed a new method to approximate the model for which the response involves more complex outputs. This method is based on a multiresolution analysis with wavelet decompositions, which is well known to produce very good approximations on highly nonlinear or discontinuous models. Finally we considered the problem of approximating the computer code when the outputs are times series. We proposed an original method for performing this task, combining the smoothing spline response surface method and wavelet decomposition. To assess the efficiency of the developed methods, numerical experiments on analytical functions and reservoir engineering test cases are presented.

Data are valuable assets to any organizations or individuals. Data are sources of useful information which is a big part of decision making. All sectors have potential to benefit from having information. Commerce, health, and research are some of the fields that have benefited from data. On the other hand, the availability of the data makes it easy for anyone to exploit the data, which in many cases are private confidential data. It is necessary to preserve the confidentiality of the data. We study two categories of privacy: Data Value Hiding and Data Pattern Hiding. Privacy is a huge concern but equally important is the concern of data utility. Data should avoid privacy breach yet be usable. Although these two objectives are contradictory and achieving both at the same time is challenging, having knowledge of the purpose and the manner in which it will be utilized helps. In this research, we focus on some particular situations for clustering and classification problems and strive to balance the utility and privacy of the data. In the first part of this dissertation, we propose Nonnegative Matrix Factorization (NMF) based techniques that accommodate constraints defined explicitly into the update rules. These constraints determine how the factorization takes place leading to the favorable results. These methods are designed to make alterations on the matrices such that user-specified cluster properties are introduced. These methods can be used to preserve data value as well as data pattern. As NMF and K-means are proven to be equivalent, NMF is an ideal choice for pattern hiding for clustering problems. In addition to the NMF based methods, we propose methods that take into account the data structures and the attribute properties for the classification problems. We separate the work into two different parts: linear classifiers and nonlinear classifiers. We propose two different solutions based on the classifiers. We study the effect of distortion on the utility of data. We propose three distortion measurement metrics which demonstrate better characteristics than the traditional metrics. The effectiveness of the measures is examined on different benchmark datasets. The result shows that the methods have the desirable properties such as invariance to translation, rotation, and scaling.