One of the main objectives of software development in scientific computing is efficiency. Being focused on highly specialized application domain, important software quality metrics, e.g., usability, extensibility ,etc may not be amongst the list of primary objectives. In this research, we have studied the design structures and iterative releases of scientific research software using Design Structure Matrix(DSM). We implemented a DSM partitioning algorithm using sparse matrix data structure Compressed Row Storage(CRS), and its timing was better than those obtained from the most widely used C++ library boost. Secondly, we computed several architectural complexity metrics, compared releases and total release costs of a number of open source scientific research software. One of the important finding is the absence of circular dependencies in studied software which attributes to the strong emphasis on computational performance of the code. Iterative release analysis indicates that there might be a correspondence between “clustering co-efficient” and “release rework cost” of the software. / x, 87 leaves : ill. ; 29 cm

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This thesis is dedicated to the active research topic of generic Visual Object Categorization(VOC), which can be widely used in many applications such as videoindexation and retrieval, video monitoring, security access control, automobile drivingsupport etc. Due to many realistic difficulties, it is still considered to be one ofthe most challenging problems in computer vision and pattern recognition. In thiscontext, we have proposed in this thesis our contributions, especially concerning thetwo main components of the methods addressing VOC problems, namely featureselection and image representation.Firstly, an Embedded Sequential Forward feature Selection algorithm (ESFS)has been proposed for VOC. Its aim is to select the most discriminant features forobtaining a good performance for the categorization. It is mainly based on thecommonly used sub-optimal search method Sequential Forward Selection (SFS),which relies on the simple principle to add incrementally most relevant features.However, ESFS not only adds incrementally most relevant features in each stepbut also merges them in an embedded way thanks to the concept of combinedmass functions from the evidence theory which also offers the benefit of obtaining acomputational cost much lower than the one of original SFS.Secondly, we have proposed novel image representations to model the visualcontent of an image, namely Polynomial Modeling and Statistical Measures basedImage Representation, called PMIR and SMIR respectively. They allow to overcomethe main drawback of the popular "bag of features" method which is the difficultyto fix the optimal size of the visual vocabulary. They have been tested along withour proposed region based features and SIFT. Two different fusion strategies, earlyand late, have also been considered to merge information from different "channels"represented by the different types of features.Thirdly, we have proposed two approaches for VOC relying on sparse representation,including a reconstructive method (R_SROC) as well as a reconstructiveand discriminative one (RD_SROC). Indeed, sparse representation model has beenoriginally used in signal processing as a powerful tool for acquiring, representingand compressing the high-dimensional signals. Thus, we have proposed to adaptthese interesting principles to the VOC problem. R_SROC relies on the intuitiveassumption that an image can be represented by a linear combination of trainingimages from the same category. Therefore, the sparse representations of images arefirst computed through solving the ℓ1 norm minimization problem and then usedas new feature vectors for images to be classified by traditional classifiers such asSVM. To improve the discrimination ability of the sparse representation to betterfit the classification problem, we have also proposed RD_SROC which includes adiscrimination term, such as Fisher discrimination measure or the output of a SVMclassifier, to the standard sparse representation objective function in order to learna reconstructive and discriminative dictionary. Moreover, we have also proposedChapter 0. Abstractto combine the reconstructive and discriminative dictionary and the adapted purereconstructive dictionary for a given category so that the discrimination power canfurther be increased.The efficiency of all the methods proposed in this thesis has been evaluated onpopular image datasets including SIMPLIcity, Caltech101 and Pascal2007.

<p>Polynomial chaos expansions provide an efficient and robust framework to analyze and quantify uncertainty in computational models. This dissertation explores the use of adaptive sparse grids to reduce the computational cost of determining a polynomial model surrogate while examining and implementing new adaptive techniques.</p><p>Determination of chaos coefficients using traditional tensor product quadrature suffers the so-called curse of dimensionality, where the number of model evaluations scales exponentially with dimension. Previous work used a sparse Smolyak quadrature to temper this dimensional scaling, and was applied successfully to an expensive Ocean General Circulation Model, HYCOM during the September 2004 passing of Hurricane Ivan through the Gulf of Mexico. Results from this investigation suggested that adaptivity could yield great gains in efficiency. However, efforts at adaptivity are hampered by quadrature accuracy requirements.</p><p>We explore the implementation of a novel adaptive strategy to design sparse ensembles of oceanic simulations suitable for constructing polynomial chaos surrogates. We use a recently developed adaptive pseudo-spectral projection (aPSP) algorithm that is based on a direct application of Smolyak's sparse grid formula, and that allows for the use of arbitrary admissible sparse grids. Such a construction ameliorates the severe restrictions posed by insufficient quadrature accuracy. The adaptive algorithm is tested using an existing simulation database of the HYCOM model during Hurricane Ivan. The {\it a priori} tests demonstrate that sparse and adaptive pseudo-spectral constructions lead to substantial savings over isotropic sparse sampling.</p><p>In order to provide a finer degree of resolution control along two distinct subsets of model parameters, we investigate two methods to build polynomial approximations. The two approaches are based with pseudo-spectral projection (PSP) methods on adaptively constructed sparse grids. The control of the error along different subsets of parameters may be needed in the case of a model depending on uncertain parameters and deterministic design variables. We first consider a nested approach where an independent adaptive sparse grid pseudo-spectral projection is performed along the first set of directions only, and at each point a sparse grid is constructed adaptively in the second set of directions. We then consider the application of aPSP in the space of all parameters, and introduce directional refinement criteria to provide a tighter control of the projection error along individual dimensions. Specifically, we use a Sobol decomposition of the projection surpluses to tune the sparse grid adaptation. The behavior and performance of the two approaches are compared for a simple two-dimensional test problem and for a shock-tube ignition model involving 22 uncertain parameters and 3 design parameters. The numerical experiments indicate that whereas both methods provide effective means for tuning the quality of the representation along distinct subsets of parameters, adaptive PSP in the global parameter space generally requires fewer model evaluations than the nested approach to achieve similar projection error. </p><p>In order to increase efficiency even further, a subsampling technique is developed to allow for local adaptivity within the aPSP algorithm. The local refinement is achieved by exploiting the hierarchical nature of nested quadrature grids to determine regions of estimated convergence. In order to achieve global representations with local refinement, synthesized model data from a lower order projection is used for the final projection. The final subsampled grid was also tested with two more robust, sparse projection techniques including compressed sensing and hybrid least-angle-regression. These methods are evaluated on two sample test functions and then as an {\it a priori} analysis of the HYCOM simulations and the shock-tube ignition model investigated earlier. Small but non-trivial efficiency gains were found in some cases and in others, a large reduction in model evaluations with only a small loss of model fidelity was realized. Further extensions and capabilities are recommended for future investigations.</p> / Dissertation

In modern power transmission systems, the double-circuit line structure is increasingly adopted. However, due to the mutual coupling between the parallel lines it is quite challenging to design accurate fault location algorithms. Moreover, the widely used series compensator and its protective device introduce harmonics and non-linearities to the transmission lines, which make fault location more difficult. To tackle these problems, this dissertation is committed to developing advanced fault location methods for double-circuit and series-compensated transmission lines. Algorithms utilizing sparse measurements for pinpointing the location of short-circuit faults on double-circuit lines are proposed. By decomposing the original network into three sequence networks, the bus impedance matrix for each network with the addition of the fictitious fault bus can be formulated. It is a function of the unknown fault location. With the augmented bus impedance matrices the sequence voltage change during the fault at any bus can be expressed in terms of the corresponding sequence fault current and the transfer impedance between the fault bus and the measured bus. Resorting to VCR the superimposed sequence current at any branch can be expressed with respect to the pertaining sequence fault current and transfer impedance terms. Obeying boundary conditions of different fault types, four different classes of fault location algorithms utilizing either voltage phasors, or phase voltage magnitudes, or current phasors, or phase current magnitudes are derived. The distinguishing charactristic of the proposed method is that the data measurements need not stem from the faulted section itself. Quite satisfactory results have been obtained using EMTP simulation studies. A fault location algorithm for series-compensated transmission lines that employs two-terminal unsynchronized voltage and current measurements has been implemented. For the distinct cases that the fault occurs either on the left or on the right side of the series compensator, two subroutines are developed. In additon, the procedure to identify the correct fault location estimate is described in this work. Simulation studies carried out with Matlab SimPowerSystems show that the fault location results are very accurate.

A limited set of Processing Element (PE) pairs in a parallel computer cover the internal communications of scalable parallel programs. We take advantage of this property using the concept of Sparse Flat Neighborhood Networks (Sparse FNNs). Sparse FNNs are network designs that provide single-switch latency and full wire bandwidth for each specified PE pair, despite using relatively few network interfaces per PE and switches that have far fewer ports than there are PEs. This dissertation discusses the design problem, runtime support, and working prototype (KASY0) for Sparse FNNs. KASY0 not only demonstrated the claimed properties, but also set world records for its price/performance and performance on a specific application. Parallel supercomputers execute many portions of an application simultaneously. For scalable programs, the more PEs the system has, the greater the potential speedup. Portions executing on different PEs may be able to work independently for short periods, but the performance desired might not be achieved due to delays in communication between PEs. The set of PE pairs that will communicate often is both predictable and small relative to the number of possible PE pairings. This sparseness property can be exploited in the design and implementation of networks for massively parallel supercomputers. The sparseness of communicating pairs is rooted in the fact that each of the human-designed communication patterns commonly used in parallel programs has the property that the number of communicating pairs grows relatively slowly as the number of PEs is increased. Additionally, the number of pairs in the union of all communication patterns used in a suite of parallel programs grows surprisingly slowly due to pair synergy: the same pair often appears in multiple communication patterns. Detailed analysis of communication patterns clearly shows that the number of PE pairs actually communicating is very sparse, although the structure of the sparseness can be complex.

Nuclei/Cell detection is usually a prerequisite procedure in many computer-aided biomedical image analysis tasks. In this thesis we propose two automatic nuclei/cell detection frameworks. One is for nuclei detection in skeletal muscle fiber images and the other is for brain tumor histopathological images. For skeletal muscle fiber images, the major challenges include: i) shape and size variations of the nuclei, ii) overlapping nuclear clumps, and iii) a series of z-stack images with out-of-focus regions. We propose a novel automatic detection algorithm consisting of the following components: 1) The original z-stack images are first converted into one all-in-focus image. 2) A sufficient number of hypothetical ellipses are then generated for each nuclei contour. 3) Next, a set of representative training samples and discriminative features are selected by a two-stage sparse model. 4) A classifier is trained using the refined training data. 5) Final nuclei detection is obtained by mean-shift clustering based on inner distance. The proposed method was tested on a set of images containing over 1500 nuclei. The results outperform the current state-of-the-art approaches. For brain tumor histopathological images, the major challenges are to handle significant variations in cell appearance and to split touching cells. The proposed novel automatic cell detection consists of: 1) Sparse reconstruction for splitting touching cells. 2) Adaptive dictionary learning for handling cell appearance variations. The proposed method was extensively tested on a data set with over 2000 cells. The result outperforms other state-of-the-art algorithms with F1 score = 0.96.

This dissertation shows that nonnegative matrix factorization (NMF) can be extended to a general and efficient clustering method. Clustering is one of the fundamental tasks in machine learning. It is useful for unsupervised knowledge discovery in a variety of applications such as text mining and genomic analysis. NMF is a dimension reduction method that approximates a nonnegative matrix by the product of two lower rank nonnegative matrices, and has shown great promise as a clustering method when a data set is represented as a nonnegative data matrix. However, challenges in the widespread use of NMF as a clustering method lie in its correctness and efficiency: First, we need to know why and when NMF could detect the true clusters and guarantee to deliver good clustering quality; second, existing algorithms for computing NMF are expensive and often take longer time than other clustering methods. We show that the original NMF can be improved from both aspects in the context of clustering. Our new NMF-based clustering methods can achieve better clustering quality and run orders of magnitude faster than the original NMF and other clustering methods. Like other clustering methods, NMF places an implicit assumption on the cluster structure. Thus, the success of NMF as a clustering method depends on whether the representation of data in a vector space satisfies that assumption. Our approach to extending the original NMF to a general clustering method is to switch from the vector space representation of data points to a graph representation. The new formulation, called Symmetric NMF, takes a pairwise similarity matrix as an input and can be viewed as a graph clustering method. We evaluate this method on document clustering and image segmentation problems and find that it achieves better clustering accuracy. In addition, for the original NMF, it is difficult but important to choose the right number of clusters. We show that the widely-used consensus NMF in genomic analysis for choosing the number of clusters have critical flaws and can produce misleading results. We propose a variation of the prediction strength measure arising from statistical inference to evaluate the stability of clusters and select the right number of clusters. Our measure shows promising performances in artificial simulation experiments. Large-scale applications bring substantial efficiency challenges to existing algorithms for computing NMF. An important example is topic modeling where users want to uncover the major themes in a large text collection. Our strategy of accelerating NMF-based clustering is to design algorithms that better suit the computer architecture as well as exploit the computing power of parallel platforms such as the graphic processing units (GPUs). A key observation is that applying rank-2 NMF that partitions a data set into two clusters in a recursive manner is much faster than applying the original NMF to obtain a flat clustering. We take advantage of a special property of rank-2 NMF and design an algorithm that runs faster than existing algorithms due to continuous memory access. Combined with a criterion to stop the recursion, our hierarchical clustering algorithm runs significantly faster and achieves even better clustering quality than existing methods. Another bottleneck of NMF algorithms, which is also a common bottleneck in many other machine learning applications, is to multiply a large sparse data matrix with a tall-and-skinny dense matrix. We use the GPUs to accelerate this routine for sparse matrices with an irregular sparsity structure. Overall, our algorithm shows significant improvement over popular topic modeling methods such as latent Dirichlet allocation, and runs more than 100 times faster on data sets with millions of documents.