abstract: Sparse learning is a powerful tool to generate models of high-dimensional data with high interpretability, and it has many important applications in areas such as bioinformatics, medical image processing, and computer vision. Recently, the a priori structural information has been shown to be powerful for improving the performance of sparse learning models. A graph is a fundamental way to represent structural information of features. This dissertation focuses on graph-based sparse learning. The first part of this dissertation aims to integrate a graph into sparse learning to improve the performance. Specifically, the problem of feature grouping and selection over a given undirected graph is considered. Three models are proposed along with efficient solvers to achieve simultaneous feature grouping and selection, enhancing estimation accuracy. One major challenge is that it is still computationally challenging to solve large scale graph-based sparse learning problems. An efficient, scalable, and parallel algorithm for one widely used graph-based sparse learning approach, called anisotropic total variation regularization is therefore proposed, by explicitly exploring the structure of a graph. The second part of this dissertation focuses on uncovering the graph structure from the data. Two issues in graphical modeling are considered. One is the joint estimation of multiple graphical models using a fused lasso penalty and the other is the estimation of hierarchical graphical models. The key technical contribution is to establish the necessary and sufficient condition for the graphs to be decomposable. Based on this key property, a simple screening rule is presented, which reduces the size of the optimization problem, dramatically reducing the computational cost. / Dissertation/Thesis / Doctoral Dissertation Computer Science 2014

abstract: Drosophila melanogaster, as an important model organism, is used to explore the mechanism which governs cell differentiation and embryonic development. Understanding the mechanism will help to reveal the effects of genes on other species or even human beings. Currently, digital camera techniques make high quality Drosophila gene expression imaging possible. On the other hand, due to the advances in biology, gene expression images which can reveal spatiotemporal patterns are generated in a high-throughput pace. Thus, an automated and efficient system that can analyze gene expression will become a necessary tool for investigating the gene functions, interactions and developmental processes. One investigation method is to compare the expression patterns of different developmental stages. Recently, however, the expression patterns are manually annotated with rough stage ranges. The work of annotation requires professional knowledge from experienced biologists. Hence, how to transfer the domain knowledge in biology into an automated system which can automatically annotate the patterns provides a challenging problem for computer scientists. In this thesis, the problem of stage annotation for Drosophila embryo is modeled in the machine learning framework. Three sparse learning algorithms and one ensemble algorithm are used to attack the problem. The sparse algorithms are Lasso, group Lasso and sparse group Lasso. The ensemble algorithm is based on a voting method. Besides that the proposed algorithms can annotate the patterns to stages instead of stage ranges with high accuracy; the decimal stage annotation algorithm presents a novel way to annotate the patterns to decimal stages. In addition, some analysis on the algorithm performance are made and corresponding explanations are given. Finally, with the proposed system, all the lateral view BDGP and FlyFish images are annotated and several interesting applications of decimal stage value are revealed. / Dissertation/Thesis / M.S. Computer Science 2012

abstract: Sparsity has become an important modeling tool in areas such as genetics, signal and audio processing, medical image processing, etc. Via the penalization of l-1 norm based regularization, the structured sparse learning algorithms can produce highly accurate models while imposing various predefined structures on the data, such as feature groups or graphs. In this thesis, I first propose to solve a sparse learning model with a general group structure, where the predefined groups may overlap with each other. Then, I present three real world applications which can benefit from the group structured sparse learning technique. In the first application, I study the Alzheimer's Disease diagnosis problem using multi-modality neuroimaging data. In this dataset, not every subject has all data sources available, exhibiting an unique and challenging block-wise missing pattern. In the second application, I study the automatic annotation and retrieval of fruit-fly gene expression pattern images. Combined with the spatial information, sparse learning techniques can be used to construct effective representation of the expression images. In the third application, I present a new computational approach to annotate developmental stage for Drosophila embryos in the gene expression images. In addition, it provides a stage score that enables one to more finely annotate each embryo so that they are divided into early and late periods of development within standard stage demarcations. Stage scores help us to illuminate global gene activities and changes much better, and more refined stage annotations improve our ability to better interpret results when expression pattern matches are discovered between genes. / Dissertation/Thesis / Ph.D. Computer Science 2013

In this research, a novel machine learning method is designed and applied to Mine Countermeasure Missions. Similarly to some kernel methods, the proposed approach seeks to compute a linear model from another higher dimensional feature space. However, no kernel is used and the feature mapping is explicit. Computation can be done directly in the accessible feature space. In the proposed approach, the feature projection is implemented by constructing a large hidden layer, which differs from traditional belief that Multi-Layer Perceptron is usually funnel-shaped and the hidden layer is used as feature extractor. The proposed approach is a general method that can be applied to various problems. It is able to improve the performance of the neural network based methods and the learning speed of support vector machine. The classification speed of the proposed approach is also faster than that of kernel machines on the mine countermeasure mission task.

abstract: Computer vision technology automatically extracts high level, meaningful information from visual data such as images or videos, and the object recognition and detection algorithms are essential in most computer vision applications. In this dissertation, we focus on developing algorithms used for real life computer vision applications, presenting innovative algorithms for object segmentation and feature extraction for objects and actions recognition in video data, and sparse feature selection algorithms for medical image analysis, as well as automated feature extraction using convolutional neural network for blood cancer grading. To detect and classify objects in video, the objects have to be separated from the background, and then the discriminant features are extracted from the region of interest before feeding to a classifier. Effective object segmentation and feature extraction are often application specific, and posing major challenges for object detection and classification tasks. In this dissertation, we address effective object flow based ROI generation algorithm for segmenting moving objects in video data, which can be applied in surveillance and self driving vehicle areas. Optical flow can also be used as features in human action recognition algorithm, and we present using optical flow feature in pre-trained convolutional neural network to improve performance of human action recognition algorithms. Both algorithms outperform the state-of-the-arts at their time. Medical images and videos pose unique challenges for image understanding mainly due to the fact that the tissues and cells are often irregularly shaped, colored, and textured, and hand selecting most discriminant features is often difficult, thus an automated feature selection method is desired. Sparse learning is a technique to extract the most discriminant and representative features from raw visual data. However, sparse learning with \textit{L1} regularization only takes the sparsity in feature dimension into consideration; we improve the algorithm so it selects the type of features as well; less important or noisy feature types are entirely removed from the feature set. We demonstrate this algorithm to analyze the endoscopy images to detect unhealthy abnormalities in esophagus and stomach, such as ulcer and cancer. Besides sparsity constraint, other application specific constraints and prior knowledge may also need to be incorporated in the loss function in sparse learning to obtain the desired results. We demonstrate how to incorporate similar-inhibition constraint, gaze and attention prior in sparse dictionary selection for gastroscopic video summarization that enable intelligent key frame extraction from gastroscopic video data. With recent advancement in multi-layer neural networks, the automatic end-to-end feature learning becomes feasible. Convolutional neural network mimics the mammal visual cortex and can extract most discriminant features automatically from training samples. We present using convolutinal neural network with hierarchical classifier to grade the severity of Follicular Lymphoma, a type of blood cancer, and it reaches 91\% accuracy, on par with analysis by expert pathologists. Developing real world computer vision applications is more than just developing core vision algorithms to extract and understand information from visual data; it is also subject to many practical requirements and constraints, such as hardware and computing infrastructure, cost, robustness to lighting changes and deformation, ease of use and deployment, etc.The general processing pipeline and system architecture for the computer vision based applications share many similar design principles and architecture. We developed common processing components and a generic framework for computer vision application, and a versatile scale adaptive template matching algorithm for object detection. We demonstrate the design principle and best practices by developing and deploying a complete computer vision application in real life, building a multi-channel water level monitoring system, where the techniques and design methodology can be generalized to other real life applications. The general software engineering principles, such as modularity, abstraction, robust to requirement change, generality, etc., are all demonstrated in this research. / Dissertation/Thesis / Doctoral Dissertation Computer Science 2018

In this research, a novel machine learning method is designed and applied to Mine Countermeasure Missions. Similarly to some kernel methods, the proposed approach seeks to compute a linear model from another higher dimensional feature space. However, no kernel is used and the feature mapping is explicit. Computation can be done directly in the accessible feature space. In the proposed approach, the feature projection is implemented by constructing a large hidden layer, which differs from traditional belief that Multi-Layer Perceptron is usually funnel-shaped and the hidden layer is used as feature extractor. The proposed approach is a general method that can be applied to various problems. It is able to improve the performance of the neural network based methods and the learning speed of support vector machine. The classification speed of the proposed approach is also faster than that of kernel machines on the mine countermeasure mission task.

No description available.

abstract: Sparse learning is a technique in machine learning for feature selection and dimensionality reduction, to find a sparse set of the most relevant features. In any machine learning problem, there is a considerable amount of irrelevant information, and separating relevant information from the irrelevant information has been a topic of focus. In supervised learning like regression, the data consists of many features and only a subset of the features may be responsible for the result. Also, the features might require special structural requirements, which introduces additional complexity for feature selection. The sparse learning package, provides a set of algorithms for learning a sparse set of the most relevant features for both regression and classification problems. Structural dependencies among features which introduce additional requirements are also provided as part of the package. The features may be grouped together, and there may exist hierarchies and over- lapping groups among these, and there may be requirements for selecting the most relevant groups among them. In spite of getting sparse solutions, the solutions are not guaranteed to be robust. For the selection to be robust, there are certain techniques which provide theoretical justification of why certain features are selected. The stability selection, is a method for feature selection which allows the use of existing sparse learning methods to select the stable set of features for a given training sample. This is done by assigning probabilities for the features: by sub-sampling the training data and using a specific sparse learning technique to learn the relevant features, and repeating this a large number of times, and counting the probability as the number of times a feature is selected. Cross-validation which is used to determine the best parameter value over a range of values, further allows to select the best parameter value. This is done by selecting the parameter value which gives the maximum accuracy score. With such a combination of algorithms, with good convergence guarantees, stable feature selection properties and the inclusion of various structural dependencies among features, the sparse learning package will be a powerful tool for machine learning research. Modular structure, C implementation, ATLAS integration for fast linear algebraic subroutines, make it one of the best tool for a large sparse setting. The varied collection of algorithms, support for group sparsity, batch algorithms, are a few of the notable functionality of the SLEP package, and these features can be used in a variety of fields to infer relevant elements. The Alzheimer Disease(AD) is a neurodegenerative disease, which gradually leads to dementia. The SLEP package is used for feature selection for getting the most relevant biomarkers from the available AD dataset, and the results show that, indeed, only a subset of the features are required to gain valuable insights. / Dissertation/Thesis / M.S. Computer Science 2011

abstract: Large-scale $\ell_1$-regularized loss minimization problems arise in high-dimensional applications such as compressed sensing and high-dimensional supervised learning, including classification and regression problems. In many applications, it remains challenging to apply the sparse learning model to large-scale problems that have massive data samples with high-dimensional features. One popular and promising strategy is to scaling up the optimization problem in parallel. Parallel solvers run multiple cores on a shared memory system or a distributed environment to speed up the computation, while the practical usage is limited by the huge dimension in the feature space and synchronization problems. In this dissertation, I carry out the research along the direction with particular focuses on scaling up the optimization of sparse learning for supervised and unsupervised learning problems. For the supervised learning, I firstly propose an asynchronous parallel solver to optimize the large-scale sparse learning model in a multithreading environment. Moreover, I propose a distributed framework to conduct the learning process when the dataset is distributed stored among different machines. Then the proposed model is further extended to the studies of risk genetic factors for Alzheimer's Disease (AD) among different research institutions, integrating a group feature selection framework to rank the top risk SNPs for AD. For the unsupervised learning problem, I propose a highly efficient solver, termed Stochastic Coordinate Coding (SCC), scaling up the optimization of dictionary learning and sparse coding problems. The common issue for the medical imaging research is that the longitudinal features of patients among different time points are beneficial to study together. To further improve the dictionary learning model, I propose a multi-task dictionary learning method, learning the different task simultaneously and utilizing shared and individual dictionary to encode both consistent and changing imaging features. / Dissertation/Thesis / Doctoral Dissertation Computer Science 2017

abstract: Many learning models have been proposed for various tasks in visual computing. Popular examples include hidden Markov models and support vector machines. Recently, sparse-representation-based learning methods have attracted a lot of attention in the computer vision field, largely because of their impressive performance in many applications. In the literature, many of such sparse learning methods focus on designing or application of some learning techniques for certain feature space without much explicit consideration on possible interaction between the underlying semantics of the visual data and the employed learning technique. Rich semantic information in most visual data, if properly incorporated into algorithm design, should help achieving improved performance while delivering intuitive interpretation of the algorithmic outcomes. My study addresses the problem of how to explicitly consider the semantic information of the visual data in the sparse learning algorithms. In this work, we identify four problems which are of great importance and broad interest to the community. Specifically, a novel approach is proposed to incorporate label information to learn a dictionary which is not only reconstructive but also discriminative; considering the formation process of face images, a novel image decomposition approach for an ensemble of correlated images is proposed, where a subspace is built from the decomposition and applied to face recognition; based on the observation that, the foreground (or salient) objects are sparse in input domain and the background is sparse in frequency domain, a novel and efficient spatio-temporal saliency detection algorithm is proposed to identify the salient regions in video; and a novel hidden Markov model learning approach is proposed by utilizing a sparse set of pairwise comparisons among the data, which is easier to obtain and more meaningful, consistent than tradition labels, in many scenarios, e.g., evaluating motion skills in surgical simulations. In those four problems, different types of semantic information are modeled and incorporated in designing sparse learning algorithms for the corresponding visual computing tasks. Several real world applications are selected to demonstrate the effectiveness of the proposed methods, including, face recognition, spatio-temporal saliency detection, abnormality detection, spatio-temporal interest point detection, motion analysis and emotion recognition. In those applications, data of different modalities are involved, ranging from audio signal, image to video. Experiments on large scale real world data with comparisons to state-of-art methods confirm the proposed approaches deliver salient advantages, showing adding those semantic information dramatically improve the performances of the general sparse learning methods. / Dissertation/Thesis / Ph.D. Computer Science 2014