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Unsupervised learning of time series data, also known as temporal clustering, is a challenging problem in machine learning. This thesis presents a novel algorithm, Deep Temporal Clustering (DTC), to naturally integrate dimensionality reduction and temporal clustering into a single end-to-end learning framework, fully unsupervised. The algorithm utilizes an autoencoder for temporal dimensionality reduction and a novel temporal clustering layer for cluster assignment. Then it jointly optimizes the clustering objective and the dimensionality reduction objective. Based on requirement and application, the temporal clustering layer can be customized with any temporal similarity metric. Several similarity metrics and state-of-the-art algorithms are considered and compared. To gain insight into temporal features that the network has learned for its clustering, a visualization method is applied that generates a region of interest heatmap for the time series. The viability of the algorithm is demonstrated using time series data from diverse domains, ranging from earthquakes to spacecraft sensor data. In each case, the proposed algorithm outperforms traditional methods. The superior performance is attributed to the fully integrated temporal dimensionality reduction and clustering criterion.
ContributorsMadiraju, NaveenSai (Author) / Liang, Jianming (Thesis advisor) / Wang, Yalin (Thesis advisor) / He, Jingrui (Committee member) / Arizona State University (Publisher)
Created2018
Description
Yersinia enterocolitica is a major foodborne pathogen found worldwide that causes approximately 87,000 human cases and approximately 1,100 hospitalizations per year in the United States. Y. enterocolitica is a very unique pathogen with the domesticated pig acting as the main animal reservoir for pathogenic bio/serotypes, and as the primary source of human infection. Similar to other gastrointestinal infections, Yersinia enterocolitica is known to trigger autoimmune responses in humans. The most frequent complication associated with Y. enterocolitica is reactive arthritis - an aseptic, asymmetrical inflammation in the peripheral and axial joints, most frequently occurring as an autoimmune response in patients with the HLA-B27 histocompatability antigen. As a foodborne illness it may prove to be a reasonable explanation for some of the cases of arthritis observed in past populations that are considered to be of unknown etiology. The goal of this dissertation project was to study the relationship between the foodborne illness -Y. enterocolitica, and the incidence of arthritis in individuals with and without contact with the domesticated pig.
ContributorsBrown, Starletta (Author) / Hurtado, Ana M (Thesis advisor) / Chowell-Puente, Gerardo (Committee member) / Hill, Kim (Committee member) / Arizona State University (Publisher)
Created2015
Description
Understanding the complexity of temporal and spatial characteristics of gene expression over brain development is one of the crucial research topics in neuroscience. An accurate description of the locations and expression status of relative genes requires extensive experiment resources. The Allen Developing Mouse Brain Atlas provides a large number of in situ hybridization (ISH) images of gene expression over seven different mouse brain developmental stages. Studying mouse brain models helps us understand the gene expressions in human brains. This atlas collects about thousands of genes and now they are manually annotated by biologists. Due to the high labor cost of manual annotation, investigating an efficient approach to perform automated gene expression annotation on mouse brain images becomes necessary. In this thesis, a novel efficient approach based on machine learning framework is proposed. Features are extracted from raw brain images, and both binary classification and multi-class classification models are built with some supervised learning methods. To generate features, one of the most adopted methods in current research effort is to apply the bag-of-words (BoW) algorithm. However, both the efficiency and the accuracy of BoW are not outstanding when dealing with large-scale data. Thus, an augmented sparse coding method, which is called Stochastic Coordinate Coding, is adopted to generate high-level features in this thesis. In addition, a new multi-label classification model is proposed in this thesis. Label hierarchy is built based on the given brain ontology structure. Experiments have been conducted on the atlas and the results show that this approach is efficient and classifies the images with a relatively higher accuracy.
ContributorsZhao, Xinlin (Author) / Ye, Jieping (Thesis advisor) / Wang, Yalin (Thesis advisor) / Li, Baoxin (Committee member) / Arizona State University (Publisher)
Created2016
Description
The rapid growth of social media in recent years provides a large amount of user-generated visual objects, e.g., images and videos. Advanced semantic understanding approaches on such visual objects are desired to better serve applications such as human-machine interaction, image retrieval, etc. Semantic visual attributes have been proposed and utilized in multiple visual computing tasks to bridge the so-called "semantic gap" between extractable low-level feature representations and high-level semantic understanding of the visual objects.
Despite years of research, there are still some unsolved problems on semantic attribute learning. First, real-world applications usually involve hundreds of attributes which requires great effort to acquire sufficient amount of labeled data for model learning. Second, existing attribute learning work for visual objects focuses primarily on images, with semantic analysis on videos left largely unexplored.
In this dissertation I conduct innovative research and propose novel approaches to tackling the aforementioned problems. In particular, I propose robust and accurate learning frameworks on both attribute ranking and prediction by exploring the correlation among multiple attributes and utilizing various types of label information. Furthermore, I propose a video-based skill coaching framework by extending attribute learning to the video domain for robust motion skill analysis. Experiments on various types of applications and datasets and comparisons with multiple state-of-the-art baseline approaches confirm that my proposed approaches can achieve significant performance improvements for the general attribute learning problem.
Despite years of research, there are still some unsolved problems on semantic attribute learning. First, real-world applications usually involve hundreds of attributes which requires great effort to acquire sufficient amount of labeled data for model learning. Second, existing attribute learning work for visual objects focuses primarily on images, with semantic analysis on videos left largely unexplored.
In this dissertation I conduct innovative research and propose novel approaches to tackling the aforementioned problems. In particular, I propose robust and accurate learning frameworks on both attribute ranking and prediction by exploring the correlation among multiple attributes and utilizing various types of label information. Furthermore, I propose a video-based skill coaching framework by extending attribute learning to the video domain for robust motion skill analysis. Experiments on various types of applications and datasets and comparisons with multiple state-of-the-art baseline approaches confirm that my proposed approaches can achieve significant performance improvements for the general attribute learning problem.
ContributorsChen, Lin (Author) / Li, Baoxin (Thesis advisor) / Turaga, Pavan (Committee member) / Wang, Yalin (Committee member) / Liu, Huan (Committee member) / Arizona State University (Publisher)
Created2016
Description
In many fields one needs to build predictive models for a set of related machine learning tasks, such as information retrieval, computer vision and biomedical informatics. Traditionally these tasks are treated independently and the inference is done separately for each task, which ignores important connections among the tasks. Multi-task learning aims at simultaneously building models for all tasks in order to improve the generalization performance, leveraging inherent relatedness of these tasks. In this thesis, I firstly propose a clustered multi-task learning (CMTL) formulation, which simultaneously learns task models and performs task clustering. I provide theoretical analysis to establish the equivalence between the CMTL formulation and the alternating structure optimization, which learns a shared low-dimensional hypothesis space for different tasks. Then I present two real-world biomedical informatics applications which can benefit from multi-task learning. In the first application, I study the disease progression problem and present multi-task learning formulations for disease progression. In the formulations, the prediction at each point is a regression task and multiple tasks at different time points are learned simultaneously, leveraging the temporal smoothness among the tasks. The proposed formulations have been tested extensively on predicting the progression of the Alzheimer's disease, and experimental results demonstrate the effectiveness of the proposed models. In the second application, I present a novel data-driven framework for densifying the electronic medical records (EMR) to overcome the sparsity problem in predictive modeling using EMR. The densification of each patient is a learning task, and the proposed algorithm simultaneously densify all patients. As such, the densification of one patient leverages useful information from other patients.
ContributorsZhou, Jiayu (Author) / Ye, Jieping (Thesis advisor) / Mittelmann, Hans (Committee member) / Li, Baoxin (Committee member) / Wang, Yalin (Committee member) / Arizona State University (Publisher)
Created2014
Description
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.
ContributorsZhang, Qiang (Author) / Li, Baoxin (Thesis advisor) / Turaga, Pavan (Committee member) / Wang, Yalin (Committee member) / Ye, Jieping (Committee member) / Arizona State University (Publisher)
Created2014
Description
In this thesis, the application of pixel-based vertical axes used within parallel coordinate plots is explored in an attempt to improve how existing tools can explain complex multivariate interactions across temporal data. Several promising visualization techniques are combined, such as: visual boosting to allow for quicker consumption of large data sets, the bond energy algorithm to find finer patterns and anomalies through contrast, multi-dimensional scaling, flow lines, user guided clustering, and row-column ordering. User input is applied on precomputed data sets to provide for real time interaction. General applicability of the techniques are tested against industrial trade, social networking, financial, and sparse data sets of varying dimensionality.
ContributorsHayden, Thomas (Author) / Maciejewski, Ross (Thesis advisor) / Wang, Yalin (Committee member) / Runger, George C. (Committee member) / Mack, Elizabeth (Committee member) / Arizona State University (Publisher)
Created2014
Description
Extraordinary medical advances have led to significant reductions in the burden of infectious diseases in humans. However, infectious diseases still account for more than 13 million annual deaths. This large burden is partly due to some pathogens having found suitable conditions to emerge and spread in denser and more connected host populations, and others having evolved to escape the pressures imposed by the rampant use of antimicrobials. It is then critical to improve our understanding of how diseases spread in these modern landscapes, characterized by new host population structures and socio-economic environments, as well as containment measures such as the deployment of drugs. Thus, the motivation of this dissertation is two-fold. First, we study, using both data-driven and modeling approaches, the the spread of infectious diseases in urban areas. As a case study, we use confirmed-cases data on sexually transmitted diseases (STDs) in the United States to assess the conduciveness of population size of urban areas and their socio-economic characteristics as predictors of STD incidence. We find that the scaling of STD incidence in cities is superlinear, and that the percent of African-Americans residing in cities largely determines these statistical patterns. Since disparities in access to health care are often exacerbated in urban areas, within this project we also develop two modeling frameworks to study the effect of health care disparities on epidemic outcomes. Discrepant results between the two approaches indicate that knowledge of the shape of the recovery period distribution, not just its mean and variance, is key for assessing the epidemiological impact of inequalities. The second project proposes to study, from a modeling perspective, the spread of drug resistance in human populations featuring vital dynamics, stochasticity and contact structure. We derive effective treatment regimes that minimize both the overall disease burden and the spread of resistance. Additionally, targeted treatment in structured host populations may lead to higher levels of drug resistance, and if drug-resistant strains are compensated, they can spread widely even when the wild-type strain is below its epidemic threshold.
ContributorsPatterson-Lomba, Oscar (Author) / Castillo-Chavez, Carlos (Thesis advisor) / Towers, Sherry (Thesis advisor) / Chowell-Puente, Gerardo (Committee member) / Arizona State University (Publisher)
Created2014
Description
Urban scaling analysis has introduced a new scientific paradigm to the study of cities. With it, the notions of size, heterogeneity and structure have taken a leading role. These notions are assumed to be behind the causes for why cities differ from one another, sometimes wildly. However, the mechanisms by which size, heterogeneity and structure shape the general statistical patterns that describe urban economic output are still unclear. Given the rapid rate of urbanization around the globe, we need precise and formal mathematical understandings of these matters. In this context, I perform in this dissertation probabilistic, distributional and computational explorations of (i) how the broadness, or narrowness, of the distribution of individual productivities within cities determines what and how we measure urban systemic output, (ii) how urban scaling may be expressed as a statistical statement when urban metrics display strong stochasticity, (iii) how the processes of aggregation constrain the variability of total urban output, and (iv) how the structure of urban skills diversification within cities induces a multiplicative process in the production of urban output.
ContributorsGómez-Liévano, Andrés (Author) / Lobo, Jose (Thesis advisor) / Muneepeerakul, Rachata (Thesis advisor) / Bettencourt, Luis M. A. (Committee member) / Chowell-Puente, Gerardo (Committee member) / Arizona State University (Publisher)
Created2014
Description
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.
ContributorsYang, Sen (Author) / Ye, Jieping (Thesis advisor) / Wonka, Peter (Thesis advisor) / Wang, Yalin (Committee member) / Li, Jing (Committee member) / Arizona State University (Publisher)
Created2014