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Description
The rate of progress in improving survival of patients with solid tumors is slow due to late stage diagnosis and poor tumor characterization processes that fail to effectively reflect the nature of tumor before treatment or the subsequent change in its dynamics because of treatment. Further advancement of targeted therapies

The rate of progress in improving survival of patients with solid tumors is slow due to late stage diagnosis and poor tumor characterization processes that fail to effectively reflect the nature of tumor before treatment or the subsequent change in its dynamics because of treatment. Further advancement of targeted therapies relies on advancements in biomarker research. In the context of solid tumors, bio-specimen samples such as biopsies serve as the main source of biomarkers used in the treatment and monitoring of cancer, even though biopsy samples are susceptible to sampling error and more importantly, are local and offer a narrow temporal scope.

Because of its established role in cancer care and its non-invasive nature imaging offers the potential to complement the findings of cancer biology. Over the past decade, a compelling body of literature has emerged suggesting a more pivotal role for imaging in the diagnosis, prognosis, and monitoring of diseases. These advances have facilitated the rise of an emerging practice known as Radiomics: the extraction and analysis of large numbers of quantitative features from medical images to improve disease characterization and prediction of outcome. It has been suggested that radiomics can contribute to biomarker discovery by detecting imaging traits that are complementary or interchangeable with other markers.

This thesis seeks further advancement of imaging biomarker discovery. This research unfolds over two aims: I) developing a comprehensive methodological pipeline for converting diagnostic imaging data into mineable sources of information, and II) investigating the utility of imaging data in clinical diagnostic applications. Four validation studies were conducted using the radiomics pipeline developed in aim I. These studies had the following goals: (1 distinguishing between benign and malignant head and neck lesions (2) differentiating benign and malignant breast cancers, (3) predicting the status of Human Papillomavirus in head and neck cancers, and (4) predicting neuropsychological performances as they relate to Alzheimer’s disease progression. The long-term objective of this thesis is to improve patient outcome and survival by facilitating incorporation of routine care imaging data into decision making processes.
ContributorsRanjbar, Sara (Author) / Kaufman, David (Thesis advisor) / Mitchell, Joseph R. (Thesis advisor) / Runger, George C. (Committee member) / Arizona State University (Publisher)
Created2017
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Description
Our ability to understand networks is important to many applications, from the analysis and modeling of biological networks to analyzing social networks. Unveiling network dynamics allows us to make predictions and decisions. Moreover, network dynamics models have inspired new ideas for computational methods involving multi-agent cooperation, offering effective solutions for

Our ability to understand networks is important to many applications, from the analysis and modeling of biological networks to analyzing social networks. Unveiling network dynamics allows us to make predictions and decisions. Moreover, network dynamics models have inspired new ideas for computational methods involving multi-agent cooperation, offering effective solutions for optimization tasks. This dissertation presents new theoretical results on network inference and multi-agent optimization, split into two parts -

The first part deals with modeling and identification of network dynamics. I study two types of network dynamics arising from social and gene networks. Based on the network dynamics, the proposed network identification method works like a `network RADAR', meaning that interaction strengths between agents are inferred by injecting `signal' into the network and observing the resultant reverberation. In social networks, this is accomplished by stubborn agents whose opinions do not change throughout a discussion. In gene networks, genes are suppressed to create desired perturbations. The steady-states under these perturbations are characterized. In contrast to the common assumption of full rank input, I take a laxer assumption where low-rank input is used, to better model the empirical network data. Importantly, a network is proven to be identifiable from low rank data of rank that grows proportional to the network's sparsity. The proposed method is applied to synthetic and empirical data, and is shown to offer superior performance compared to prior work. The second part is concerned with algorithms on networks. I develop three consensus-based algorithms for multi-agent optimization. The first method is a decentralized Frank-Wolfe (DeFW) algorithm. The main advantage of DeFW lies on its projection-free nature, where we can replace the costly projection step in traditional algorithms by a low-cost linear optimization step. I prove the convergence rates of DeFW for convex and non-convex problems. I also develop two consensus-based alternating optimization algorithms --- one for least square problems and one for non-convex problems. These algorithms exploit the problem structure for faster convergence and their efficacy is demonstrated by numerical simulations.

I conclude this dissertation by describing future research directions.
ContributorsWai, Hoi To (Author) / Scaglione, Anna (Thesis advisor) / Berisha, Visar (Committee member) / Nedich, Angelia (Committee member) / Ying, Lei (Committee member) / Arizona State University (Publisher)
Created2017
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Description
The subliminal impact of framing of social, political and environmental issues such as climate change has been studied for decades in political science and communications research. Media framing offers an “interpretative package" for average citizens on how to make sense of climate change and its consequences to their livelihoods, how

The subliminal impact of framing of social, political and environmental issues such as climate change has been studied for decades in political science and communications research. Media framing offers an “interpretative package" for average citizens on how to make sense of climate change and its consequences to their livelihoods, how to deal with its negative impacts, and which mitigation or adaptation policies to support. A line of related work has used bag of words and word-level features to detect frames automatically in text. Such works face limitations since standard keyword based features may not generalize well to accommodate surface variations in text when different keywords are used for similar concepts.

This thesis develops a unique type of textual features that generalize triplets extracted from text, by clustering them into high-level concepts. These concepts are utilized as features to detect frames in text. Compared to uni-gram and bi-gram based models, classification and clustering using generalized concepts yield better discriminating features and a higher classification accuracy with a 12% boost (i.e. from 74% to 83% F-measure) and 0.91 clustering purity for Frame/Non-Frame detection.

The automatic discovery of complex causal chains among interlinked events and their participating actors has not yet been thoroughly studied. Previous studies related to extracting causal relationships from text were based on laborious and incomplete hand-developed lists of explicit causal verbs, such as “causes" and “results in." Such approaches result in limited recall because standard causal verbs may not generalize well to accommodate surface variations in texts when different keywords and phrases are used to express similar causal effects. Therefore, I present a system that utilizes generalized concepts to extract causal relationships. The proposed algorithms overcome surface variations in written expressions of causal relationships and discover the domino effects between climate events and human security. This semi-supervised approach alleviates the need for labor intensive keyword list development and annotated datasets. Experimental evaluations by domain experts achieve an average precision of 82%. Qualitative assessments of causal chains show that results are consistent with the 2014 IPCC report illuminating causal mechanisms underlying the linkages between climatic stresses and social instability.
ContributorsAlashri, Saud (Author) / Davulcu, Hasan (Thesis advisor) / Desouza, Kevin C. (Committee member) / Maciejewski, Ross (Committee member) / Hsiao, Sharon (Committee member) / Arizona State University (Publisher)
Created2018
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Description
The performance of most of the visual computing tasks depends on the quality of the features extracted from the raw data. Insightful feature representation increases the performance of many learning algorithms by exposing the underlying explanatory factors of the output for the unobserved input. A good representation should also handle

The performance of most of the visual computing tasks depends on the quality of the features extracted from the raw data. Insightful feature representation increases the performance of many learning algorithms by exposing the underlying explanatory factors of the output for the unobserved input. A good representation should also handle anomalies in the data such as missing samples and noisy input caused by the undesired, external factors of variation. It should also reduce the data redundancy. Over the years, many feature extraction processes have been invented to produce good representations of raw images and videos.

The feature extraction processes can be categorized into three groups. The first group contains processes that are hand-crafted for a specific task. Hand-engineering features requires the knowledge of domain experts and manual labor. However, the feature extraction process is interpretable and explainable. Next group contains the latent-feature extraction processes. While the original feature lies in a high-dimensional space, the relevant factors for a task often lie on a lower dimensional manifold. The latent-feature extraction employs hidden variables to expose the underlying data properties that cannot be directly measured from the input. Latent features seek a specific structure such as sparsity or low-rank into the derived representation through sophisticated optimization techniques. The last category is that of deep features. These are obtained by passing raw input data with minimal pre-processing through a deep network. Its parameters are computed by iteratively minimizing a task-based loss.

In this dissertation, I present four pieces of work where I create and learn suitable data representations. The first task employs hand-crafted features to perform clinically-relevant retrieval of diabetic retinopathy images. The second task uses latent features to perform content-adaptive image enhancement. The third task ranks a pair of images based on their aestheticism. The goal of the last task is to capture localized image artifacts in small datasets with patch-level labels. For both these tasks, I propose novel deep architectures and show significant improvement over the previous state-of-art approaches. A suitable combination of feature representations augmented with an appropriate learning approach can increase performance for most visual computing tasks.
ContributorsChandakkar, Parag Shridhar (Author) / Li, Baoxin (Thesis advisor) / Yang, Yezhou (Committee member) / Turaga, Pavan (Committee member) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2017
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Description
Machine learning models convert raw data in the form of video, images, audio,

text, etc. into feature representations that are convenient for computational process-

ing. Deep neural networks have proven to be very efficient feature extractors for a

variety of machine learning tasks. Generative models based on deep neural networks

introduce constraints on the

Machine learning models convert raw data in the form of video, images, audio,

text, etc. into feature representations that are convenient for computational process-

ing. Deep neural networks have proven to be very efficient feature extractors for a

variety of machine learning tasks. Generative models based on deep neural networks

introduce constraints on the feature space to learn transferable and disentangled rep-

resentations. Transferable feature representations help in training machine learning

models that are robust across different distributions of data. For example, with the

application of transferable features in domain adaptation, models trained on a source

distribution can be applied to a data from a target distribution even though the dis-

tributions may be different. In style transfer and image-to-image translation, disen-

tangled representations allow for the separation of style and content when translating

images.

This thesis examines learning transferable data representations in novel deep gen-

erative models. The Semi-Supervised Adversarial Translator (SAT) utilizes adversar-

ial methods and cross-domain weight sharing in a neural network to extract trans-

ferable representations. These transferable interpretations can then be decoded into

the original image or a similar image in another domain. The Explicit Disentangling

Network (EDN) utilizes generative methods to disentangle images into their core at-

tributes and then segments sets of related attributes. The EDN can separate these

attributes by controlling the ow of information using a novel combination of losses

and network architecture. This separation of attributes allows precise modi_cations

to speci_c components of the data representation, boosting the performance of ma-

chine learning tasks. The effectiveness of these models is evaluated across domain

adaptation, style transfer, and image-to-image translation tasks.
ContributorsEusebio, Jose Miguel Ang (Author) / Panchanathan, Sethuraman (Thesis advisor) / Davulcu, Hasan (Committee member) / Venkateswara, Hemanth (Committee member) / Arizona State University (Publisher)
Created2018
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Description
It is well known that the overall performance of a solar cell is limited by the worst performing areas of the device. These areas are usually micro and nano-scale defects inhomogenously distributed throughout the material. Mitigating and/or engineering these effects is necessary to provide a path towards increasing the efficiency

It is well known that the overall performance of a solar cell is limited by the worst performing areas of the device. These areas are usually micro and nano-scale defects inhomogenously distributed throughout the material. Mitigating and/or engineering these effects is necessary to provide a path towards increasing the efficiency of state-of-the-art solar cells. The first big challenge is to identify the nature, origin and impact of such defects across length scales that span multiple orders of magnitude, and dimensions (time, temperature etc.). In this work, I present a framework based on correlative X-ray microscopy and big data analytics to identify micro and nanoscale defects and their impact on material properties in CuIn1-xGaxSe2 (CIGS) solar cells.

Synchrotron based X-ray Fluorescence (XRF) and X-ray Beam Induced Current (XBIC) are used to study the effect that compositional variations, between grains and at grain boundaries, have on CIGS device properties. An experimental approach is presented to correcting XRF and XBIC quantification of CIGS thin film solar cells. When applying XRF and XBIC to study low and high gallium CIGS devices, it was determined that increased copper and gallium at grain boundaries leads to increased collection efficiency at grain boundaries in low gallium absorbers. However, composition variations were not correlated with changes in collection efficiency in high gallium absorbers, despite the decreased collection efficiency observed at grain boundaries.

Understanding the nature and impact of these defects is only half the battle; controlling or mitigating their impact is the next challenge. This requires a thorough understanding of the origin of these defects and their kinetics. For such a study, a temperature and atmosphere controlled in situ stage was developed. The stage was utilized to study CIGS films during a rapid thermal growth process. Comparing composition variations across different acquisition times and growth temperatures required the implementation of machine learning techniques, including clustering and classification algorithms. From the analysis, copper was determined to segregate the faster than indium and gallium, and clustering techniques showed consistent elemental segregation into copper rich and copper poor regions. Ways to improve the current framework and new applications are also discussed.
ContributorsWest, Bradley (Author) / Bertoni, Mariana I (Thesis advisor) / Verebelyi, Darren (Committee member) / Holman, Zachary (Committee member) / Rose, Volker (Committee member) / Arizona State University (Publisher)
Created2018
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Description
The goal of diagnostic assessment is to discriminate between groups. In many cases, a binary decision is made conditional on a cut score from a continuous scale. Psychometric methods can improve assessment by modeling a latent variable using item response theory (IRT), and IRT scores can subsequently be used to

The goal of diagnostic assessment is to discriminate between groups. In many cases, a binary decision is made conditional on a cut score from a continuous scale. Psychometric methods can improve assessment by modeling a latent variable using item response theory (IRT), and IRT scores can subsequently be used to determine a cut score using receiver operating characteristic (ROC) curves. Psychometric methods provide reliable and interpretable scores, but the prediction of the diagnosis is not the primary product of the measurement process. In contrast, machine learning methods, such as regularization or binary recursive partitioning, can build a model from the assessment items to predict the probability of diagnosis. Machine learning predicts the diagnosis directly, but does not provide an inferential framework to explain why item responses are related to the diagnosis. It remains unclear whether psychometric and machine learning methods have comparable accuracy or if one method is preferable in some situations. In this study, Monte Carlo simulation methods were used to compare psychometric and machine learning methods on diagnostic classification accuracy. Results suggest that classification accuracy of psychometric models depends on the diagnostic-test correlation and prevalence of diagnosis. Also, machine learning methods that reduce prediction error have inflated specificity and very low sensitivity compared to the data-generating model, especially when prevalence is low. Finally, machine learning methods that use ROC curves to determine probability thresholds have comparable classification accuracy to the psychometric models as sample size, number of items, and number of item categories increase. Therefore, results suggest that machine learning models could provide a viable alternative for classification in diagnostic assessments. Strengths and limitations for each of the methods are discussed, and future directions are considered.
ContributorsGonzález, Oscar (Author) / Mackinnon, David P (Thesis advisor) / Edwards, Michael C (Thesis advisor) / Grimm, Kevin J. (Committee member) / Zheng, Yi (Committee member) / Arizona State University (Publisher)
Created2018
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Description
This research start utilizing an efficient sparse inverse covariance matrix (precision matrix) estimation technique to identify a set of highly correlated discriminative perspectives between radical and counter-radical groups. A ranking system has been developed that utilizes ranked perspectives to map Islamic organizations on a set of socio-cultural, political and behavioral

This research start utilizing an efficient sparse inverse covariance matrix (precision matrix) estimation technique to identify a set of highly correlated discriminative perspectives between radical and counter-radical groups. A ranking system has been developed that utilizes ranked perspectives to map Islamic organizations on a set of socio-cultural, political and behavioral scales based on their web site corpus. Simultaneously, a gold standard ranking of these organizations was created through domain experts and compute expert-to-expert agreements and present experimental results comparing the performance of the QUIC based scaling system to another baseline method for organizations. The QUIC based algorithm not only outperforms the baseline methods, but it is also the only system that consistently performs at area expert-level accuracies for all scales. Also, a multi-scale ideological model has been developed and it investigates the correlates of Islamic extremism in Indonesia, Nigeria and UK. This analysis demonstrate that violence does not correlate strongly with broad Muslim theological or sectarian orientations; it shows that religious diversity intolerance is the only consistent and statistically significant ideological correlate of Islamic extremism in these countries, alongside desire for political change in UK and Indonesia, and social change in Nigeria. Next, dynamic issues and communities tracking system based on NMF(Non-negative Matrix Factorization) co-clustering algorithm has been built to better understand the dynamics of virtual communities. The system used between Iran and Saudi Arabia to build and apply a multi-party agent-based model that can demonstrate the role of wedges and spoilers in a complex environment where coalitions are dynamic. Lastly, a visual intelligence platform for tracking the diffusion of online social movements has been developed called LookingGlass to track the geographical footprint, shifting positions and flows of individuals, topics and perspectives between groups. The algorithm utilize large amounts of text collected from a wide variety of organizations’ media outlets to discover their hotly debated topics, and their discriminative perspectives voiced by opposing camps organized into multiple scales. Discriminating perspectives is utilized to classify and map individual Tweeter’s message content to social movements based on the perspectives expressed in their tweets.
ContributorsKim, Nyunsu (Author) / Davulcu, Hasan (Thesis advisor) / Sen, Arunabha (Committee member) / Hsiao, Sharon (Committee member) / Corman, Steven (Committee member) / Arizona State University (Publisher)
Created2018
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Description
In healthcare facilities, health information systems (HISs) are used to serve different purposes. The radiology department adopts multiple HISs in managing their operations and patient care. In general, the HISs that touch radiology fall into two categories: tracking HISs and archive HISs. Electronic Health Records (EHR) is a typical tracking

In healthcare facilities, health information systems (HISs) are used to serve different purposes. The radiology department adopts multiple HISs in managing their operations and patient care. In general, the HISs that touch radiology fall into two categories: tracking HISs and archive HISs. Electronic Health Records (EHR) is a typical tracking HIS, which tracks the care each patient receives at multiple encounters and facilities. Archive HISs are typically specialized databases to store large-size data collected as part of the patient care. A typical example of an archive HIS is the Picture Archive and Communication System (PACS), which provides economical storage and convenient access to diagnostic images from multiple modalities. How to integrate such HISs and best utilize their data remains a challenging problem due to the disparity of HISs as well as high-dimensionality and heterogeneity of the data. My PhD dissertation research includes three inter-connected and integrated topics and focuses on designing integrated HISs and further developing statistical models and machine learning algorithms for process and patient care improvement.

Topic 1: Design of super-HIS and tracking of quality of care (QoC). My research developed an information technology that integrates multiple HISs in radiology, and proposed QoC metrics defined upon the data that measure various dimensions of care. The DDD assisted the clinical practices and enabled an effective intervention for reducing lengthy radiologist turnaround times for patients.

Topic 2: Monitoring and change detection of QoC data streams for process improvement. With the super-HIS in place, high-dimensional data streams of QoC metrics are generated. I developed a statistical model for monitoring high- dimensional data streams that integrated Singular Vector Decomposition (SVD) and process control. The algorithm was applied to QoC metrics data, and additionally extended to another application of monitoring traffic data in communication networks.

Topic 3: Deep transfer learning of archive HIS data for computer-aided diagnosis (CAD). The novelty of the CAD system is the development of a deep transfer learning algorithm that combines the ideas of transfer learning and multi- modality image integration under the deep learning framework. Our system achieved high accuracy in breast cancer diagnosis compared with conventional machine learning algorithms.
ContributorsWang, Kun (Author) / Li, Jing (Thesis advisor) / Wu, Teresa (Committee member) / Pan, Rong (Committee member) / Zwart, Christine M. (Committee member) / Arizona State University (Publisher)
Created2018
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Description
The recent technological advances enable the collection of various complex, heterogeneous and high-dimensional data in biomedical domains. The increasing availability of the high-dimensional biomedical data creates the needs of new machine learning models for effective data analysis and knowledge discovery. This dissertation introduces several unsupervised and supervised methods to hel

The recent technological advances enable the collection of various complex, heterogeneous and high-dimensional data in biomedical domains. The increasing availability of the high-dimensional biomedical data creates the needs of new machine learning models for effective data analysis and knowledge discovery. This dissertation introduces several unsupervised and supervised methods to help understand the data, discover the patterns and improve the decision making. All the proposed methods can generalize to other industrial fields.

The first topic of this dissertation focuses on the data clustering. Data clustering is often the first step for analyzing a dataset without the label information. Clustering high-dimensional data with mixed categorical and numeric attributes remains a challenging, yet important task. A clustering algorithm based on tree ensembles, CRAFTER, is proposed to tackle this task in a scalable manner.

The second part of this dissertation aims to develop data representation methods for genome sequencing data, a special type of high-dimensional data in the biomedical domain. The proposed data representation method, Bag-of-Segments, can summarize the key characteristics of the genome sequence into a small number of features with good interpretability.

The third part of this dissertation introduces an end-to-end deep neural network model, GCRNN, for time series classification with emphasis on both the accuracy and the interpretation. GCRNN contains a convolutional network component to extract high-level features, and a recurrent network component to enhance the modeling of the temporal characteristics. A feed-forward fully connected network with the sparse group lasso regularization is used to generate the final classification and provide good interpretability.

The last topic centers around the dimensionality reduction methods for time series data. A good dimensionality reduction method is important for the storage, decision making and pattern visualization for time series data. The CRNN autoencoder is proposed to not only achieve low reconstruction error, but also generate discriminative features. A variational version of this autoencoder has great potential for applications such as anomaly detection and process control.
ContributorsLin, Sangdi (Author) / Runger, George C. (Thesis advisor) / Kocher, Jean-Pierre A (Committee member) / Pan, Rong (Committee member) / Escobedo, Adolfo R. (Committee member) / Arizona State University (Publisher)
Created2018