Physical Sciences and Mathematics Commons^™

Machine Learning And Geostatistical Approaches For Discovery Of Weather And Climate Events Related To El Niño Phenomena, Sachi Perera

Computational and Data Sciences (PhD) Dissertations

El Nino and La Nina are worldwide environmental phenomena brought about by repetitive changes in the water temperature of the Pacific Ocean. Even though the El-Nino impact focuses on a smaller area in the Pacific Ocean near the Equator, these developments have global repercussions, where temperature and precipitation are influenced across the globe, causing droughts and floods simultaneously. In this dissertation, we first derived a drought vulnerability index for the Nile basin, identifying regions with high and low drought risk under ENSO conditions. Next, we evaluated the coherence and periodicity of the ENSO signal to detect its implications on MENA …

A Novel Correction For The Multivariate Ljung-Box Test, Minhao Huang

Computational and Data Sciences (PhD) Dissertations

This research introduces an analytical improvement to the Multivariate Ljung-Box test that addresses significant deviations of the original test from the nominal Type I error rates under almost all scenarios. Prior attempts to mitigate this issue have been directed at modification of the test statistics or correction of the test distribution to achieve precise results in finite samples. In previous studies, focused on designing corrections to the univariate Ljung-Box, a method that specifically adjusts the test rejection region has been the most successful of attaining the best Type I error rates. We adopt the same approach for the more complex, …

Random Variable Spaces: Mathematical Properties And An Extension To Programming Computable Functions, Mohammed Kurd-Misto

Computational and Data Sciences (PhD) Dissertations

This dissertation aims to extend the boundaries of Programming Computable Functions (PCF) by introducing a novel collection of categories referred to as Random Variable Spaces. Originating as a generalization of Quasi-Borel Spaces, Random Variable Spaces are rigorously defined as categories where objects are sets paired with a collection of random variables from an underlying measurable space. These spaces offer a theoretical foundation for extending PCF to natively handle stochastic elements.

The dissertation is structured into seven chapters that provide a multi-disciplinary background, from PCF and Measure Theory to Category Theory with special attention to Monads and the Giry Monad. The …

Computational Analysis Of Antibody Binding Mechanisms To The Omicron Rbd Of Sars-Cov-2 Spike Protein: Identification Of Epitopes And Hotspots For Developing Effective Therapeutic Strategies, Mohammed Alshahrani

Computational and Data Sciences (PhD) Dissertations

The advent of the Omicron strain of SARS-CoV-2 has elicited apprehension regarding its potential influence on the effectiveness of current vaccines and antibody treatments. The present investigation involved the implementation of mutational scanning analyses to examine the impact of Omicron mutations on the binding affinity of four categories of antibodies that target the Omicron receptor binding domain (RBD) of the Spike protein. The study demonstrates that the Omicron variant harbors 23 unique mutations across the RBD regions I, II, III, and IV. Of these mutations, seven are shared between RBD regions I and II, while three are shared among RBD …

Causal Inference Methods For Estimation Of Survival And General Health Status Measures Of Alzheimer’S Disease Patients, Ehsan Yaghmaei

Computational and Data Sciences (PhD) Dissertations

Identifying optimal treatment options with respect to survival of Alzheimer's disease patients is crucially important and previously uninvestigated research question. Our objective was to estimate the causal effects of the most prevalent classes of Alzheimer’s disease drugs, Donepezil and Memantine, and their combined use on Survival and General Health Status Measures of Alzheimer's disease patients for the first five years after initial diagnosis. We carried out a thorough causal inference study using doubly robust estimators, nonparametric bootstrap confidence intervals, Bonferroni corrections for multiple comparisons and analyzing one of the largest high-quality medical databases containing millions of de-identified electronic health records …

Computational Modeling Of Superconductivity From The Set Of Time-Dependent Ginzburg-Landau Equations For Advancements In Theory And Applications, Iris Mowgood

Computational and Data Sciences (PhD) Dissertations

A full review of the research conducted and published during my PhD studies in Computational and Data Sciences at Chapman University, under the advisement of Dr. Armen Gulian, are presented. Using the set of time-dependent Ginzburg-Landau (TDGL) equations with inclusion of the interference current and the non-equilibrium phonon term, we modeled the dynamics of superconductors in various theory revealing states and practical purposes. A review of the history and phenomenon of superconductivity, including modern applications, is introduced. The Josephson effect and associated Josephson junction are discussed for comparison to our analogous results with the 1-D superconducting wire. The mathematics of …

Perturbation Modeling For Molecular Design Of Protein Tyrosine Kinase Inhibitors Using Unsupervised Machine Learning, Keerthi Krishnan

Computational and Data Sciences (MS) Theses

The field of computational drug discovery and development has grown, with the aid of new computational tools for novel molecule discovery. In specific, generative deep learning models have excelled as tools to aid in navigating the large space of known molecules and in the creation of new molecules. These models are fed various representations of molecules as inputs and learn to perform a variety of things, such as the optimization of these molecules towards a targeted property. Ultimately, these generative learning models allow us to build bridges between chemical and continuous spaces to understand the compromise between invoking small incremental …

Causalmodels: An R Library For Estimating Causal Effects, Joshua Wolff Anderson

Computational and Data Sciences (MS) Theses

Free and open source software for statistical modeling and machine learning have advanced productivity in data science significantly. Packages such as SciPy in Python and caret in R provide fundamental tools for statistical modeling and machine learning in the two most popular programming languages used by data scientists. Unfortunately, robust tools similar to these are limited in terms of causal inference. The tools in R that exist lack consistent and standardized methodologies and inputs. R lacks a comprehensive package that offers traditional causal inference methods such as standardization, IP weighting, G-estimation, outcome regression, and propensity matching in one common package. …

Computational Approaches To Facilitate Automated Interchange Between Music And Art, Rao Hamza Ali

Computational and Data Sciences (PhD) Dissertations

Recently, there has been a tremendous increase in generating and synthesizing music and art using various computational techniques. An area that is still under-researched, however, is how one medium can be converted into the other, while maintaining the overall aesthetics. Over the last few centuries, artists, composers, and scholars, have attempted to use substitute one form of art for the other: by proposing techniques where music notes are synonymous to colors, by inventing instruments that combine the aesthetics of music and visual art, and by incorporating the two media in live performances. A widely accepted computational approach, for the conversion, …

Quantum State Estimation And Tracking For Superconducting Processors Using Machine Learning, Shiva Lotfallahzadeh Barzili

Computational and Data Sciences (PhD) Dissertations

Quantum technology has been rapidly growing; in particular, the experiments that have been performed with superconducting qubits and circuit QED have allowed us to explore the light-matter interaction at its most fundamental level. The study of coherent dynamics between two-level systems and resonator modes can provide insight into fundamental aspects of quantum physics, such as how the state of a system evolves while being continuously observed. To study such an evolving quantum system, experimenters need to verify the accuracy of state preparation and control since quantum systems are very fragile and sensitive to environmental disturbance. In this thesis, I look …

An Information-Theoretic Analysis Of Adherence To Physical Exercise Routines, Lily Foster

Computational and Data Sciences (MS) Theses

One of the most common recommendations in healthcare is to simply form healthy habits, but little research has been done to understand the formation and continuation of a healthy habit that isn’t heavily influenced by an individual’s interpretation. Arizona State University’s WalkIT study aimed to analyze how goal setting and financial reinforcement can influence moderate-to-vigorous physical activity (MVPA) in adults, while using data from accelerometers to alleviate individual bias. In this trial, 512 insufficiently active adults were recruited to wear an accelerometer for 1 year and were then randomly assigned to one of the four study groups. Each group had …

Automated Parsing Of Flexible Molecular Systems Using Principal Component Analysis And K-Means Clustering Techniques, Matthew J. Nwerem

Computational and Data Sciences (MS) Theses

Computational investigation of molecular structures and reactions of biological and pharmaceutical interests remains a grand scientific challenge due to the size and conformational flexibility of these systems. The work requires parsing and analyzing thousands of conformations in each molecular state for meaningful chemical information and subjecting the ensemble to costly quantum chemical calculations. The current status quo typically involves a manual process where the investigator must look at each conformation, separating each into structural families. This process is time-intensive and tedious, making this process infeasible in some cases, and limiting the ability of theoreticians to study these systems. However, the …

Multi-Modal Data Fusion, Image Segmentation, And Object Identification Using Unsupervised Machine Learning: Conception, Validation, Applications, And A Basis For Multi-Modal Object Detection And Tracking, Nicholas Lahaye

Computational and Data Sciences (PhD) Dissertations

Remote sensing and instrumentation is constantly improving and increasing in capability. Included within this, is the increase in amount of different instrument types, with various combinations of spatial and spectral resolutions, pointing angles, and various other instrument-specific qualities. While the increase in instruments, and therefore datasets, is a boon for those aiming to study the complexities of the various Earth systems, it can also present a large number of new challenges. With this information in mind, our group has set our aims on combining datasets with different spatial and spectral resolutions in an effective and as-general-as-possible way, with as little …

Exploring Behaviors Of Software Developers And Their Code Through Computational And Statistical Methods, Elia Eiroa Lledo

Computational and Data Sciences (PhD) Dissertations

As Artificial Intelligence (AI) increasingly penetrates all aspects of society, many obstacles emerge. This thesis identifies and discusses the issues facing Computer Vision and significant deficiencies in the Software Development Life-cycle that need to be resolved to facilitate the evolution toward true artificial intelligence. We explicitly review the concepts behind Convolutional Neural Network (CNN) models, the benchmark for computer vision. Chapter 2 highlights the mechanisms that have popularized CNNs while also specifying significant gaps that could garner the model inadequate for future use in safety-critical systems. We put forward two main limitations. Namely, CNNs do not use lack of information …

Enhancing Microbiome Host Disease Prediction With Variational Autoencoders, Celeste Manughian-Peter

Computational and Data Sciences (MS) Theses

Advancements in genetic sequencing methods for microbiomes in recent decades have permitted the collection of taxonomic and functional profiles of microbial communities, accelerating the discovery of the functional aspects of the microbiome and generating an increased interest among clinicians in applying these techniques with patients. This advancement has coincided with software and hardware improvements in the field of machine learning and deep learning. Combined, these advancements implicate further potential for progress in disease diagnosis and treatment in humans. The ability to classify a human microbiome profile into a disease category, and additionally identify the differentiating factors within the profile between …

Optimal Analytical Methods For High Accuracy Cardiac Disease Classification And Treatment Based On Ecg Data, Jianwei Zheng

Computational and Data Sciences (PhD) Dissertations

This work constitutes six projects. In the first project, a newly inaugurated research database for 12-lead electrocardiogram signals was created under the auspices of Chapman University and Shaoxing People's Hospital (Shaoxing Hospital Zhejiang University School of Medicine). This database aims to enable the scientific community in conducting new studies on arrhythmia and other cardiovascular conditions. In the second project, we created a new 12-lead ECG database under the auspices of Chapman University and Ningbo First Hospital of Zhejiang University that aims to provide high quality data enabling detection of the distinctions between idiopathic ventricular arrhythmia from right ventricular outflow tract …

Assessing The Re-Identification Risk In Ecg Datasets And An Application Of Privacy Preserving Techniques In Ecg Analysis, Arin Ghazarian

Computational and Data Sciences (PhD) Dissertations

In this work, first we investigate the use of ECG signal as a biometric in human identification systems using deep learning models. We train convolutional neural network models on ECG samples from approximately 81k patients. Our models achieved an over-all accuracy of 95.69%. Further, we assess the accuracy of our ECG identification model for distinct groups of patients with particular heart conditions and combinations of such conditions. For example, we observed that the identification accuracy was the highest (99.7%) for patients with both ST changes and supraventricular tachycardia. On the other hand, we also found that the identification rate was …

Novel Applications Of Statistical And Machine Learning Methods To Analyze Trial-Level Data From Cognitive Measures, Chelsea Parlett

Computational and Data Sciences (PhD) Dissertations

Many cognitive tasks and measures can benefit from trial-level analyses including Item Response Theory models as well as other Bayesian and Machine Learning models. Specifically, this dissertation focuses mainly on task-based measures of metamemory and how within-set variability as well as item-level characteristics can improve the inferences researchers make about these measures.First, a clustering analysis of judgements of learning across a task is examined in order to detect different participant strategies on a metamemory task and whether strategy use differs by age. Second, the benefits of using item response theory models to analyze both individual and item-level differences in metamemory …

Forecasting The Prices Of Cryptocurrencies Using A Novel Parameter Optimization Of Varima Models, Alexander Barrett

Computational and Data Sciences (PhD) Dissertations

This work is a comparative study of different univariate and multivariate time series predictive models as applied to Bitcoin, other cryptocurrencies, and other related financial time series data. ARIMA models, long regarded as the gold standard of univariate financial time series prediction due to both its flexibility and simplicity, are used a baseline for prediction. Given the highly correlative nature amongst different cryptocurrencies, this work aims to show the benefit of forecasting with multivariate time series models—primarily focusing on a novel parameter optimization of VARIMA models outlined in this paper.

These models are trained on 3 years of historical data, …

Applications Of Machine Learning To Facilitate Software Engineering And Scientific Computing, Natalie Best

Computational and Data Sciences (PhD) Dissertations

The use of machine learning has risen in recent years, though many areas remain unexplored due to lack of data or lack of computational tools. This dissertation explores machine learning approaches in case studies involving image classification and natural language processing. In addition, a software library in the form of two-way bridge connecting deep learning models in Keras with ones available in the Fortran programming language is also presented.

In Chapter 2, we explore the applicability of transfer learning utilizing models pre-trained on non-software engineering data applied to the problem of classifying software unified modeling language diagrams where data is …

Gaining Computational Insight Into Psychological Data: Applications Of Machine Learning With Eating Disorders And Autism Spectrum Disorder, Natalia Rosenfield

Computational and Data Sciences (PhD) Dissertations

Over the past 100 years, assessment tools have been developed that allow us to explore mental and behavioral processes that could not be measured before. However, conventional statistical models used for psychological data are lacking in thoroughness and predictability. This provides a perfect opportunity to use machine learning to study the data in a novel way. In this paper, we present examples of using machine learning techniques with data in three areas: eating disorders, body satisfaction, and Autism Spectrum Disorder (ASD). We explore clustering algorithms as well as virtual reality (VR).

Our first study employs the k-means clustering algorithm to …

A Novel Correction For The Adjusted Box-Pierce Test — New Risk Factors For Emergency Department Return Visits Within 72 Hours For Children With Respiratory Conditions — General Pediatric Model For Understanding And Predicting Prolonged Length Of Stay, Sidy Danioko

Computational and Data Sciences (PhD) Dissertations

This thesis represents the results of three research projects that underline the breadth and depth of my interests.

Firstly, I devoted some efforts to the well-known Box-Pierce goodness-of-fit tests for time series models which has been an important research topic over the last few decades. All previously proposed tests are focused on changes of the test statistics. Instead, I adopted a different approach that takes the best performing test and modifying the rejection region. Thus, I developed a semiparametric correction of the Adjusted Box-Pierce test that attains the best I error rates for all sample sizes and lags and outperforms …

Integrated Machine Learning And Bioinformatics Approaches For Prediction Of Cancer-Driving Gene Mutations, Oluyemi Odeyemi

Computational and Data Sciences (PhD) Dissertations

Cancer arises from the accumulation of somatic mutations and genetic alterations in cell division checkpoints and apoptosis, this often leads to abnormal tumor proliferation. Proper classification of cancer-linked driver mutations will considerably help our understanding of the molecular dynamics of cancer. In this study, we compared several cancer-specific predictive models for prediction of driver mutations in cancer-linked genes that were validated on canonical data sets of functionally validated mutations and applied to a raw cancer genomics data. By analyzing pathogenicity prediction and conservation scores, we have shown that evolutionary conservation scores play a pivotal role in the classification of cancer …

On Quantum Effects Of Vector Potentials And Generalizations Of Functional Analysis, Ismael L. Paiva

Computational and Data Sciences (PhD) Dissertations

This is a dissertation in two parts. In the first one, the Aharonov-Bohm effect is investigated. It is shown that solenoids (or flux lines) can be seen as barriers for quantum charges. In particular, a charge can be trapped in a sector of a long cavity by two flux lines. Also, grids of flux lines can approximate the force associated with continuous two-dimensional distributions of magnetic fields. More, if it is assumed that the lines can be as close to each other as desirable, it is explained how the classical magnetic force can emerge from the Aharonov-Bohm effect. Continuing, the …

Connecting The Dots For People With Autism: A Data-Driven Approach To Designing And Evaluating A Global Filter, Viseth Sean

Computational and Data Sciences (PhD) Dissertations

"Social communication is the use of language in social contexts. It encompasses social interaction, social cognition, pragmatics, and language processing” [3]. One presumed prerequisite of social communication is visual attention–the focus of this work. “Visual attention is a process that directs a tiny fraction of the information arriving at primary visual cortex to high-level centers involved in visual working memory and pattern recognition” [7]. This process involves the integration of two streams: the global and local streams; the global stream rapidly processes the scene, and the local stream processes details. This integration is important to social communication in that attending …

Exploring The Employment Landscape For Individuals With Autism Spectrum Disorders Using Supervised And Unsupervised Machine Learning, Kayleigh Hyde

Computational and Data Sciences (PhD) Dissertations

Autism Spectrum Disorders (ASD) are a class of neurodevelopmental disorders which usually present with difficulties in social interactions, verbal and nonverbal forms of communication, repetitive behaviors, and restricted interests. Employment rates of young adults with ASD is a national concern, and research suggests that young adults with “high functioning” ASD experience significant difficulty in transitioning to work. One of the goals of this study was to identify the barriers associated with these individuals’ transition into the world of work. A classification tree analysis was used with a sample of 236 caregivers of individuals with ASD or the individuals themselves, who …

Long Term Ground Based Precipitation Data Analysis: Spatial And Temporal Variability, Luciano Rodriguez

Computational and Data Sciences (PhD) Dissertations

This dissertation evaluates response variables (classifiers) on various models applied to the detection of El Niño Southern Oscillation (ENSO) on California’s seven climate divisions by using modeled and gauge (in-situ/ground) precipitation measurements and various climate indices. Three scientific studies were conducted as part of this research for evaluation of spatial and temporal ENSO events from modeled and gauge data using: 1) Wavelets 2) Autoregressive-moving-average (ARMA) model / Empirical Mode Decomposition (EMD) 3) Vector Generalized Linear Model (VGLM). This dissertation aims to propose and evaluate a methodology for developing a model to measure ENSO events accurately. The hypothesis is that precipitation …

Image Restoration Using Automatic Damaged Regions Detection And Machine Learning-Based Inpainting Technique, Chloe Martin-King

Computational and Data Sciences (PhD) Dissertations

In this dissertation we propose two novel image restoration schemes. The first pertains to automatic detection of damaged regions in old photographs and digital images of cracked paintings. In cases when inpainting mask generation cannot be completely automatic, our detection algorithm facilitates precise mask creation, particularly useful for images containing damage that is tedious to annotate or difficult to geometrically define. The main contribution of this dissertation is the development and utilization of a new inpainting technique, region hiding, to repair a single image by training a convolutional neural network on various transformations of that image. Region hiding is also …

Employing Earth Observations And Artificial Intelligence To Address Key Global Environmental Challenges In Service Of The Sdgs, Wenzhao Li

Computational and Data Sciences (PhD) Dissertations

Earth Observation (EO) data provides the capability to integrate data from multiple sources and helps to produce more relevant, frequent, and accurate information about complex processes. EO, empowered by methodologies from Artificial Intelligence (AI), supports various aspects of the UN’s Sustainable Development Goals (SDGs). This dissertation presents author’s major studies using EO to fill in knowledge gaps and develop methodologies and cloud-based applications in selected SDGs, including SDG 6 (Clean Water and Sanitation), SDG 11 (Sustainable Cities and Communities), SDG 14 (Life below Water) and SDG 15 (Life on Land). For SDG 6, the study focuses on spatiotemporal water recharge …

Classifying Challenging Behaviors In Autism Spectrum Disorder With Neural Document Embeddings, Abigail Atchison

Computational and Data Sciences (MS) Theses

The understanding and treatment of challenging behaviors in individuals with Autism Spectrum Disorder is paramount to enabling the success of behavioral therapy; an essential step in this process being the labeling of challenging behaviors demonstrated in therapy sessions. These manifestations differ across individuals and within individuals over time and thus, the appropriate classification of a challenging behavior when considering purely qualitative factors can be unclear. In this thesis we seek to add quantitative depth to this otherwise qualitative task of challenging behavior classification. We do so through the application of natural language processing techniques to behavioral descriptions extracted from the …