Digital Commons Network^™

Model-Based Deep Autoencoders For Clustering Single-Cell Rna Sequencing Data With Side Information, Xiang Lin

Dissertations

Clustering analysis has been conducted extensively in single-cell RNA sequencing (scRNA-seq) studies. scRNA-seq can profile tens of thousands of genes' activities within a single cell. Thousands or tens of thousands of cells can be captured simultaneously in a typical scRNA-seq experiment. Biologists would like to cluster these cells for exploring and elucidating cell types or subtypes. Numerous methods have been designed for clustering scRNA-seq data. Yet, single-cell technologies develop so fast in the past few years that those existing methods do not catch up with these rapid changes and fail to fully fulfil their potential. For instance, besides profiling transcription …

Mitigating The Shortcomings Of Language Models: Strategies For Handling Memorization & Adversarial Attacks, Aly Kassem

Electronic Theses and Dissertations

Deep learning models have recently achieved remarkable progress in Natural Language Processing (NLP), specifically in classification, question-answering, and machine translation. However, NLP models face challenges related to security and privacy. Security-wise, even small perturbations in the input can significantly impact a model's prediction. This highlights the importance of generating natural adversarial attacks to analyze the weaknesses of NLP models and bolster their robustness through adversarial training (AT). Conversely, Large Language Models (LLMs) are trained on vast amounts of data, which may include sensitive information. If exposed, this poses a risk to personal privacy. LLMs can memorize portions of their training …

Advanced Deep Learning Multivariate Multi-Time Series Framework For A Novel Covid-19 Dataset, Swastik Bagga

Electronic Theses and Dissertations

This thesis introduces an innovative framework aimed at addressing the complexities of predicting outcomes in multivariate multi time series datasets in regression analysis. By applying this framework to a novel COVID-19 dataset, it enhances predictive analytics by providing accurate forecasts for epidemic trends at regional or provincial levels, going beyond national-level analysis. The framework incorporates advanced data preprocessing, feature selection, engineering, encoding, and model architecture, effectively capturing intricate variable interactions and temporal dependencies. This makes it a powerful tool for tackling multivariate multi time series regression challenges, offering valuable insights for informed decision-making. Predicting outcomes in such datasets is challenging …

Enhancing Urban Life: A Policy-Based Autonomic Smart City Management System For Efficient, Sustainable, And Self-Adaptive Urban Environments, Elham Okhovat

Electronic Thesis and Dissertation Repository

This thesis proposes the concept of the Policy-based Autonomic Smart City Management System, an innovative framework designed to comprehensively manage diverse aspects of urban environments, ranging from environmental conditions such as temperature and air quality to the infrastructure which comprises multiple layers of infrastructure, from sensors and devices to advanced IoT platforms and applications. Efficient management requires continuous monitoring of devices and infrastructure, data analysis, and real-time resource assessment to ensure seamless city operations and improve residents' quality of life. Automating data monitoring is essential due to the vast array of hardware and data exchanges, and round-the-clock monitoring is critical. …

Smart Applications And Resource Management In Internet Of Things, Zeinab Akhavan

Computer Science ETDs

Internet of Things (IoT) technologies are currently the principal solutions driving smart cities. These new technologies such as Cyber Physical Systems, 5G and data analytic have emerged to address various cities' infrastructure issues ranging from transportation and energy management to healthcare systems. An IoT setting primarily consists of a wide range of users and devices as a massive network interacting with different layers of the city infrastructure resulting in generating sheer volume of data to enable smart city services. The goal of smart city services is to create value for the entire ecosystem, whether this is health, education, transportation, energy, …

Computational Study Of The Effect Of Geometry On Molecular Interactions, Sarika Kumar

Computer Science ETDs

The specificity and predictability of DNA make it an excellent programmable material and have allowed bio-programmers to build sophisticated molecular circuits. These molecular devices should be precise, correct, and function as intended. In order to implement these circuits, the challenge is to build a robust, reliable, and scalable logic circuit with ideally minimum unwanted signal release. Performing experiments are expensive and time-consuming, so modeling and analyzing these bio-molecular systems become crucial in designing molecular circuits. This dissertation aimed to develop algorithms and build computational tools for automated analysis of molecular circuits that incorporate the molecular geometry of nanostructures. Molecular circuits …

Roadside Lidar Data Processing For Intelligent Transportation System, Md Parvez Mollah

Computer Science ETDs

Roadside LiDAR (Light Detection and Ranging) sensors are recently being explored for Intelligent Transportation System aiming at safer and faster traffic management and vehicular operations. However, massive data volume, occlusion, and limited viewing angles are significant obstacles to the widespread use of roadside LiDARs. In this dissertation, we address three major challenges to enable applications of Intelligent Transportation System through roadside LiDAR data: (i) real-time transmission of the massive point-cloud data from the roadside LiDAR devices to the cloud using 5G network, (ii) mitigating sensor occlusion problem to increase coverage and detect events occurred in occluded regions of a sensor, …

Context-Driven Behavior: Improved Contextual Reasoning For Context-Aware Agents, Christian L. Wilson

Electronic Theses and Dissertations

Over the last three decades, a considerable amount of research has been dedicated to improving an artificial agent's ability to recognize and deal effectively with context. In this paper, I discuss a framework for a novel form of contextual reasoning. Unlike existing contextual reasoning frameworks, which allow an agent to apply its contextual knowledge after it is operating in an instance of a known context, the model I discuss allows an agent to reason about context proactively. With a proactive model, an agent forecasts the future contexts it will encounter, then takes steps to ensure its behaviors are appropriate for …

Learning Mortality Risk For Covid-19 Using Machine Learning And Statistical Methods, Shaoshi Zhang

Electronic Thesis and Dissertation Repository

This research investigates the mortality risk of COVID-19 patients across different variant waves, using the data from Centers for Disease Control and Prevention (CDC) websites. By analyzing the available data, including patient medical records, vaccination rates, and hospital capacities, we aim to discern patterns and factors associated with COVID-19-related deaths.

To explore features linked to COVID-19 mortality, we employ different techniques such as Filter, Wrapper, and Embedded methods for feature selection. Furthermore, we apply various machine learning methods, including support vector machines, decision trees, random forests, logistic regression, K-nearest neighbours, na¨ıve Bayes methods, and artificial neural networks, to uncover underlying …

Probing And Enhancing The Reliance Of Transformer Models On Poetic Information, Almas Abdibayev

Dartmouth College Ph.D Dissertations

Transformer models have achieved remarkable success in the widest variety of domains, spanning not just a multitude of tasks within natural language processing, but also those in computer vision, speech, and reinforcement learning. The key to this success is largely attributed to the self-attention mechanism, particularly its ability to scale in performance as it grows in the number of parameters. Extensive effort has been underway to study the major linguistic properties learned by these models during the course of their pretraining. However, the role of certain finer linguistic phenomena present in language and their utilization by Transformers has not been …

Cta’S ‘L’ System Visualization And Animation, Julia Finegan

Honors Capstones

The Chicago Transit Authority (CTA) is a vital public transportation system for the city of Chicago and the surrounding suburbs, and all of its ‘L’ train data was recorded from March 2022 to February 2023 for this research. The main goal of this project was to create interactive/animated charts, graphs, and/or transit maps to present this raw data in a meaningful form that could help future researchers learn more about the CTA system, its patterns, and/or its unexplained inconsistencies/irregularities. A simple animation of the ‘L’ trains running within a specified time frame was created with the Python libraries Pandas, Shapely, …

Cm-Ii Meditation As An Intervention To Reduce Stress And Improve Attention: A Study Of Ml Detection, Spectral Analysis, And Hrv Metrics, Sreekanth Gopi

Master of Science in Computer Science Theses

Students frequently face heightened stress due to academic and social pressures, particularly in de- manding fields like computer science and engineering. These challenges are often associated with serious mental health issues, including ADHD (Attention Deficit Hyperactivity Disorder), depression, and an increased risk of suicide. The average student attention span has notably decreased from 21⁄2 minutes to just 47 seconds, and now it typically takes about 25 minutes to switch attention to a new task (Mark, 2023). Research findings suggest that over 95% of individuals who die by suicide have been diagnosed with depression (Shahtahmasebi, 2013), and almost 20% of students …

Phenotyping Cotton Compactness Using Machine Learning And Uas Multispectral Imagery, Joshua Carl Waldbieser

Theses and Dissertations

Breeding compact cotton plants is desirable for many reasons, but current research for this is restricted by manual data collection. Using unmanned aircraft system imagery shows potential for high-throughput automation of this process. Using multispectral orthomosaics and ground truth measurements, I developed supervised models with a wide range of hyperparameters to predict three compactness traits. Extreme gradient boosting using a feature matrix as input was able to predict the height-related metric with R2=0.829 and RMSE=0.331. The breadth metrics require higher-detailed data and more complex models to predict accurately.

Designing An Artificial Immune Inspired Intrusion Detection System, William Hosier Anderson

Theses and Dissertations

The domain of Intrusion Detection Systems (IDS) has witnessed growing interest in recent years due to the escalating threats posed by cyberattacks. As Internet of Things (IoT) becomes increasingly integrated into our every day lives, we widen our attack surface and expose more of our personal lives to risk. In the same way the Human Immune System (HIS) safeguards our physical self, a similar solution is needed to safeguard our digital self. This thesis presents the Artificial Immune inspired Intrusion Detection System (AIS-IDS), an IDS modeled after the HIS. This thesis proposes an architecture for AIS-IDS, instantiates an AIS-IDS model …

A Conceptual Decentralized Identity Solution For State Government, Martin Duclos

Theses and Dissertations

In recent years, state governments, exemplified by Mississippi, have significantly expanded their online service offerings to reduce costs and improve efficiency. However, this shift has led to challenges in managing digital identities effectively, with multiple fragmented solutions in use. This paper proposes a Self-Sovereign Identity (SSI) framework based on distributed ledger technology. SSI grants individuals control over their digital identities, enhancing privacy and security without relying on a centralized authority. The contributions of this research include increased efficiency, improved privacy and security, enhanced user satisfaction, and reduced costs in state government digital identity management. The paper provides background on digital …

Study Of Augmentations On Historical Manuscripts Using Trocr, Erez Meoded

Theses and Dissertations

Historical manuscripts are an essential source of original content. For many reasons, it is hard to recognize these manuscripts as text. This thesis used a state-of-the-art Handwritten Text Recognizer, TrOCR, to recognize a 16^th-century manuscript. TrOCR uses a vision transformer to encode the input images and a language transformer to decode them back to text. We showed that carefully preprocessed images and designed augmentations can improve the performance of TrOCR. We suggest an ensemble of augmented models to achieve an even better performance.

Brain-Inspired Spatio-Temporal Learning With Application To Robotics, Thiago André Ferreira Medeiros

USF Tampa Graduate Theses and Dissertations

The human brain still has many mysteries and one of them is how it encodes information. The following study intends to unravel at least one such mechanism. For this it will be demonstrated how a set of specialized neurons may use spatial and temporal information to encode information. These neurons, called Place Cells, become active when the animal enters a place in the environment, allowing it to build a cognitive map of the environment. In a recent paper by Scleidorovich et al. in 2022, it was demonstrated that it was possible to differentiate between two sequences of activations of a …

High-Performance Computing In Covariant Loop Quantum Gravity, Pietropaolo Frisoni

Electronic Thesis and Dissertation Repository

This Ph.D. thesis presents a compilation of the scientific papers I published over the last three years during my Ph.D. in loop quantum gravity (LQG). First, we comprehensively introduce spinfoam calculations with a practical pedagogical paper. We highlight LQG's unique features and mathematical formalism and emphasize the computational complexities associated with its calculations. The subsequent articles delve into specific aspects of employing high-performance computing (HPC) in LQG research. We discuss the results obtained by applying numerical methods to studying spinfoams' infrared divergences, or ``bubbles''. This research direction is crucial to define the continuum limit of LQG properly. We investigate the …

Overcoming Foreign Language Anxiety In An Emotionally Intelligent Tutoring System, Daneih Ismail

College of Computing and Digital Media Dissertations

Learning a foreign language entails cognitive and emotional obstacles. It involves complicated mental processes that affect learning and emotions. Positive emotions such as motivation, encouragement, and satisfaction increase learning achievement, while negative emotions like anxiety, frustration, and confusion may reduce performance. Foreign Language Anxiety (FLA) is a specific type of anxiety accompanying learning a foreign language. It is considered a main impediment that hinders learning, reduces achievements, and diminishes interest in learning.

Detecting FLA is the first step toward reducing and eventually overcoming it. Previously, researchers have been detecting FLA using physical measurements and self-reports. Using physical measures is direct …

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 …

Enhanced Content-Based Fake News Detection Methods With Context-Labeled News Sources, Duncan Arnfield

Electronic Theses and Dissertations

This work examined the relative effectiveness of multilayer perceptron, random forest, and multinomial naïve Bayes classifiers, trained using bag of words and term frequency-inverse dense frequency transformations of documents in the Fake News Corpus and Fake and Real News Dataset. The goal of this work was to help meet the formidable challenges posed by proliferation of fake news to society, including the erosion of public trust, disruption of social harmony, and endangerment of lives. This training included the use of context-categorized fake news in an effort to enhance the tools’ effectiveness. It was found that term frequency-inverse dense frequency provided …

Generalized Differentiable Neural Architecture Search With Performance And Stability Improvements, Emily J. Herron

Doctoral Dissertations

This work introduces improvements to the stability and generalizability of Cyclic DARTS (CDARTS). CDARTS is a Differentiable Architecture Search (DARTS)-based approach to neural architecture search (NAS) that uses a cyclic feedback mechanism to train search and evaluation networks concurrently, thereby optimizing the search process by enforcing that the networks produce similar outputs. However, the dissimilarity between the loss functions used by the evaluation networks during the search and retraining phases results in a search-phase evaluation network, a sub-optimal proxy for the final evaluation network utilized during retraining. ICDARTS, a revised algorithm that reformulates the search phase loss functions to ensure …

Towards Safer Code Reuse: Investigating And Mitigating Security Vulnerabilities And License Violations In Copy-Based Reuse Scenarios, David Reid

Doctoral Dissertations

Background: A key benefit of open source software is the ability to copy code to reuse in other projects. Code reuse provides benefits such as faster development time, lower cost, and improved quality. There are several ways to reuse open source software in new projects including copy-based reuse, library reuse, and the use of package managers. This work specifically looks at copy-based code reuse.

Motivation: Code reuse has many benefits, but also has inherent risks, including security and legal risks. The reused code may contain security vulnerabilities, license violations, or other issues. Security vulnerabilities may persist in projects that copy …

Towards Expressive And Versatile Visualization-As-A-Service (Vaas), Tanner C. Hobson

Doctoral Dissertations

The rapid growth of data in scientific visualization has posed significant challenges to the scalability and availability of interactive visualization tools. These challenges can be largely attributed to the limitations of traditional monolithic applications in handling large datasets and accommodating multiple users or devices. To address these issues, the Visualization-as-a-Service (VaaS) architecture has emerged as a promising solution. VaaS leverages cloud-based visualization capabilities to provide on-demand and cost-effective interactive visualization. Existing VaaS has been simplistic by design with focuses on task-parallelism with single-user-per-device tasks for predetermined visualizations. This dissertation aims to extend the capabilities of VaaS by exploring data-parallel visualization …

Leveraging Artificial Intelligence For Team Cognition In Human-Ai Teams, Beau Schelble

All Dissertations

Advances in artificial intelligence (AI) technologies have enabled AI to be applied across a wide variety of new fields like cryptography, art, and data analysis. Several of these fields are social in nature, including decision-making and teaming, which introduces a new set of challenges for AI research. While each of these fields has its unique challenges, the area of human-AI teaming is beset with many that center around the expectations and abilities of AI teammates. One such challenge is understanding team cognition in these human-AI teams and AI teammates' ability to contribute towards, support, and encourage it. Team cognition is …

Towards A Model Of The Mapping Between English And Spanish Prosody, Jonathan Avila

Open Access Theses & Dissertations

Current speech-to-speech translation systems face challenges in effectively translating the nuances of prosody, which plays a pivotal role in conveying speaker intent and stance in dialog. This limitation restricts cross-lingual communication, especially in situations demanding deeper interpersonal understanding. To address this, this research delves into the relationships between prosody and its pragmatic functions, in English and Spanish. First, I discuss a data collection protocol in which bilingual speakers re-enact utterances from an earlier conversation in their other language, then describe an English-Spanish corpus, consisting of 3816 matched utterance pairs. Second, I describe a prosodic dissimilarity metric based on Euclidean distance …

Leveraging Agile Software Methodologies Within Software Development To Introduce A Novel Educational Software Methodology, Montserrat Guadalupe Molina

Open Access Theses & Dissertations

Agile Software Development has been growing increasingly popular in the software engineering industry as a way to produce working software in a quick and people-centered manner. Agile methodologies require practitioners to have strong technical and non-technical skills, such as teamwork, project management, and communication skills. Students graduating from the software engineering discipline have been found to be lacking in these areas, leading to many difficulties faced by recent graduates as they begin their professional careers. Given that Agile Software Development is the most popular software development lifecycle currently used by practitioners in industry, it is important to expose students to …

Context-Aware Temporal Embeddings For Text And Video Data, Ahnaf Farhan

Open Access Theses & Dissertations

Recent years have seen an exponential increase in unstructured data, primarily in the form of text, images, and videos. Extracting useful features and trends from large-scale unstructured datasets -- such as news outlets, scientific papers, and videos like security cameras or body cam recordings -- is faced with substantial challenges of volume, scalability, complexity, and semantic understanding. In analyzing trends, comprehending the temporal context is vital for uncovering patterns and narratives that are not apparent from a single video frame or text document. Despite its importance, many existing data mining and machine learning approaches overlook extracting evolutionary contextual features in …

Decoding Usage And Adoption Behavior Of The Low-Carbon Transportation Market: An Ai-Driven Exploration, Vuban Chowdhury

Graduate Theses and Dissertations

The transportation sector stands as a significant contributor to greenhouse gas emissions in the United States, with its environmental impact steadily escalating over the past few decades. This has prompted government agencies to facilitate the adoption and usage of low-carbon transportation (LCT) options as alternatives to fossil-fuel-powered transportation. LCTs include modes of transportation that minimize the overall carbon footprint of the transportation sector by relying on energy sources that are environmentally sustainable. These sustainable transportation options have also garnered significant interest in the transportation research community. For government agencies and researchers alike, a comprehensive understanding of the adoption and usage …

Integrating Machine Learning Methods For Medical Diagnosis, Jazmin Quezada

Open Access Theses & Dissertations

Abstract:The rapid advancement of machine learning techniques has revolutionized the field of medical diagnosis by offering powerful tools to analyze complex data sets and make accurate predictions. In this proposed method, we present a novel approach that integrates machine learning and optimization models to enhance the accuracy of medical diagnoses. Our method focuses on fine-tuning and optimizing the parameters of machine learning algorithms commonly used in medical diagnosis, such as logistic regression, support vector machines, and neural networks. By employing optimization techniques, we systematically explore the parameter space of these algorithms to discover the most optimal configurations. Moreover, by representing …