Physical Sciences and Mathematics Commons^™

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 …

Making Data Meaningful: Stakeholder Perceptions On Data Visualization And Data Management Practices Within A Multi-Tiered System Of Supports (Mtss), Domenick Saia

Dissertations

Data-driven decision-making and collaboration are core pillars of a multi-tiered system of supports (MTSS); however, timely and accessible data use, as well as data literacy and visualization literacy skills, are challenges school leaders and educators face related to implementing such frameworks. I hypothesized efficient data management systems and data visualization tools enable school teams to predict student learning outcomes, readily communicate, and better understand student data. The purpose of this study design was to highlight a need for more efficient data structures that allow school stakeholders to balance their roles within an MTSS framework more effectively. The context of this …

A Novel Multi-Model Patient Similarity Network Driven By Federated Data Quality And Resource Profiling, Alramzana Nujum Navaz

Dissertations

Smart and Connected Health (SCH) is revolutionizing healthcare by leveraging extensive healthcare data for precise, personalized medicine. At its core, SCH relies on the concept of patient similarity, which involves the comparative analysis of newly encountered patients with those who exhibit comparable similarities from the existing patient cohort. Yet, this approach faces significant challenges, including data heterogeneity and dimensionality. Our research introduces a multi-dimensional Patient Similarity Network (PSN) Fusion model tailored to handle both static and dynamic features. The static data analysis focuses on extracting contextual information using Bidirectional Encoder Representations from Transformers (BERT), while dynamic features are captured through …

Models And Algorithms For Promoting Diverse And Fair Query Results, Md Mouinul Islam

Dissertations

Ensuring fairness and diversity in search results are two key concerns in compelling search and recommendation applications. This work explicitly studies these two aspects given multiple users' preferences as inputs, in an effort to create a single ranking or top-k result set that satisfies different fairness and diversity criteria. From group fairness standpoint, it adapts demographic parity like group fairness criteria and proposes new models that are suitable for ranking or producing top-k set of results. This dissertation also studies equitable exposure of individual search results in long tail data, a concept related to individual fairness. First, the dissertation focuses …

Quantifying Balance: Computational And Learning Frameworks For The Characterization Of Balance In Bipedal Systems, Kubra Akbas

Dissertations

In clinical practice and general healthcare settings, the lack of reliable and objective balance and stability assessment metrics hinders the tracking of patient performance progression during rehabilitation; the assessment of bipedal balance plays a crucial role in understanding stability and falls in humans and other bipeds, while providing clinicians important information regarding rehabilitation outcomes. Bipedal balance has often been examined through kinematic or kinetic quantities, such as the Zero Moment Point and Center of Pressure; however, analyzing balance specifically through the body's Center of Mass (COM) state offers a holistic and easily comprehensible view of balance and stability.

Building upon …

Learning Representations For Effective And Explainable Software Bug Detection And Fixing, Yi Li

Dissertations

Software has an integral role in modern life; hence software bugs, which undermine software quality and reliability, have substantial societal and economic implications. The advent of machine learning and deep learning in software engineering has led to major advances in bug detection and fixing approaches, yet they fall short of desired precision and recall. This shortfall arises from the absence of a 'bridge,' known as learning code representations, that can transform information from source code into a suitable representation for effective processing via machine and deep learning.

This dissertation builds such a bridge. Specifically, it presents solutions for effectively learning …

Fortifying Robustness: Unveiling The Intricacies Of Training And Inference Vulnerabilities In Centralized And Federated Neural Networks, Guanxiong Liu

Dissertations

Neural network (NN) classifiers have gained significant traction in diverse domains such as natural language processing, computer vision, and cybersecurity, owing to their remarkable ability to approximate complex latent distributions from data. Nevertheless, the conventional assumption of an attack-free operating environment has been challenged by the emergence of adversarial examples. These perturbed samples, which are typically imperceptible to human observers, can lead to misclassifications by the NN classifiers. Moreover, recent studies have uncovered the ability of poisoned training data to generate Trojan backdoored classifiers that exhibit misclassification behavior triggered by predefined patterns.

In recent years, significant research efforts have been …

Bacterial Motion And Spread In Porous Environments, Yasser Almoteri

Dissertations

Micro-swimmers are ubiquitous in nature from soil and water to mammalian bodies and even many technological processes. Common known examples are microbes such as bacteria, micro-algae and micro-plankton, cells such as spermatozoa and organisms such as nematodes. These swimmers live and have evolved in multiplex environments and complex flows in the presence of other swimmers and types, inert particles and fibers, interfaces and non-trivial confinements and more. Understanding the locomotion and interactions of these individual micro-swimmers in such impure viscous fluids is crucial to understanding the emergent dynamics of such complex systems, and to further enabling us to control and …

Diversification And Fairness In Top-K Ranking Algorithms, Mahsa Asadi

Dissertations

Given a user query, the typical user interfaces, such as search engines and recommender systems, only allow a small number of results to be returned to the user. Hence, figuring out what would be the top-k results is an important task in information retrieval, as it helps to ensure that the most relevant results are presented to the user. There exists an extensive body of research that studies how to score the records and return top-k to the user. Moreover, there exists an extensive set of criteria that researchers identify to present the user with top-k results, and result diversification …

Human-Ai Complex Task Planning, Sepideh Nikookar

Dissertations

The process of complex task planning is ubiquitous and arises in a variety of compelling applications. A few leading examples include designing a personalized course plan or trip plan, designing music playlists/work sessions in web applications, or even planning routes of naval assets to collaboratively discover an unknown destination. For all of these aforementioned applications, creating a plan requires satisfying a basic construct, i.e., composing a sequence of sub-tasks (or items) that optimizes several criteria and satisfies constraints. For instance, in course planning, sub-tasks or items are core and elective courses, and degree requirements capture their complex dependencies as constraints. …

Program Analysis For Android Security And Reliability, Sydur Rahaman

Dissertations

The recent, widespread growth and adoption of mobile devices have revolutionized the way users interact with technology. As mobile apps have become increasingly prevalent, concerns regarding their security and reliability have gained significant attention. The ever-expanding mobile app ecosystem presents unique challenges in ensuring the protection of user data and maintaining app robustness. This dissertation expands the field of program analysis with techniques and abstractions tailored explicitly to enhancing Android security and reliability. This research introduces approaches for addressing critical issues related to sensitive information leakage, device and user fingerprinting, mobile medical score calculators, as well as termination-induced data loss. …

Toward Smart And Efficient Scientific Data Management, Jinzhen Wang

Dissertations

Scientific research generates vast amounts of data, and the scale of data has significantly increased with advancements in scientific applications. To manage this data effectively, lossy data compression techniques are necessary to reduce storage and transmission costs. Nevertheless, the use of lossy compression introduces uncertainties related to its performance. This dissertation aims to answer key questions surrounding lossy data compression, such as how the performance changes, how much reduction can be achieved, and how to optimize these techniques for modern scientific data management workflows.

One of the major challenges in adopting lossy compression techniques is the trade-off between data accuracy …

Data-Driven 2d Materials Discovery For Next-Generation Electronics, Zeyu Zhang

Dissertations

The development of material discovery and design has lasted centuries in human history. After the concept of modern chemistry and material science was established, the strategy of material discovery relies on the experiments. Such a strategy becomes expensive and time-consuming with the increasing number of materials nowadays. Therefore, a novel strategy that is faster and more comprehensive is urgently needed. In this dissertation, an experiment-guided material discovery strategy is developed and explained using metal-organic frameworks (MOFs) as instances. The advent of 7r-stacked layered MOFs, which offer electrical conductivity on top of permanent porosity and high surface area, opened up new …

On Phishing: Proposing A Host-Based Multi-Layer Passive/Active Anti-Phishing Approach Combating Counterfeit Websites, Wesam Harbi Fadheel

Dissertations

Phishing is the starting point of most cyberattacks, mainly categorized as Email, Websites, Social Networks, Phone calls (Vishing), and SMS messaging (Smishing). Phishing refers to an attempt to collect sensitive data, typically in the form of usernames, passwords, credit card numbers, bank account information, etc., or other crucial facts, intending to use or sell the information obtained. Similar to how a fisherman uses bait to catch a fish, an attacker will pose as a trustworthy source to attract and deceive the victim.

This study explores the efficacy of host-side APT (Anti-Phishing Techniques) based onWebsite features like Lexical, Host-Based, or Content-Based …

Stream-Evolving Bot Detection Framework Using Graph-Based And Feature-Based Approaches For Identifying Social Bots On Twitter, Eiman Alothali

Dissertations

This dissertation focuses on the problem of evolving social bots in online social networks, particularly Twitter. Such accounts spread misinformation and inflate social network content to mislead the masses. The main objective of this dissertation is to propose a stream-based evolving bot detection framework (SEBD), which was constructed using both graph- and feature-based models. It was built using Python, a real-time streaming engine (Apache Kafka version 3.2), and our pretrained model (bot multi-view graph attention network (Bot-MGAT)). The feature-based model was used to identify predictive features for bot detection and evaluate the SEBD predictions. The graph-based model was used to …

Blockchain-Enabled Ehr Sharing In Healthcare Federation: Sharding And Interblockchain Communication, Faiza Hashim

Dissertations

Electronic Health Records (EHRs) are crucial components of the healthcare system, facilitating accurate and efficient diagnosis. Blockchain technology has emerged as a promising solution to improve EHRs sharing among medical practitioners while ensuring privacy and security. By leveraging its decentralized, distributed, immutable, and secure architecture, blockchain has the potential to revolutionize the healthcare system. However, due to security concerns, blockchain networks in healthcare typically operate in private or consortium modes, resulting in isolated networks within a federation. Scalability remains a significant challenge for blockchain networks, as the number of participating nodes increases within each network of the federation. Consensus mechanisms …

Machine Learning And Network Embedding Methods For Gene Co-Expression Networks, Niloofar Aghaieabiane

Dissertations

High-throughput technologies such as DNA microarrays and RNA-seq are used to measure the expression levels of large numbers of genes simultaneously. To support the extraction of biological knowledge, individual gene expression levels are transformed into Gene Co-expression Networks (GCNs). GCNs are analyzed to discover gene modules. GCN construction and analysis is a well-studied topic, for nearly two decades. While new types of sequencing and the corresponding data are now available, the software package WGCNA and its most recent variants are still widely used, contributing to biological discovery.

The discovery of biologically significant modules of genes from raw expression data is …

Trustworthy Machine Learning Through The Lens Of Privacy And Security, Thi Kim Phung Lai

Dissertations

Nowadays, machine learning (ML) becomes ubiquitous and it is transforming society. However, there are still many incidents caused by ML-based systems when ML is deployed in real-world scenarios. Therefore, to allow wide adoption of ML in the real world, especially in critical applications such as healthcare, finance, etc., it is crucial to develop ML models that are not only accurate but also trustworthy (e.g., explainable, privacy-preserving, secure, and robust). Achieving trustworthy ML with different machine learning paradigms (e.g., deep learning, centralized learning, federated learning, etc.), and application domains (e.g., computer vision, natural language, human study, malware systems, etc.) is challenging, …

Mapping Programs To Equations, Hessamaldin Mohammadi

Dissertations

Extracting the function of a program from a static analysis of its source code is a valuable capability in software engineering; at a time when there is increasing talk of using AI (Artificial Intelligence) to generate software from natural language specifications, it becomes increasingly important to determine the exact function of software as written, to figure out what AI has understood the natural language specification to mean. For all its criticality, the ability to derive the domain-to-range function of a program has proved to be an elusive goal, due primarily to the difficulty of deriving the function of iterative statements. …

Deep Hybrid Modeling Of Neuronal Dynamics Using Generative Adversarial Networks, Soheil Saghafi

Dissertations

Mechanistic modeling and machine learning methods are powerful techniques for approximating biological systems and making accurate predictions from data. However, when used in isolation these approaches suffer from distinct shortcomings: model and parameter uncertainty limit mechanistic modeling, whereas machine learning methods disregard the underlying biophysical mechanisms. This dissertation constructs Deep Hybrid Models that address these shortcomings by combining deep learning with mechanistic modeling. In particular, this dissertation uses Generative Adversarial Networks (GANs) to provide an inverse mapping of data to mechanistic models and identifies the distributions of mechanistic model parameters coherent to the data.

Chapter 1 provides background information on …

Loss Scaling And Step Size In Deep Learning Optimizatio, Nora Alosily

Dissertations

Deep learning training consumes ever-increasing time and resources, and that is
due to the complexity of the model, the number of updates taken to reach good
results, and both the amount and dimensionality of the data. In this dissertation,
we will focus on making the process of training more efficient by focusing on the
step size to reduce the number of computations for parameters in each update.
We achieved our objective in two new ways: we use loss scaling as a proxy for
the learning rate, and we use learnable layer-wise optimizers. Although our work
is perhaps not the first …

Socially Aware Natural Language Processing With Commonsense Reasoning And Fairness In Intelligent Systems, Sirwe Saeedi

Dissertations

Although Artificial Intelligence (AI) promises to deliver ever more user-friendly consumer applications, recent mishaps involving fake information and biased treatment serve as vivid reminders of the pitfalls of AI. AI can harbor latent biases and flaws that can cause harm in diverse and unexpected ways. It is crucial to understand the reasons for, mechanisms behind, and circumstances under which AI can fail. For instance, a lack of commonsense reasoning can lead to biased or unfair decisions made by Machine Learning (ML) systems. For example, if an ML system is trained on data that is biased or unrepresentative of the real …

Identification Of Students At Risk Of Low Performance By Combining Rule-Based Models, Enhanced Machine Learning, And Knowledge Graph Techniques, Balqis Mubarak Al Braiki

Dissertations

Technologies and online learning platforms have changed the contemporary educational paradigm, giving institutions more alternatives in a complex and competitive environment. Online learning platforms, learning-based analytics, and data mining tools are increasingly complementing and replacing traditional education techniques. However, academic underachievement, graduation delays, and student dropouts remain common problems in educational institutions. One potential method of preventing these issues is by predicting student performance through the use of institution data and advanced technologies. However, to date, scholars have yet to develop a module that can accurately predict students’ academic achievement and commitment. This dissertation attempts to bridge that gap by …

Using Materialized Views For Answering Graph Pattern Queries, Michael Lan

Dissertations

Discovering patterns in graphs by evaluating graph pattern queries involving direct (edge-to-edge mapping) and reachability (edge-to-path mapping) relationships under homomorphisms on data graphs has been extensively studied. Previous studies have aimed to reduce the evaluation time of graph pattern queries due to the potentially numerous matches on large data graphs.

In this work, the concept of the summary graph is developed to improve the evaluation of tree pattern queries and graph pattern queries. The summary graph first filters out candidate matches which violate certain reachability constraints, and then finds local matches of query edges. This reduces redundancy in the representation …

Android Security: Analysis And Applications, Raina Samuel

Dissertations

The Android mobile system is home to millions of apps that offer a wide range of functionalities. Users rely on Android apps in various facets of daily life, including critical, e.g., medical, settings. Generally, users trust that apps perform their stated purpose safely and accurately. However, despite the platform’s efforts to maintain a safe environment, apps routinely manage to evade scrutiny. This dissertation analyzes Android app behavior and has revealed several weakness: lapses in device authentication schemes, deceptive practices such as apps covering their traces, as well as behavioral and descriptive inaccuracies in medical apps. Examining a large corpus of …

Machine Learning-Based Data Analytics For Understanding Space Weather And Climate, Yasser Abduallah

Dissertations

This dissertation addresses multiple crucial problems in space weather and climate, presenting new machine learning-based data analytics algorithms and models for tackling the problems.

First, the dissertation presents two new approaches to predicting solar flares. One approach, called DeepSun, predicts solar flares by utilizing a machine-learning-as-a-service (MLaaS) platform. The DeepSun system provides a friendly interface for Web users and an application programming interface (API) for remote programming users. It adopts an ensemble learning method that employs several machine learning algorithms to perform multiclass flare prediction. The other approach, named SolarFlareNet, forecasts the occurrence of solar flares within the next 24 …

Software Protection And Secure Authentication For Autonomous Vehicular Cloud Computing, Muhammad Hataba

Dissertations

Artificial Intelligence (AI) is changing every technology we deal with. Autonomy has been a sought-after goal in vehicles, and now more than ever we are very close to that goal. Vehicles before were dumb mechanical devices, now they are becoming smart, computerized, and connected coined as Autonomous Vehicles (AVs). Moreover, researchers found a way to make more use of these enormous capabilities and introduced Autonomous Vehicles Cloud Computing (AVCC). In these platforms, vehicles can lend their unused resources and sensory data to join AVCC.

In this dissertation, we investigate security and privacy issues in AVCC. As background, we built our …

Computation Of Risk Measures In Finance And Parallel Real-Time Scheduling, Yajuan Li

Dissertations

Many application areas employ various risk measures, such as a quantile, to assess risks. For example, in finance, risk managers employ a quantile to help determine appropriate levels of capital needed to be able to absorb (with high probability) large unexpected losses in credit portfolios comprising loans, bonds, and other financial instruments subject to default. This dissertation discusses the computation of risk measures in finance and parallel real-time scheduling.

Firstly, two estimation approaches are compared for one risk measure, a quantile, via randomized quasi-Monte Carlo (RQMC) in an asymptotic setting where the number of randomizations for RQMC grows large, but …

Low-Reynolds-Number Locomotion Via Reinforcement Learning, Yuexin Liu

Dissertations

This dissertation summarizes computational results from applying reinforcement learning and deep neural network to the designs of artificial microswimmers in the inertialess regime, where the viscous dissipation in the surrounding fluid environment dominates and the swimmer’s inertia is completely negligible. In particular, works in this dissertation consist of four interrelated studies of the design of microswimmers for different tasks: (1) a one-dimensional microswimmer in free-space that moves towards the target via translation, (2) a one-dimensional microswimmer in a periodic domain that rotates to reach the target, (3) a two-dimensional microswimmer that switches gaits to navigate to the designated targets in …

Data Collection And Machine Learning Methods For Automated Pedestrian Facility Detection And Mensuration, Joseph Bailey Luttrell Iv

Dissertations

Large-scale collection of pedestrian facility (crosswalks, sidewalks, etc.) presence data is vital to the success of efforts to improve pedestrian facility management, safety analysis, and road network planning. However, this kind of data is typically not available on a large scale due to the high labor and time costs that are the result of relying on manual data collection methods. Therefore, methods for automating this process using techniques such as machine learning are currently being explored by researchers. In our work, we mainly focus on machine learning methods for the detection of crosswalks and sidewalks from both aerial and street-view …