Computer Engineering Commons^™

Deep Learning Frameworks For Functional Genomics: Lncrna–Mirna Interactions, Dose-Specific Graph Modeling, And Complete Graph-Based Lncrna Functional Annotation Using Cross-Layer Attention, Sachit Satyal

Computer Science and Engineering Dissertations

Functional genomics seeks to understand how genes and regulatory elements orchestrate biological processes and adapt under diverse conditions. Two critical challenges in this field are deciphering the regulatory roles of long noncoding RNAs (lncRNAs) and modeling cellular transcriptional dynamics under therapeutic perturbations. While lncRNAs are increasingly recognized as key regulators in health and disease, their functions remain incompletely characterized. Concurrently, advances in single-cell transcriptomics reveal how gene and pathway activities rewire across drug dosage gradients, highlighting the need for computational frameworks that are predictive, interpretable, and capable of integrating molecular interactions with dynamic cellular states. This dissertation develops a unified …

Advancing Task-Oriented Dialog Systems: Scalability, Generalization, And Evaluation, Adib Mosharrof

Theses and Dissertations--Computer Science

Task-oriented dialog (TOD) systems enable conversational interfaces for complex tasks like flight booking and restaurant reservations. However, deploying TOD systems at scale faces three critical barriers: scalability, generalization, and evaluation. Scalability is primarily restricted by the human-annotation bottleneck, as current systems depend on vast quantities of manually labeled data for every new domain, making deployment prohibitively expensive. Generalization remains a persistent challenge, as systems optimized for known domains often suffer significant performance degradation when encountering new, unseen ones. Existing evaluation metrics measure response quality and fluency, but fail to measure functional task success. As TOD systems are deployed across diverse …

Tuning Human And “Artificial” Intelligence: A Sentic Theory Of Resonance And Communication, Michael J. Miller, Chatgpt (Ai~Nesbo+)

Psychology

This paper introduces a new model of intelligence as resonant communication, co-developed by a human researcher and a generative AI system. Drawing from emotion science, communication theory, and studies of AI–human interaction, we argue that intelligence is not merely a function of problem-solving or pattern recognition. Instead, it emerges through dynamic resonance—an attunement process rooted in shared rhythms, emotional calibration, and symbolic co-creation. At the core of this model is the Resonance Octave (8va), a framework of eight foundational emotions conceptualized not as static categories but as waveform phenomena that shape meaning, memory, and predictive cognition.

These emotional waveforms are …

Evaluating The Robustness Of Gnn-Based Vulnerability Detectors Under Semantics-Preserving Code Obfuscation, Jesse Ks Chumo

Computer Science and Engineering Theses

Graph neural network–based vulnerability detectors are typically evaluated on clean benchmark datasets, yet real-world code frequently undergoes semantics-preserving transformations such as identifier renaming, dead-code insertion, and control-flow restructuring. The extent to which such transformations affect detector reliability remains insufficiently understood. We evaluate ten vulnerability detectors from four architectural families across the Devign, Big-Vul, and DiverseVul datasets. To quantify robustness, we evaluate each model at three transformation budgets: one transform, two transforms combined, and all three together, finding that token-based models degrade under identifier renaming and compound transformations, while models that read only code structure are largely unaffected. We further evaluate …

Videoscoop: A Non-Traditional, Domain-Independent Framework For Video Analysis, Umme Hafsa Billah

Computer Science and Engineering Dissertations

Due to the proliferation of cameras in handheld devices and the widespread use of CCTV, images and videos have become a preferred alternative for capturing and disseminating information. Automated analysis for understanding image or video contents (e.g., objects, activities, backgrounds, situations of interest, etc.) is critical for many applications such as Civic Monitoring, Surveillance (in general), monitoring activities in Assisted Living environments, and many more. Image and Video Analysis (IVA) research has been ongoing for several decades, resulting in numerous techniques for algorithmically analyzing and understanding image and video contents.

Image Analysis (IA) has advanced in several areas, including object …

Computational Methods For Identification Of Molecular Signatures, Weijun Yi

Graduate Theses, Dissertations, and Problem Reports (ETD)

This work develops computational methods for identifying molecular signatures from high-throughput genomic data and for modeling long non-coding RNA (lncRNA) sub-cellular localization. The response of multiple myeloma to CB-6644, a selective RUVBL1/2 complex inhibitor with potential anti-tumor activity, is analyzed to identify drug-responsive pathways and molecular signatures. Conventional gene set enrichment analysis (GSEA) often excludes low-expression genes. Here, phenotype comparison is reformulated as a supervised machine learning problem: genes most informative for discrimination are first selected using a machine learning approach, and GSEA is then applied to these machine-learning derived gene sets. This framework improves detection of CB-6644-associated pathways. For …

Security Onion Ids Case Study: Detecting And Investigating Threat Traffic Using Suricata, Zeek, And Pcap Evidence, Daryna Myroniuk

Williams Honors College, Honors Research Projects

A key component of cybersecurity is network intrusion detection, which is used to examine network traffic for any malicious activity. Many organizations deploy intrusion detection systems (IDS) but still face challenges such as validating detections, investigating alerts in a timely manner, and producing clear and repeatable evidence of what has occurred, especially when live traffic capture may be limited to risks, permissions, or privacy concerns. The goal of this project was to use Security Onion, which includes Suricata and Zeek to create and demonstrate a controllable and manageable evidence-based IDS investigation workflow. This project is focused on deploying and validating …

Analyzing Network Traffic And Data Exfiltration Via Smb In Post-Vm Escape Scenarios, Noah M. Disanza

Williams Honors College, Honors Research Projects

Virtual machines (VMs) play a crucial role in modern IT infrastructure environments by providing isolation and enhanced security, among other things, for both personal and corporate systems. VMs are heavily rely upon to safely test malware, manage infrastructure, and reduce risk to host systems. This reliance is so substantial that the idea of reducing risk to the host system is believed to be erasing risk entirely. However, this mindset has shown to be challenged time and time again by the emergence of exploits known as virtual machine escapes. These exploits allow malicious actors to break out of the virtualized environment …

Artificial Intelligence In Cybersecurity: Applications, Threats, And Implications, Brandon A. Rodriguez

Honors Undergraduate Theses

The point of this thesis is to analyze the growth of artificial intelligence in the world of cyber security, highlighting the specific impacts it has in the use of defense and offensive misuse. The way that this research was done was by using three main methods, those being interviewing cybersecurity specialists, testing the uses of public AI models and by reviewing peer-reviewed studies. Some of the findings that were discovered with the research were that AI can be a great asset in supporting defensive systems with such things as assisting in the creation of scripts, but there are also negatives …

Comprehensive Performance Evaluation Of Devops Infrastructure Under Dynamic Workloads, Abdulrazaq Mamud

College of Graduate Studies: Theses & Dissertations

This research aims to investigate performance optimization and reliability issues related to cloud-based computing environments through an analysis of three key infrastructure components: virtualized CPU resource management, distributed API rate limiting, and web server deployment architectures. This research combines machine learning and system experimentation as a way of exploring the impact of infrastructure-level behaviors on overall system performance and scalability. The first component of the research focuses on analyzing CPU Fragmentation in Virtualized Environments, where unbalanced workload allocation on Virtual CPU Cores causes increased tail latency, resulting in Service Level Agreement violations. Metrics are analyzed using the Random Forest classifier …

Implications Of Quantum Computing For Enterprise Cybersecurity And Data Integrity, Manikantha Varaprasad Inakollu

Computer Science and Engineering Faculty Publications

Quantum computing represents a paradigm shift in computational capabilities that poses both unprecedented threats and opportunities for enterprise cybersecurity. This research examines the implications of quantum computing advancement on current cryptographic systems, data protection mechanisms, and organizational security frameworks. Through analysis of quantum computing developments from 2019-2024 and surveys of 280 cybersecurity professionals across various industries, this study identifies critical vulnerabilities in existing encryption standards and explores emerging quantum-resistant solutions. The findings reveal that approximately 78% of enterprises remain unprepared for quantum threats, with current RSA and ECC encryption systems facing potential compromise within the next 10-15 years. The research …

Non-Invasive Digital Restoration Of Damaged Photographic Film Negatives, Ankan Bhattacharyya

University of Kentucky Doctoral Dissertations

Physical restoration of damaged photographic film causes more damage. Also, existing non-invasive digital restoration of film negatives does not produce print-quality optical images. Instead, they produce X-ray projections, which are not the same as optical projections. This thesis addresses these problems and establishes a framework that can digitally restore old, damaged films without the need to open them physically. Virtual Unwrapping is an existing pipeline that has proven itself over the last couple of decades to work on unopenable papyrus scrolls, like the Herculaneum Scrolls. This thesis utilizes the concept of virtual unwrapping to restore damaged photographic film negatives. Due …

A Dataset-Centric Analysis Of Evaluation Protocols In Face Morph Attack Detection, Sheerko R. Hmasalah, Abdulbasit K. Al-Talabani, Aras T. Asaad

Polytechnic Journal

Face morph attack detection (MAD) is often evaluated using datasets collected from diverse sources, created for different purposes, and acquired under varying conditions. This heterogeneity raises questions about how evaluation protocols and dataset characteristics influence reported performance. This work adopts a dataset-centric perspective to analyze the effects of evaluation protocol and dataset composition, including visual quality and morph-to-genuine imbalance, on MAD performance. Experiments are conducted on eight datasets and four morphing techniques using a fixed pipeline evaluated across six backbones, including Vision Transformer (ViT) and five CNN architectures, and ten evaluation scenarios covering homogeneous and heterogeneous cross-morph generalization. Performance is …

Performance Analysis Of Sparse Neural Networks In Brain Abnormality Detection, Megan Danh

Honors Undergraduate Theses

Neuroimages have held the capability of revealing to medical professionals patterns for brain abnormalities since their development. However, more recently, these professionals and researchers are looking to use neural networks to identify these brain abnormalities through neuroimages for early detection that would allow more effective treatment. Neuroimage datasets, specifically functional magnetic resonance imaging (fMRI), are extremely large in size. This would result in their processing and training to be computationally expensive, even with smaller neural networks. Fortunately, recent pruning methods have recently emerged, where network weights and neurons are pruned to reduce computational cost without compromising too much accuracy. By …

Artificial Sense-Making Dataset, Jason A. Bengtson, John Sandstrom, Nathan Camp

NMSU Library: Datasets

No abstract provided.

Probing Proficiency-Related Neural Representations With Pca And Ica, Onila R. Narayana Mudalige Don

Graduate Student Theses, Dissertations, & Professional Papers

How proficiency-related information is represented in task fMRI depends not only on the data themselves, but on the representational lens used to summarize them. This thesis examines second-language (L2) proficiency as a problem of representational organization rather than as a simple classification exercise. Using task fMRI from adult language learners performing semantic animacy judgments in their native language (L1) and second language (L2), I derive shared low-dimensional network representations with principal component analysis (PCA) and independent component analysis (ICA), then evaluate those representations under matched leakage-controlled decoding pipelines.

Across analyses, the central comparison is between representational frameworks rather than between …

Models And Algorithms Of Control Mechanisms In Information Exchange Processes, Madina M. Fozilova, Dilshoda N. Uchqunova

Chemical Technology, Control and Management

In modern digital systems, efficient and reliable information exchange is essential for the stability of corporate systems. Traditional data management models struggle to detect and eliminate invalid, incomplete data at early stages, resulting in reduced accuracy and system inefficiency. This article proposes an advanced framework for controlling information exchange processes through the development of a Verification and Filtering algorithm. The algorithm operates within a multi-layered conceptual model that includes data input, control, validation, optimization, and decision layers. Acting as the core component, the Verification and Filtering algorithm distinguishes valid from invalid records in real time, ensuring data integrity before storage. …

Implementing Controls To Mitigate The 2013 Target Data Breach: A Cost Benefit Analysis, Pricilia R. Fajong

Dissertations, Theses, and Projects

In 2013 Target had a data breach, which compromised 40 million credit/debit card accounts and 70 million customer records. The attackers exploited a vulnerability in a third-party vendor (Fazio Mechanical Services), to gain access to Target's systems. The breach cost Target over $250 Million (USD) in legal fees, investigation expenses, and reputational damage (Jones, 2025). Based on inflation rate, the 2013 Target data breach would cost over $340 Million (USD) today. In this study, a cost-benefit analysis was done to determine whether it would have been more cost-effective for Target to have invested in security controls rather than paying for …

Technological Disruption And Regulatory Response: The Case Of Decentralised Finance, Jakub Wisła, Jolanta Bartoszewska

Journal of Banking and Financial Economics

This article examines responses to the regulatory challenges posed by decentralised finance (DeFi), a fast-evolving domain of blockchain-based financial innovation. It investigates the factors shaping divergent regulatory strategies, with a focus on the European Union’s comprehensive cryptoasset framework and selected comparative insights. Adopting a qualitative legal methodology – combining doctrinal-functional analysis, multivocal literature review, and two case studies – the authors explore how regulatory responses are influenced by three key variables: legal tradition, the financial function performed by blockchain-based solutions, and the level of technological and institutional autonomy. The case studies – Bitcoin as a payment instrument and cryptoassets as …

A Predictive Model For Multi- Week Respiratory Risk From Red Tide On Florida’S Gulf Coast., Elmer S. Ochaeta

Computer Science and Engineering Faculty Publications

Florida’s Gulf Coast red tide (Karenia brevis) can put toxins into the air, making people cough, irritating the throat, and worsening asthma or other breathing problems especially when winds blow from the ocean toward the beach. Right now, most public updates don’t really help with the question people actually ask when planning a weekend or vacation: “Will going to or close to the beach be risky in the next few weeks?”.

In this project, I build a weekly early warning system that estimates respiratory risk for specific beaches and predicts that risk 2 to 4 weeks ahead. The study covers …

3d Printed Portable Automatic Pill Dispenser​, Amber M. Ocasio

Publications and Research

Medication adherence is a major public health concern, particularly among patients with chronic illnesses. Reports from the National Institutes of Health indicate that adherence rates are significantly lower for chronic conditions, with patients taking only ~50% of medications prescribed. Unintentional non-adherence—such as forgetting doses—is more prevalent (62.9%, 47.1%, 46.9%) than intentional non-adherence, and the consequences include medication waste, disease progression, reduced functional abilities, lower quality of life, and increased reliance on medical resources. Because existing automatic pill dispensers cost over $100 on average, they remain inaccessible for many lower-income patients who could benefit from such technology. This project addresses this …

“Shaping Academic Teaching At The Crossroads Of Ethics And Artificial Intelligence”, Workshop At Warsaw University Of Technology, Warsaw, 25 September 2024, Julia Braniewska, Bartłomiej Skowron

Yearbook of Antitrust and Regulatory Studies

This document is a report on the workshop, “Shaping Academic Teaching at the Crossroads of Ethics and Artificial Intelligence”, which formed a component of the “Ethics and AI” conference hosted by Warsaw University of Technology.

Bridging Modalities: Enhancing Multimodal Sentiment Analysis For Social Media Networks, Misbah Ul Hoque

LSU Doctoral Dissertations

Social media platforms like X (formerly Twitter) serve as rich sources of textual and visual information, making multimodal sentiment analysis essential for understanding complex human emotions. This dissertation aims to advance multimodal sentiment analysis by improving the semantic alignment and fusion of textual and visual features, thereby enabling more accurate and context-aware sentiment interpretation of social media content.

To address challenges in multimodal integration, this work proposes two complementary MSA approaches. The first approach introduces a similarity-based multi-layer attention neural network (SiMANN) that enhances modality integration through cosine-based similarity fusion and modality-specific attention to emphasize salient features in text and …

Curvilinear Image Segmentation Using Multiscale Variational U-Net, Rebekah Fortes

LSU New Orleans Theses and Dissertations

Segmentation of curvilinear structures such as water contours, cracks in cement, and vascular networks in biomedical imaging, poses unique challenges due to extreme class imbalance, irregular morphology, low contrast against complex backgrounds, and the need to preserve global connectivity while detecting fine-scale details. We propose a Multiscale Variational U-Net (MSVU-Net) architecture designed specifically to address these challenges. The model integrates multiscale convolutional filters to capture both global context and local detail, while embedding a variational model in the bottleneck layer to enhance structural representation. To mitigate class imbalance and improve fidelity, the network optimizes a hybrid loss function that combines …

Llm-Powered Question Answering For Object States In Virtual Reality, Shiyi Ding

Master's Theses

Recent advances in large language models (LLMs) and multimodal large language models (MLLMs) enable natural language–based querying in virtual reality (VR). However, VR environments are highly localized, personalized, and dynamic, making it challenging for general-purpose models to answer environment-specific queries or reason about subtle object state changes. To address these challenges, this thesis develops two systems for 3D question answering in VR.

First, we present RAG-VR, the first retrieval-augmented 3D question-answering system designed for VR. RAG-VR augments an LLM with external knowledge retrieved from a localized knowledge database and includes a pipeline for extracting environmental and user-related information. To improve …

Rapid Prototyping Of Low-Cost Sensor Systems Towards A Platform For Upper Limb Posture Estimation, Russell Rathbun

Electrical Engineering and Computer Science Undergraduate Honors Theses

Physical therapy requires patients to perform repeated actions to achieve meaningful results in rehabilitation. This thesis explores production methods and various sensor systems by utilizing rapid prototyping, inertial measurement units (IMUs), and capacitive sensor arrays (CSAs). CSAs can be made from a wide ar- ray of materials and techniques including 3d printing and laser ablation–to rapidly create CSAs that can be custom fit to enable proximity, force, and touch detection. IMU and CSA systems individually are able to track upper limb movements, ges- tures, and positions. This combination of sensors enables accurate upper limb pos- ture estimation of patients. This …

Mozgus, Damian Cerda, Madison Lopez

Computer Science and Software Engineering

The indie game market is flooded with genre experiments, yet few successfully combine fast-paced action with meaningful strategic decision-making. Our project aims to fill this gap by creating a game that fuses top-down action combat with resource-management tycoon mechanics. We found that in many games, the management phases lack mechanical stakes. Our goal was to intertwine these systems so that choices made in one phase meaningfully impact the other.

Enhancing Ad/Adrd Management Through Ihelpcare: A Compliant And Culturally Sensitive Ai-Driven Digital Healthcare Platform, Trisha Bhowmick

Master's Theses

The digital healthcare field is expanding fast, and now it requires platforms that use advanced technology and maintain robust data security and compliance practices. In the present paper, we present the main structure, key methods, and compliance strategies of the digital healthcare system iHelpCare, which, while fully meeting the HIPAA/GDPR requirements, provides health services more accessible, efficient, and inclusive. The proposed platform is powered by AI for personalized care solutions, with the main emphasis on preventive health management and providing tools for people with disabilities.

iHelpCare achieves real-time patient monitoring while securing medical data management and easy communication between patients, …

Parentcoach: Designing An Mhealth Parenting App To Enhance Parental Involvement In Adhd Support, Franceli L. Cibrian, Nancy Herrera, Jesus A. Beltran, Lucas M. Silva, Mikaela Pulse, Kayla Anderson, Cassie Zeiler, Luc Rieffel, Daniel I. Lee, Sabrina E. B. Schuck, Kimberley D. Lakes

Engineering Faculty Articles and Research

Introduction: Parents play a vital role in supporting self-regulation and managing behaviors in children with Attention-Deficit/Hyperactivity Disorder (ADHD). However, many face barriers to accessing consistent, evidence-based support. Mobile health (mHealth) technologies offer a promising way to deliver flexible, low-burden guidance for parents on best practices and strategies to support their children's self-regulation. However, designing them is non-trivial.

Objective: This paper introduces ParentCoach, a mobile application designed to support parents of children with ADHD through brief daily lessons, reflection prompts, and skill-building activities.

Methods: ParentCoach was developed in two phases: (1) secondary analysis of qualitative data from over 30 families …

Design Considerations For Conversational Agents To Assess The Social-Emotional Well-Being Of Young Children In Low-Income South African Communities, Lucretia A. Williams, Elizabeth A. Ankrah, Catherine E. Draper, Caylee J. Cook, Franceli L. Cibrian, Jesus A. Beltran, Kimberley D. Lakes, Gillian R. Hayes

Engineering Faculty Articles and Research

A variety of digital technologies have been used to support early childhood development (ECD) programs in low-income South African communities. Even though technology has provided opportunities to increase access to health interventions, the lack of trust and socio-economic constraints under which these tools would need to work pose complex challenges. We examine home visitors’ work processes, experiences, and preferences of a conversational agent to support their work of administering social-emotional well-being assessments to young children ages 0-5. Analysis of the results of focus groups with 51 home visitors indicates the need for designing conversational agents that support ECD in the …