Computer Engineering Commons^™

Exploring Gene Regulatory Neural Network Biocomputing Of Bacteria, Adrian Merle Ratwatte

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Artificial Intelligence (AI) has evolved from brain-inspired algorithms into a discipline that increasingly integrates with biological systems. While silicon-based platforms have advanced machine learning, they remain limited in energy efficiency and operation in environments beyond silicon. This motivates biological computing as an alternative, enabling efficient, resource-aware, and reconfigurable computing within living systems. This dissertation addresses these limitations by introducing a bacterial computing framework that models Gene Regulatory Networks (GRNs) as Gene Regulatory Neural Networks (GRNNs). The GRNN mirrors the structure and function of Artificial Neural Networks (ANNs) through gene-gene interactions across trans-omic layers, enabling natural, self-regulating information processing within living …

Lightweight Attestation Techniques For The Industrial Internet Of Things, Syed Owais Athar

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

The Industrial Internet of Things (IIoT) has transformed critical infrastructure by integrating programmable logic controllers (PLCs) with connected sensors, actuators, and supervisory systems. While these advancements enhance operational efficiency, they also increase exposure to sophisticated cyber-physical threats, particularly through malicious modifications of PLC programs. Existing attestation methods either impose significant computational burdens by performing continuous verification or rely on detailed physical models that are often impractical to maintain across heterogeneous environments.

The first part of this thesis focuses on DuAtt, a dual-layer attestation scheme that integrates a physical process–based anomaly detection mechanism with a targeted attestation of the PLC program. …

Application Of Maritime Non-Line-Of-Sight Relay Attack On Wireless Digital Communication, Nathan Meyer

School of Computing: Dissertations, Theses, and Student Research

As wireless communication becomes increasingly prevalent, securing information over wireless channels is an ongoing challenge, especially in maritime environments where communication depends on radio links. While higher layer wireless attacks have been widely studied, lower level physical-layer relay attacks in maritime settings have received less attention. This thesis presents a simulation of a maritime relay attack in a beyond line-of-sight wireless environment for study. A three antenna communication model is developed where a legitimate transmitter sends a digital wireless signal, an attacking antenna intercepts, modifies, and retransmits the signal, and a final receiver observes both the direct and relay transmission. …

A Webcam Eye Tracking Infrastructure For Software Engineering Tasks, Zachary M. Kozak

School of Computing: Dissertations, Theses, and Student Research

Performing eye tracking utilizing commodity webcams has been explored for over a decade, but limited camera quality and sensitivity to head movements have hindered its adoption in research settings. Recent advances in consumer-grade webcams and machine learning methods present an opportunity to improve the accuracy of webcam eye tracking and extend the feasibility of studies beyond controlled laboratory environments.

Current popular webcam eye tracking methods restrict implementations to the browser and rely on continuous user interactions for calibration, limiting the kinds of studies that can be conducted. This thesis presents a feature-based gaze prediction system that incorporates eye geometry and …

Leveraging Code Embeddings To Identify And Address Blind Spots In Benchmark Creation, Charles Moloney

School of Computing: Dissertations, Theses, and Student Research

Formal software verification remains critical for early vulnerability detection, yet benchmarking these tools is costly and often reliant on centralized datasets such as SV-COMP. While such repositories enable standardized evaluation, they introduce risks of overfitting and bias, particularly due to first-party benchmark contributions. To address these limitations, we extend ARG-V, our tool for generating SV-COMP-compatible benchmarks from real-world Java code, with a novel approach of using code embedding techniques to selectively sample from mined code. By leveraging Nomic Embed Code and a cosine-based Minimum Hyperspherical Energy (MHE) objective, we systematically select and transform benchmarks from scraped GitHub code that …

Open Multi-Agent Systems: The Free-Range-Zoo Framework And Moasei Competition, Ceferino J. Patino Iv

School of Computing: Dissertations, Theses, and Student Research

The field of multi-agent reinforcement learning (MARL) has made significant strides in addressing sequential decision-making problems under uncertainty. However, traditional MARL frameworks assume closed-world settings with fixed agent sets, static task distributions, and unchanging environment dynamics. This thesis presents two complementary contributions that advance the state of open-world multi-agent systems research: (1) the free-range-zoo framework, an open-source environment suite for MARL in open environments featuring dynamic agent populations, evolving task sets, and changing operational frames; and (2) the MOASEI Competition, an international benchmarking event that leverages free-range-zoo to evaluate how artificial agents handle openness in complex, partially observable domains. The …

Integration Of Bayesian Networks And Neural Networks For High-Dimensional Data Analysis, Cooper Schmer

Department of Electrical and Computer Engineering: Dissertations, Theses, and Student Research

High-dimensional biomedical datasets, such as omics data, present significant challenges for predictive modeling due to noise, redundancy, and computational complexity. This thesis proposes a hybrid framework that integrates Bayesian Networks (BNs) and Artificial Neural Networks (NNs) to improve classification performance of such data sets while reducing input dimensionality. Central to this work is a novel feature selection method based on d-separation, a structural property of Bayesian networks that encodes conditional independence relationships.

The proposed approach introduces a count-based d-separation metric to quantify the relevance of variables to a target outcome, along with a thresholding scheme to balance feature selection robustness …

A Software-Defined Radio Testbed For Mimo-Ofdm Communications, Chaz G. Maschman

Department of Electrical and Computer Engineering: Dissertations, Theses, and Student Research

In this thesis, we implement a testbed for multiple-input multiple-output orthogonal frequency division multiplexing (MIMO-OFDM) systems via GNU Radio. Specifically, we implement a configurable framework for the construction of MIMO-OFDM software-defined radio (SDR) systems as a GNU Radio module. The GNU Radio MIMO-OFDM module consists of multiple algorithmic blocks necessary for implementation of a MIMO-OFDM system. This includes a library for the generation of orthogonal or pseudo-random pilot sequences, amendments to the Schmidl-Cox protocol for MIMO synchronization, and the creation of click-and-drag GNU Radio blocks implementing the conversion of arbitrary data sent via external programs to MIMO-OFDM frames, the initial …

A Low-Power Mixed-Signal Potentiostat System-On-Chip With Integrated Dual-Slope Adc, Seth Mcrobert

Department of Electrical and Computer Engineering: Dissertations, Theses, and Student Research

This thesis presents the design and characterization of a low-power mixed-signal potentiostat that was integrated with a 65 nm core in a SoC for low-power electrochemical sensing applications. The system integrates a low-noise transimpedance-based potentiostat front end with a 12-bit dual-slope analog-to-digital converter (ADC) for accurate current-to-digital conversion. The potentiostat core—comprising the control amplifier, current-mirror network, and transimpedance amplifier—consumes 38.2 µA from a 2.5 V supply (95.5 µW) and achieves an input-referred noise floor of 113 µVRMS over a 330 Hz bandwidth, while having an input current range from 1 nA to 20 µA and a noise-limited sensitivity of 56.4 …

Reinforcement Learning Based Security Schemes For Distributed Ai Systems, Ashan Chamath Gunawardena

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Distributed machine learning (DML) is a component of modern intelligent systems, enabling collaborative training across devices such as mobile clients, vehicles, and edge networks. However, the decentralized nature of these systems introduces vulnerabilities, particularly data poisoning attacks that compromise model integrity and degrade performance. Traditional defenses, such as statistical filtering, robust aggregation, and privacy-preserving techniques, often struggle to adapt to overwhelming adversaries or operate under strict privacy and real-time constraints. This dissertation proposes the use of reinforcement learning (RL) and deep reinforcement learning (DRL) based misbehavior detection schemes that dynamically identify poisoning attempts in distributed AI systems, including federated learning, …

Making Deep Neural Networks Trustworthy: Intelligibility And Safety Through Symbolic Methods, Eleanor Catherine Quint

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

The rapid adoption of deep learning has come at the cost of properties long valued in artificial intelligence: intelligibility and safety. This dissertation develops methods that restore these properties by coupling neural networks with symbolic structure.

First, for supervised classification, I propose a differentiable decision tree integrated with a supervised variational autoencoder. The resulting model maintains competitive accuracy and generative performance while exposing clear macro-features in its latent space, improving interpretability.

Second, for reinforcement learning, I extend constrained Markov decision processes by specifying constraints in formal languages. This formal language constrained MDP enables the use of automata for state augmentation, …

Securing Connected And Autonomous Vehicles, Owana Marzia Moushi

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

A vehicular network is susceptible to various security flaws and attacks. Cryptographic techniques are used in vehicular networks but these alone cannot provide proper security to the network. Identifying various types of attacks is necessary to secure vehicular communication networks. In this dissertation, we focused on detecting various insider attacks in vehicular networks to enhance the security of the network.

Our first contribution in this dissertation is the detection of both binary and multi-class data replay and data replay Sybil attacks in vehicular networks. A publicly available dataset, VeReMi-Extension is used to detect these attacks. This dataset has been reformulated …

Real-Time, Co-Regulated Design For Cyber-Physical, Multi-Rotor Uas Swarms, Grant Simon Phillips

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

Uncrewed Aerial Systems (UAS) have been integrated into a wide range of research and industrial applications, with growing interest in extending mission duration and spatial coverage through coordinated multi-UAS systems, or swarms. While swarming offers the potential for extended mission endurance and robustness through advanced path-planning, control, and estimation algorithms, significant challenges arise when implementing these methods on decentralized platforms composed of size, weight, and power-constrained (SWaP) vehicles. Limitations in onboard computational capacity and congested communication channels can break critical design-time assumptions, which at best, will degrade application quality of service, and at worst, destabilize the fleet through excessive delays …

Learn To Fly: Enabling Deep Learning Based Perception And Control In Aerial Robotics, Krishna Muvva

School of Computing: Dissertations, Theses, and Student Research

Uncrewed Aerial Vehicles (UAVs) are increasingly deployed in dynamic, GPS degraded, and cluttered environments, yet their autonomy remains fundamentally constrained by limitations in onboard perception and real-time control. This dissertation addresses these challenges by proposing a unified framework that co-designs deep learning-based perception and model-based control, organized around three core thrusts: Learn to Track, Learn to Localize, and Learn to Evade.

Learn to Track develops dynamic and adaptive perception control mechanisms that optimize CNN inference for target tracking. A control-aware CNN framework dynamically adjusts inference frequency based on UAV motion, reducing latency while maintaining visual lock. An adaptive CNN with …

Traffic Prediction For Research And Education Networks: Anomaly-Aware Deep Learning And Benchmarking, Mohammad Arafath Uddin Shariff

School of Computing: Dissertations, Theses, and Student Research

Research and Education Networks (RENs) and High-Performance Computing (HPC) environments are critical infrastructures for modern scientific discovery, demanding sustained high-throughput and low-latency data transfers. Unlike commercial networks, RENs exhibit unique traffic characteristics, including predominant “elephant flows,” inherent burstiness, and complex temporal-spatial dynamics often decoupled from human-driven cycles. Traditional traffic forecasting methods, tailored for commercial Wide Area Networks (WANs), consistently fail to capture these distinct REN dynamics, leading to inefficient resource management and potential impediments to scientific progress.

This thesis addresses this critical gap by developing and validating a robust, scalable, and anomaly-aware traffic forecasting framework specifically tailored for REN/HPC networks. …

How Developers Use Type-System Related Programming Language Features, Samuel W. Flint

School of Computing: Dissertations, Theses, and Student Research

Optional type annotations are a popular feature of programming languages that allow developers to omit explicit type information in code while, in some cases, retaining many of the benefits of static typing, such as in-code documentation, improved detection of type errors, or enforcement of code properties. However, how developers use and understand optional type annotations is not clear. The focus of this dissertation is to understand the use and comprehension of optional type annotations.

Optional type annotations are examined through four lenses: first, by examining the evolution of usage in a statically typed programming language (Kotlin, the default language for …

Intelligent Multi-Layer Optical Network Design And Network Softwarization, Boyang Hu

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

The growing demand for high-capacity, low-latency services has placed significant pressure on the design and operation of optical transport networks. Multi-layer optical network design—which coordinates the physical layer with higher-layer protocols—has emerged as a critical strategy to enhance resource efficiency, service flexibility, and fault resilience. Enabled by advancements in software-defined networking (SDN) and network softwarization, intelligent multi-layer architectures allow for adaptive, cross-layer control of routing, grooming, and protection mechanisms, ultimately reducing both capital and operational expenditures.

This dissertation investigates the intelligent design and simulation of multi-layer optical networks through the integration of SDN, machine learning, and high-fidelity physical-layer modeling. We …

Investigating The Impact Of Agent Openness On Planning In Multi-Agent Systems, Bala Subramanyam Duggirala

School of Computing: Dissertations, Theses, and Student Research

Multi-agent systems (MAS) possess significant potential for modeling real-world scenarios requiring coordinated actions (like wildfire fighting or ridesharing) among autonomous entities or agents (e.g., wildfire fighting agents) in complex, dynamic environments. Effective decision-theoretic planning (where each agent must carefully consider both the immediate and the future situations or states, and coordinate with the other agents (neighbors) to evaluate what needs to be done at present) within MAS, especially multiagent planning, where the planning agent directly models its neighbors in order to estimate their optimal actions, is critical, yet challenged by factors like partial observability, openness, and diverse agent types with …

Analysis Of Vision Transformers And Domain Adaptation In Long-Range Facial Recognition, Zachary Michael Swanson

Department of Electrical and Computer Engineering: Dissertations, Theses, and Student Research

Atmospheric turbulence presents a significant barrier to long-range facial recognition, introducing severe geometric distortions and blur that degrade image quality. This thesis investigates deep learning approaches for mitigating these effects, with a focus on transformer based architectures and domain adaptation strategies.

An in-depth benchmarking study was performed using convolutional neural networks (CNNs) and vision transformers (ViTs) on the Husker BRIAR Research Collection from up to 500m (HBRC-500) face dataset. The results demonstrated that vision transformers, particularly hierarchical vision transformers like the shifted-window (Swin) transformer, outperform CNN-based models at long distances due to their ability to model global spatial relationships and …

Biocomputing Approach To Modeling And Modulating Calcium Signaling, Sehee Sun

School of Computing: Dissertations, Theses, and Student Research

Biocomputing is an emerging field that seeks to perform computational tasks using biological substrates and processes. Unlike conventional computing systems based on silicon hardware, biocomputing leverages the parallelism, energy efficiency, and complex dynamics of living systems. Among various cellular mechanisms, calcium (Ca2+) signaling stands out as a central regulator of diverse biological functions, offering a promising basis for programmable logic and control in living cells.

This thesis introduces a novel framework for modeling and modulating Ca2+ dynamics using biologically inspired Boolean logic circuits. Specifically, we propose the Ca2+ Boolean Logic (CaBL) model, in which Ca2+ fluxes and interactions are abstracted …

A Uas-Centered Investigation Of Vorticity Characteristics And Cold Pool Structure Across Forward And Left-Flank Boundaries In Supercells, Mark R. De Bruin

Department of Earth and Atmospheric Sciences: Dissertations, Theses, and Student Research

Supercell internal boundaries are the locus of tornadogenesis; thus, understanding the characteristics of these boundaries, particularly in terms of vorticity, is important for identifying the role they play in tornado formation. Insight into the overall characteristics of internal boundaries and their possible role in tornadogenesis have been driven by studies reliant on numerical modeling-based experiments. Observational studies often neglect above-surface conditions or, when these observations are made, lack the spatial resolution to resolve boundary characteristics. During TORUS (Targeted Observation by Radars and UAS of Supercells) 2019 and TORUS-LItE (TORUS Left-flank Intensive Experiment) 2023, uncrewed aircraft systems (UAS) and mobile mesonets …

Farmnav-Uav: A Field-Ready Autonomous Uav For Tracking Static And Dynamic Trajectories In Agricultural Applications, Veera Venkata Ram Murali Krishna Rao Muvva

Department of Agricultural and Biological Systems Engineering: Dissertations, Theses, and Student Research

This study presents the design and development of a custom-built uncrewed aerial vehicle (UAV) tailored for precision agriculture. Unlike commercial UAVs, which are often constrained by proprietary systems and limited hardware customization, the proposed platform emphasizes modularity, upgradeability, and cost-effectiveness. The UAV is equipped with a Cube Blue flight controller for reliable low-level actuation and a Raspberry Pi 4 companion computer that executes a Model Predictive Control (MPC) algorithm for high-level trajectory optimization and stability enhancement.

Most conventional UAV autopilot systems rely on non-optimal control strategies, such as proportional–integral–derivative (PID) controllers, which can be inadequate for dynamic or resource-constrained environments. …

Ecen191/Robo150 Robotics Tools: Evaluating The Impact Of Project-Based Learning On Teaching Effectiveness, Nikhil Satyala

UNL Faculty Course Portfolios

The course selected for this study aims to introduce the skills and knowledge needed to utilize software and hardware tools used to design and operate robots. In this introductory course, undergraduate students in the Robotics Engineering major are provided with the opportunity to broaden their skill set with focus on specializing in one of three engineering disciplines (Software, Electrical and Mechanical). The primary goal of this course is to teach how develop the proficiency in basic concepts in robotics and enable the students to build and program a small-scale fully functional robotic arm. In this portfolio study, I investigated the …

Benefits And Applications Of Learning With Virtual Reality, Michael W. Timm

Honors Program: Senior Projects (Public)

Education is a fundamental pillar of society. It equips students for employment and interpersonal relations. Virtual reality (VR) has emerged as a transformative technology in the field of education. The aim of this paper is to synthesize existing research in order to determine the benefits of utilizing virtual reality in a variety of education settings, such as K-12 classrooms, universities, and workplace training. This paper observes significant benefits of virtual reality in constructivist and experiential learning, gamified learning, and tailored practice. This analysis also finds that virtual reality is advantageous for educational accessibility, particularly for absentee students and impoverished students. …

From In-The-Head To In-The-World: Frameworks For Understanding And Applying Computational Thinking, Justin Olmanson, Gretchen K. Larsen, Azadeh Hassani

Department of Teaching, Learning, and Teacher Education: Faculty Publications

In the five decades since Papert coined the term Computational Thinking (CT), it has become a core framework for thinking about learning, problem-solving, design, and creativity. Although CT is most commonly, and initially, associated with the cognitive orientations involved in coding and learning to code, it also includes situated and critical processes related to computational problem solving. Herein we unpack ways researchers in different fields and points in time have organized CT. We include creative coding as a uniquely generative lens for rethinking CT, outlining its potential as an expressive, constructionist, and culturally situated practice. In doing so, we explore …

Conversion Of Thermal Energy Stored In Conductive Concrete To Electricity With Thermoelectric Generators, Moustafa M. Al Adawi

Department of Electrical and Computer Engineering: Dissertations, Theses, and Student Research

This paper presents a proof-of-concept experimental study on the use of conductive concrete as thermal energy storage and its conversion into electricity. The conductive concrete is heated to 100°C by supplying electricity, and the stored thermal energy is converted back into electricity using thermoelectric generators (TEGs). Measurement results demonstrate that the conductive concrete effectively stores thermal energy up to 100°C, and this energy can be successfully converted into electricity. The findings highlight the potential of conductive concrete as a reliable medium for thermal energy storage.

Advisor: Lim Nguyen

A Machine Learning Framework For Packet Anomaly Detection In Smartgrid Substation Networks, Sowmya Bandari

School of Computing: Dissertations, Theses, and Student Research

The increasing reliance on Smart Grid Substation Networks for efficient electricity distribution has amplified cybersecurity vulnerabilities, particularly within Supervisory Control and Data Acquisition (SCADA) systems. The IEC 60870-5-104 (IEC-104) protocol, widely adopted for communication between Remote Terminal Units (RTUs) and Human-Machine Interfaces (HMIs), lacks inherent encryption and authentication mechanisms, rendering it susceptible to sophisticated cyberattacks. Threats such as False Data Injection Attacks (FDIAs), command injection, covert attacks and replay attacks pose significant risks by manipulating grid control signals, potentially leading to undetected operational disruptions, cascading failures, or system-wide instability. Conventional signature-based Intrusion Detection Systems (IDS) often fail to identify zero-day …

Physics Embedded Neural Network: A Novel Data-Free Numerical Method For Solving Computational Physics Problems, Pawan Gaire

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

A novel approach for solving partial differential equations (PDEs) using neural networks for scientific computing is introduced. The proposed approach, referred to as physics-embedded neural network (PENN), features a unique architecture that incorporates the PDE and boundary conditions information directly within the final fully-connected layer of the feed-forward neural network (NN). The key aspect of PENN is the parallel numerical embedding of a differential equation associated with physical problems within the activation function of the network’s final layer. This integration leads to a new class of computational solvers competitive with classical methods like the Finite Element Method (FEM) and capable …

Robot-Integrated 4d Building Information Modeling (4d Bim): Framework For Planning Safe Autonomous Construction Operations In Dynamic Environments, Hafiz Oyedimeji Oyediran

Dissertations and Doctoral Documents, University of Nebraska-Lincoln, 2023–

In the construction industry, the use of autonomous robots is considered a solution to overcome the heavy reliance on human workers to perform repetitive, strenuous, and hazardous tasks. While these robots offer the advantage of autonomous operation, ensuring their safe and efficient integration within construction sites requires precise planning. Such planning must account for the varying project complexities such as scope, site layout, tasks, timelines, existence of human workers, and other spatiotemporal conditions of the construction site. Currently, there are no methods to safely plan autonomous robot operations considering these factors within the overarching construction planning process. Thus, autonomous robots …

Enhancing Remote Sensing Imagery Temporal Resolution Using Starfm Data Fusion Approach For Improved Land Surface Monitoring, Ahmadreza Pourghodrat

School of Computing: Dissertations, Theses, and Student Research

High-resolution remote sensing imagery plays a critical role in various domains, such as farm-level agricultural operations, environmental monitoring, and natural resource management. However, data with high spatial resolution typically have low temporal resolution, and those with high temporal resolution often lack spatial detail. For example, Landsat 8 and 9 satellites deliver high spatial resolution images with a 30-meter pixel size but suffer from low temporal resolution, with a 16-day revisit cycle. In contrast, satellites like MODIS and VIIRS provide daily images but with a much coarser spatial resolution (375 meters or more), reducing spatial details. Additionally, there is a lack …