Defense Notices

This thesis addresses two related problems in the optical manipulation of microscopic particles: the efficient generation of holograms for holographic optical tweezers and the simulation of multi-particle optical binding. Holographic optical tweezers use phase-only spatial light modulators to create programmable optical trapping fields, enabling dynamic control over the number, position, and relative strength of optical traps. Because the quality of the trapping field depends strongly on the computed hologram, the first part of this work focuses on improving hologram-generation methods used in these systems.

A new phase-induced compressive sensing algorithm is presented for holographic optical tweezers, along with weighted and unweighted variants. These methods are developed from the Gerchberg-Saxton framework and are designed to improve computational efficiency while preserving favorable trapping characteristics such as uniformity and optical efficiency. By combining compressive sensing with phase induction, the proposed algorithms reduce the computational burden associated with iterative hologram generation while maintaining strong performance across a variety of trapping arrangements. Comparative simulations are used to evaluate these methods against several established hologram-generation algorithms, and the results show that the proposed approaches offer meaningful improvements in convergence behavior and overall performance.

The second part of this thesis examines optical binding, a phenomenon in which multiple particles interact through both the incident optical field and the fields scattered by neighboring particles. To study this process, a numerical simulation is developed that incorporates gradient forces, radiation pressure, and light-mediated particle-particle interactions in both two- and three-dimensional configurations. The simulation is used to investigate how particles evolve under different initial conditions and illumination states, and how collective effects influence the formation of stable or semi-stable arrangements. These results provide insight into the role of scattering-mediated forces in many-particle optical systems and highlight differences between two-dimensional and three-dimensional behavior.

Although hologram generation and optical binding are treated as separate problems in this work, they are connected by a common goal: understanding how structured optical fields can be designed and applied to control microscopic matter. Together, the results of this thesis contribute to the broader study of computational beam shaping and many-body optical interactions, with relevance to advanced optical trapping, particle organization, and dynamically reconfigurable light-driven systems.

Runtime estimation plays a structural role in reservation-based scheduling for High Performance Computing (HPC) systems, where predicted walltimes directly influence reservation timing, backfilling feasibility, and overall queue dynamics. This raises a fundamental question of whether improved runtime prediction accuracy necessarily translates into improved scheduling performance. In this work, we conduct an empirical study of runtime estimation under EASY Backfilling using an application-driven workload consisting of MRI-based brain segmentation jobs. Despite identical configurations and uniform metadata, runtimes exhibit substantial variability driven by intrinsic input structure. To capture this variability, we develop a feature-driven machine learning (ML) framework that extracts region-wise features from MRI volumes to predict job runtimes without relying on historical execution traces or scheduling metadata. We integrate these ML-derived predictions into an EASY Backfilling scheduler implemented in the Batsim simulation framework. Our results show that regression accuracy alone does not determine scheduling performance. Instead, scheduling performance depends strongly on estimation bias and its effect on reservation timing and runtime exceedances. In particular, mild multiplicative calibration of ML-based runtime estimates stabilizes scheduler behavior and yields consistently competitive performance across workload and system configurations. Comparable performance can also be observed with certain levels of uniform overestimation; however, calibrated ML predictions provide a systematic mechanism to control estimation bias without relying on arbitrary static inflation. In contrast, underestimation consistently leads to severe performance degradation and cascading job terminations. These findings highlight runtime estimation as a structural control input in backfilling-based HPC scheduling and demonstrate the importance of evaluating prediction models jointly with scheduling dynamics rather than through regression metrics alone.

The University of Kansas maintains hundreds of departmental and unit websites, leaving students without a unified way to find information. General-purpose chatbots hallucinate KU-specific facts, and static FAQ pages cannot hold a conversation. This work presents BabyJay, a Retrieval-Augmented Generation chatbot that answers student questions using content scraped from official KU sources, with inline citations on every response. The pipeline combines query preprocessing and decomposition, an intent classifier that routes most queries to fast JSON lookups, hybrid retrieval (BM25 and ChromaDB vector search merged via Reciprocal Rank Fusion), a cross-encoder re-ranker, and generation by Claude Sonnet 4.6 under a context-only system prompt. Evaluation on 46 question-answer pairs across five difficulty tiers and eight domains produced a composite score of 0.72, entity precision of 93%, and zero runtime errors. Retrieval, rather than generation, emerged as the primary bottleneck, motivating future work on multi-domain query handling.

Modern intelligent systems increasingly rely on continuous sensor data streams for perception, decision-making, and control, making sensors a critical yet underexplored attack surface. While prior research has demonstrated the feasibility of sensor-based attacks, recent advances in mobile operating systems and machine learning-based defenses have significantly reduced their practicality, rendering them more detectable, resource-intensive, and constrained by evolving permission and context-aware security models.

This dissertation revisits sensor exploitation under these modern constraints and develops a unified, cross-layer perspective that improves both practicality and stealth of sensor-enabled attacks. We identify three fundamental challenges: (i) the difficulty of reliably manipulating physical sensor signals in noisy, real-world environments; (ii) the effectiveness of context-aware defenses in detecting anomalous sensor behavior on mobile devices, and (iii) the lack of lightweight coordination for practical sensor-based side- and covert-channels.

To address the first challenge, we propose a physical-domain attack framework that integrates signal modeling, simulation-guided attack synthesis, and real-time adaptive targeting, enabling robust adversarial perturbations with high attack success rates even under environmental uncertainty. As a case study, we demonstrate an infrared laser-based adversarial example attack against face recognition systems, which achieves consistently high success rates across diverse conditions with practical execution overhead.

To improve attack stealth against context-aware defenses, we introduce an auto-contextualization mechanism that synchronizes malicious sensor actuation with legitimate application activity. By aligning injected signals with both statistical patterns and semantic context of benign behavior, the approach renders attacks indistinguishable from normal system operations and benign sensor usage. We validate this design using three Android logic bombs, showing that auto-contextualized triggers can evade both rule-based and learning-based detection mechanisms.

Finally, we extend sensor exploitation beyond the traditional attack-channel plane by introducing a lightweight control-plane protocol embedded within sensor data streams. This protocol encodes control signals directly into sensor observations and leverages simple signal-processing primitives to coordinate multi-stage attacks without relying on privileged APls or explicit inter-process communication. The resulting design enables low-overhead, stealthy coordination of cross-device side- and covert-channels.

Together, these contributions establish a new paradigm for sensor exploitation that spans physical, contextual, and control-plane dimensions. By bridging these layers, this dissertation demonstrates that sensor-based attacks remain not only feasible but also practical and stealthy in modern computer systems.

Modern phased-array antenna calibration is essential for advanced radar systems to achieve precise beamforming, sidelobe control, and coherent processing. While mutual coupling-based calibration provides a valuable internal alternative to external far-field references by exploiting near-field element interactions, the problem is fundamentally ill-posed. Measured responses depend simultaneously on transmit coefficients, receive coefficients, and the coupling matrix, making it difficult to isolate true channel errors from array-model mismatch without additional structure.

This thesis presents a Bayesian Maximum A Posteriori (MAP) calibration framework that resolves this ambiguity by embedding physically motivated prior information into the estimation problem. The nominal coupling matrix is decomposed into Infinite, Symmetric, and Reciprocal components, which define low-dimensional parameterizations and prior covariance models. A Maximum Likelihood (ML) stage first generates a data-consistent transceiver initialization, followed by a MAP estimator that refines the solution by jointly addressing structured coupling deviations and measurement uncertainty.

Evaluations using Computational Electromagnetic (CEM) models and measured WaDES array data reveal that the physical array contains more higher-order structural content than the nominal CEM model. Across Monte Carlo trials, highly structured MAP estimators generally achieve lower aggregate error than unconstrained ML and Log Least Squares (LLS) methods. The overlapping-subspace M family offers an optimal balance of structural flexibility, zero-centered phase and magnitude behavior, and tuning robustness. Additionally, parametric sweeps highlight that prior covariance scaling is a critical design parameter: tight reciprocal priors prevent spurious structural absorption, whereas overly loose priors allow model mismatch to contaminate transceiver estimates.

Ultimately, this work demonstrates that internal mutual coupling calibration can achieve autonomy and robustness against model mismatch by parameterizing the nominal coupling matrix into structured components and integrating them as Bayesian priors.

Substance use remains a major public health issue in the United States that significantly impacts individuals, families, and society. Many individuals who suffer from substance use disorder (SUD) face incarceration due to drug-related offenses. Drug courts have emerged as an alternative to imprisonment and offer the opportunity for individuals to participate in a drug rehabilitation program instead. Drug courts mainly focus on those with non-violent drug-related offenses. One of the challenges of decision making in drug courts is assessing the likelihood of participants graduating from the drug court and avoiding recidivism after graduation. This study investigates the use of machine learning models to predict success in drug courts using data from a substance use drug court in Missouri. Success is measured in terms of graduation from the program, and the model includes a wide range of potential predictors including demographic characteristics, family and social factors, substance use history, legal involvement, physical and mental health history, employment history as well as drug court participation data. The results will be beneficial to drug court teams and presiding judges in predicting client success, evaluating risk factors during treatment for participants, informing person-centered treatment planning, and the development of after-care plans for high-risk participants to reduce the likelihood of recidivism. 

Optical Neural Networks (ONNs) have gained traction as an alternative to the conventional computing architectures used in modern CPUs and GPUs, largely because light enables massive parallelism, ultrafast inference, and minimal power consumption. 

As with conventional deep neural networks (DNNs), free-space ONNs require two main layers: (1) a nonlinear activation function which exists to separate adjacent linear layers, and (2) weighting layers that applies a linear transformation given an input.

Firstly, a Resonant Semiconductor Saturable Absorption Mirror (RSAM) was investigated as a viable nonlinear activation function. Several mechanisms have been used to create nonlinear activation functions, such as cold atoms, vapor absorption cells, and polaritons, but these implementations are bulky and must operate under tightly controlled environments while RSAMs is a passive device. Compared to typical SESAMs, the resonance structure of RSAM also reduces the saturation fluence compared to non-resonant SAMs, allowing low power laser sources to be used. A fiber-based optical testbed demonstrated notable improvement of 8.1% in classification accuracy compared to a linear only network trained with the MNIST dataset.

Secondly, Micro-electromechanical-system-based phase light modulators (PLMs) were evaluated as an alternative to LC-SLMs for in-situ reinforcement learning. PLMs can operate at kilohertz-scale frame rates at a substantially lower cost compared to LC-SLMs but have lower phase resolution and non-uniform quantization which impacts fidelity. Despite these disadvantages, the high-speed nature of PLMs allows for significant decrease in optimization time, which not only allows for reduction in training time, but also allows for larger datasets and more complex models with more learnable parameters. A single layer optical network was implemented using policy-based learning with discrete action-space to minimize impact of quantization. The testbed achieves 90.1%, 79.7%, and 76.9% training, validation, and test accuracy, respectively, on 3,000 images from the MNIST dataset. Additionally, we achieved 79.9%, 72.1%, and 71.7% accuracy on 3,000 images from the Fashion MNIST dataset. At 14 minutes per epoch during training, it is at least a magnitude lower in training time compared to LC-SLMs based models.

Checkpointing strategies in high-performance computing traditionally employ the Young-Daly for-

mula to determine the (first-order) optimal duration between checkpoints, which assumes a known

mean time between faults (MTBF). However, in practice, the MTBF may not be known accurately

or may vary, causing Young-Daly checkpointing to perform sub-optimally. In 2021, Sigdel et al.

introduced the CHORE (CHeckpointing Overhead and Rework Equated) checkpointing strategy,

which is MTBF-agnostic yet demonstrates a bounded increase in overhead compared to the op-

timal strategy. This thesis analyzed and extends the CHORE framework in several ways. First,

it verifies Sigdel et al.’s claims about the relative overhead of the CHORE strategy through both

event-driven simulations and expected runtimes derived from the underlying probablistic model.

Second, it extends the CHORE strategy to silent errors, which must be deliberately checked for to

be detected. In this scenario, the overhead compared to optimal checkpointing is once more ana-

lyzed through simulations and expected runtimes. Third, a heuristic is proposed to offer improved

performance of the CHORE algorithm under typical runtime scenarios by interpreting CHORE as

an additive-increase multiplicative-decrease model and tuning the parameters.

Ultrawideband (UWB) Interferometric Synthetic Aperture Radar (InSAR) integrated with multi-rotor Uncrewed Aerial Vehicle (UAV), or UIMU in this work for brevity, provides ultrafine-resolution, all-weather, 3D surface imagery at any time of day. UIMU can be rapidly deployable and low-cost, and therefore a critical new tool for low-altitude remote sensing applications, such as disaster response, environmental monitoring, and intelligence surveillance and reconnaissance (ISR). Traditional repeat-pass data collection methods reduce the phase coherence required for InSAR processing of ultrafine-resolution datasets due to the unstable flight behavior of multi-rotor UAVs. Collecting Synthetic Aperture Radar (SAR) datasets using two receive channels during a single-pass will improve phase coherence and the ability to produce ultrafine-resolution 3D InSAR imagery.

This work proposes to quantify and characterize 3D target-position accuracy for a dual-channel 6 GHz bandwidth (2 cm range resolution) frequency modulated continuous wave (FMCW) radar integrated with the Aurela X6 hexacopter to establish novel single-pass UWB InSAR data collection methods and processing algorithms for multi-rotor UAV. The feasibility of the proposed investigation is demonstrated by the preliminary qualitative analysis of single-pass InSAR imagery presented in this proposal. Fieldwork will be conducted to measure the positions of GPS located corner reflectors using the UIMU system. Algorithms for motion tolerant Time-Domain Backprojection (TDBP), InSAR coregistration, and digital elevation mapping novel to multi-rotor UAV at UWB will be developed and presented. An analysis of vehicle motion induced phase decoherence, and InSAR imagery signal to noise ratio (SNR) will be presented. The TDBP SNR performance will be compared to the Open Polar Radar Omega-K algorithm to attempt to quantify motion tolerance between the different SAR processing algorithms.

This work will establish a foundation for future investigations of real-time image processing, separated transmission and receive platforms (bistatic), or swarm configurations for UIMU systems.

Graph Neural Networks (GNNs) achieve state-of-the-art performance in modeling complex biological and behavioral systems, yet their "black-box" nature limits their utility for scientific discovery and clinical translation. Standard post-hoc explainability methods typically attribute importance to low-level features, such as individual nodes or edges, which often fail to map onto the high-level, domain-specific concepts utilized by experts. To address this gap, this thesis explores diverse methodological strategies for achieving Concept-Level Interpretability in GNNs, demonstrating how deep learning models can be structurally and analytically aligned with expert domain knowledge. This theme is explored through two distinct methodological paradigms applied to critical challenges in neuroscience and clinical psychology. First, we introduce an interpretable-by-design approach for modeling brain structure-function coupling. By employing an ensemble of GNNs conceptually biased via input graph filtering, the model enforces verifiably disentangled node embeddings. This allows for the quantitative testing of specific structural hypotheses, revealing that a minority of strong anatomical connections disproportionately drives functional connectivity predictions. Second, we present a post-hoc conceptual alignment paradigm for quantifying atypical motor signatures in Autism Spectrum Disorder (ASD). Utilizing a Spatio-Temporal Graph Autoencoder (STGCN-AE) trained on normative skeletal data, we establish an unsupervised anomaly detection system. To provide clinical interpretability, the model's reconstruction error is systematically aligned with a library of human-interpretable kinematic features, such as postural sway and limb jerk. Explanatory meta-modeling via XGBoost and SHAP analysis further translates this abstract loss into a multidimensional clinical signature. Together, these applications demonstrate that integrating concept-level interpretability through either architectural design or systematic post-hoc alignment enables GNNs to serve as robust tools for hypothesis testing and clinical assessment.