Physical Sciences and Mathematics Commons^™

Attention-Based Multi-Omics Fusion For Drug Synergy Prediction, Kusal Debnath, Pratip Rana, Preetam Ghosh

Computer Science Faculty Publications

Drug combination therapy in disease management gained popularity in the last few decades. Computational modeling of such combinations is an active area of research in the drug discovery domain. While earlier approaches solely emphasized on the structural features of participating drugs for designing synergistic models, they lack other crucial factors directly linked with drug administration - omics expressions. As differential omics expression is a downstream consequence of the administered drug combinations, utilizing such expressions while designing synergistic models promises robust and dynamic modeling. In this work, we propose SynergyLM that fuses multi-omics features with drug embeddings to build an omics-aware …

Towards Sample-Efficient Deep Reinforcement Learning, Guang Yang

Theses and Dissertations

Deep reinforcement learning (DRL), combining reinforcement learning and high-performance function approximations such as deep neural networks (DNN), is a powerful approach to solving complex sequential decision-making problems. However, due to the complex solution space of the sequential decision-making problems and the inefficient design of the DRL algorithms, DRL algorithms usually require a prohibitively large number of data samples to train effective strategies. Consequently, it is difficult to apply these DRL algorithms to complex real-world problems that require high costs to collect a large volume of data samples. This dissertation proposes new mechanisms to address this sample inefficiency issue, realizing sample-efficient …

Medical Linear Accelerator Water Tank Measurements Optimization For Commissioning, Tyler R. Laugh

Theses and Dissertations

Beam commissioning is a critical component of linear accelerator (LINAC) implementation, requiring accurate measurement of percent depth dose (PDD), beam profiles, and output factors across a wide range of field sizes. Conventional commissioning workflows often require multiple detectors and can be time-intensive, particularly for small-field dosimetry where measurement accuracy is highly sensitive to detector characteristics. This study evaluated the performance of a plastic scintillation detector (BP-PSD) for full water tank commissioning and its potential to improve efficiency while maintaining dosimetric accuracy.

Beam data were acquired for field sizes ranging from 1 × 1 cm² to 40 × 40 cm² using …

An Integrated Data-Driven Framework For Arctic Shipping: Analyzing Vessel Speed, Environmental And Ecological Factors Through Innovative Statistical Spatio-Temporal Methods, Inverse Optimization And Machine Learning, Mauli Pant

Theses and Dissertations

This dissertation develops an integrated data-driven framework to analyze vessel navigation and ecological risk in the United States Arctic from 2010 to 2019. As environmental change and maritime activity increase in the region, understanding how vessels respond to dynamic conditions and how those responses interact with marine ecosystems has become increasingly important. A central theme of this dissertation is the treatment of vessel speed as both an observed outcome and a decision variable reflecting trade- offs among operational, environmental, and ecological factors. The first chapter develops a predictive framework for vessel speed over ground (SOG) using Gaussian Process Boosting (GPBoost), …

Plumbed 3-Manifolds And Neumann Moves, Noah J. Pope

Theses and Dissertations

We give a constructive proof that every weakly negative definite plumbing tree can be transformed into a negative definite one by a finite sequence of Neumann moves. The argument combines Neumann’s plumbing calculus with the diagonalization algorithm of Duchon, Eisenbud, and Neumann, which extracts the eigenvalues of the framing matrix directly from the combinatorics of the tree. We show that any positive eigenvalues are supported on linear branches and can be eliminated systematically via controlled applications of Neumann moves. This provides an explicit algorithm reducing weakly negative definite plumbing trees to negative definite ones.

A Mathematical Frameworks For Singular, Nonlinear Phenomena: Applications To Nematocyst Firing And Inhomogeneous Nls With Coulomb Potential, Abdulrahman Alharbi

Theses and Dissertations

Nematocysts are specialized cellular organelles found in all cnidarians, including corals and jellyfish, as well as in some single-celled protists such as dinoflagellates. These organelles display remarkable diversity in morphology and function, playing roles in prey capture and defense. The firing of a nematocyst is one of the fastest accelerations in nature, yet the underlying physical mechanisms remain not fully understood. In this work, we address key questions: how sufficient force is generated to overcome the fluid boundary layer, whether fluid–structure interaction models can reproduce observed dynamics, and what mechanisms trigger discharge.

Our research investigates models based on osmotic pressure …

Advancing Cybersecurity Through Userland Memory Forensics: From Runtime Analysis To Security Applications, Hala Ali

Theses and Dissertations

Memory forensics has become a crucial component of digital investigations, particularly for detecting malware operating solely in system memory. As operating system vendors implemented kernel access restrictions, malware authors shifted to userland malware. However, existing memory forensics techniques have largely focused on kernel-level analysis, leaving userland runtimes insufficiently covered. This dissertation addresses this gap by expanding memory analysis capabilities across two distinct paradigms: interpreted and compiled runtimes. The first phase targets the Python runtime, developing automated recovery techniques that enable several security applications. For malware detection, these techniques extract critical forensic artifacts such as encryption keys and command-and-control configurations. For …

A Comprehensive Review Of Cyber Security And Current Practices In Global Mining Critical Infrastructure, Abu Barkat Ullah, Wanli Ma, Mohiuddin Ahmed, Bazlur Rashid, Munir Ahmad Saeed, Omer Arshad, Utkarsh Raghav

Research outputs 2022 to 2026

The purpose of the study is to explore the reasons behind the low uptake of Information Security Management Standards (ISMS), Asset Management, and Business Continuity Plans despite increasing cyber threats to the mining sector. Mining companies need to modernize and automate to keep up with the ‘Fourth Industrial Revolution’, driven by disruptive technology, forcing systems and technologies to become more integrated, increasing cyber attack threats. To address this, we conducted a literature review analyzing the mining industry across various regions. The research is based on a qualitative analysis of diversified literature. The results highlighted factors behind the low uptake of …

Quantifying Uncertainty In Landscape Evolution And Provenance Analysis: Insights From Statistical And Numerical Modelling, Vivian Carmello Grom

LSU Doctoral Dissertations

Landscape evolution models (LEMs) and detrital zircon provenance are widely used to investigate Earth surface processes, yet both face challenges related to quantifying model behavior and interpreting sedimentary signals under realistic, heterogeneous conditions. This thesis addresses these challenges through analysis and case studies that develop and apply new approaches for analyzing landscape dynamics and assessing uncertainties in sediment provenance.

Chapter 1 introduces a quantitative framework for evaluating LEM outputs using Shannon Entropy, Moran’s I, and Geary’s C. Applied to simulations with steady uplift, periodic uplift, spatially variable uplift, and a timeseries of DEMs, these metrics capture spatial organization and information …

Beyond Full Fine-Tuning: The New Playbook For Adapting Deep Neural Networks, Cristian S. Mcgee

Honors Undergraduate Theses

Fine-tuning is the process of teaching and specializing a pre-trained neural network on a downstream task. Fine-tuning is a rapidly growing topic in artificial intelligence domains; however, many fine-tuning endeavors are highly specialized without a coherent framework connecting them. This work presents a unified perspective on fine-tuning methods and performance metrics. Our perspective organizes the methods in terms of how they are applied to fine-tuning. This framework showcases methods that (i) update effective subspaces of the pre-trained model, (ii) change the adaptation optimization procedure, and (iii) alter the representations of the embedded input. Additionally, we present unconventional metrics such as …

Deep Learning Approaches For Voltammetric Analysis Of Coffee, Ryan Koes

Honors Theses

This thesis investigates deep learning approaches for voltammetric analysis of brewed coffee using a low-cost electrochemical system and screen-printed electrodes (SPEs). Traditional analytical methods, such as high-performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS), provide precise quantification of key compounds but require expensive instrumentation and specialized expertise, limiting accessibility. While SPEs offer a more accessible alternative, they yielded poor results with traditional processing; however, when combined with a neural network, the system proved more effective. In experiments with 132 coffee samples, mean errors for caffeine, CGA, and TDS predictions were 52.98 ppm, 70.48 ppm, and 0.08%, respectively. These findings …

Sedimentology, Paleontology, And Depositional Environments Of The Upper Devonian Lock Haven Formation In West Burlington Quarry, North-Central Pa, Michael Harman

Honors Theses

The Upper Devonian Lock Haven Formation in north-central Pennsylvania preserves evidence of significant climactic and evolutionary transitions, including the fin-to-limb transition and initial arborescence. The formation contains abundant sedimentary features, palynomorphs, trace fossils, and fish body fossils, making it crucial for reconstructing these paleoenvironments. However, integrated studies on the Lock Haven Formation are rare. This study characterizes the depositional environments, ichnology, paleontology, and age of the Lock Haven Formation. A recent exposure at the Insinger-Ward West Burlington Quarry reveals three middle to early late Famennian lithofacies associations (FAs). FA1 consists of red sandstone, shale, and mudstone containing rhizoliths (deeply penetrating …

Utilizing Computer Modeling To Optimize Electric Fields Within Xenon Time Projection Chambers, Miles Meloni

Honors Theses

XENONnT is a physics experiment designed with the goal of detecting dark matter particles. The detector is a time projection chamber; a series of charged electrodes creates an electric field, surrounding a central body filled with liquid and gaseous xenon. Photomultiplier tubes (PMTs), positioned on either end of the chamber, serve to detect light signals. We seek to minimize the root mean square of the electric field norms experienced by the PMTs. This quantity corresponds to the variance in the electric field observed by the PMTs. Establishing a consistent electric field is important to maintaining these sensitive components. The electric …

Inequality In The Urban Forest: Modeling Tree Canopy Dynamics Through Demographics And Restoration Strategies, Eve Johansson

Honors Theses

Urban tree canopies play an important role in environmental quality, public health, and neighborhood livability, yet their distribution is highly uneven and often reflects historical patterns of inequality. In Brooklyn, long-term processes such as redlining, uneven development, and demographic change have contributed to persistent disparities in access to green space.

This thesis examines how urban tree canopy evolves across space and time in Brooklyn and how different restoration strategies affect long-run outcomes. The analysis uses demographic and canopy data from 1990-2020, considering race, income, employment, and educational attainment. Among these, education is the most consistent predictor of canopy coverage, with …

A Web-Based Wizard-Of-Oz Platform For Collaborative And Reproducible Human-Robot Interaction Research, Sean O'Connor

Honors Theses

The Wizard-of-Oz (WoZ) technique is widely used in Human-Robot Interaction (HRI) research, but two persistent problems limit its effectiveness: existing tools impose technical barriers that exclude non-engineering domain experts (the Accessibility Problem), and the fragmented landscape of robot-specific implementations makes interaction scripts difficult to port across platforms (the Reproducibility Problem- concerning execution consistency and portability, not third-party replication). Through a literature review, I identified three design principles to address both: a hierarchical specification model, an event-driven execution model, and a plugin architecture that decouples experiment logic from robot-specific implementations. I realized these principles in HRIStudio, an open-source, web-based platform providing …

Barriers To Immunity: Understanding Covid-19 Vaccine Uptake In Africa, Emilia Blechschmidt

Honors Theses

This thesis examines the factors influencing COVID-19 vaccine uptake across African countries, with a focus on structural, informational, and behavioral barriers to immunization. Drawing on cross-country data, the study analyzes how access to transportation, reliable information, and healthcare resources shape vaccination rates, alongside the effect of demographics and institutional factors in shaping individual perceptions of risk and vaccine safety.

The findings emphasize that the broader strength and preparedness of national health systems strongly influence vaccine uptake. Countries that demonstrated higher coverage of routine childhood immunizations, such as polio and hepatitis B, also tended to perform better in COVID-19 uptake efficiency …

Group-Based Integer Factorization: Theory And Performance, Phuong Cao

Honors Theses

Integer factorization, the problem of finding a nontrivial factor of a composite integer N=pq for large primes p,q, particularly at the size of RSA moduli, is a notoriously difficult challenge that takes classical methods such as Trial Division and Fermat’s Algorithm trillions of years to solve. This thesis studies four probabilistic algorithms that exploit algebraic group structures to achieve significantly better, subexponential efficiency for certain classes of N: Pollard’s p-1, Williams’ p+1, Lenstra’s Elliptic Curve Method, and Pell’s Conic Method. In each case, the algorithm operates on a group over ℤ/Nℤ that decomposes, via the Chinese Remainder Theorem, into corresponding …

Paleoflood Chronology For The West Branch Of The Susquehanna River Using Abandoned Chute Channel Sediments, Pennsylvania, Usa, Juliette A. Vanluven

Honors Theses

Anthropogenic climate change is altering the hydrologic cycle, increasing flood frequency and severity, with associated increased risks in population exposure. This is associated with increasing risks to the population of the Susquehanna River Valley, which supports over 600,000 people today. However, our understanding of the frequencies of large floods is limited by relatively short instrumental records. By studying sediments from an abandoned chute channel in the Robert Allen Natural Area near Williamsport, PA, we can extend the existing flood records using paleoflood slackwater sediments along the West Branch of the Susquehanna River.  Sylvan Dell is an abandoned chute channel that …

Sedimentological Characterization Of Main And Chute Channel Scroll Bars Along The Kantishna River, Alaska, Cooper Sentz

Honors Theses

Scroll bars, arcuate sediment ridges found along the inner banks of river bends, are common floodplain features in meandering river systems that form during lateral channel migration. Two hypothesized formation mechanisms described in prior studies are the aggradation of suspended load onto abandoned inner bank levee (IBL) deposits during overbank flow and the migration of transverse bar packages from the channel bed up onto the point bar during flooding events. To study the sedimentology and geometry of these features, we conduct remote sensing and field analysis on a 60 km portion of the Kantishna River, AK: a highly sinuous, pro-glacial …

Anuran Occupancy Of Created Wetlands Within Reforested Legacy Surface Mines In Kentucky And West Virginia, Jillian C. Newman, Steve Price, Jacquelyn C. Guzy, Joshua Castle, John J. Cox, Jeffery L. Larkin, Christopher D. Barton

Forestry and Natural Resources Faculty Publications

Restoration of habitat is an important component of wildlife management. Surface coal mining has altered forest cover in the Central Appalachians, and most reclamation activities on previously mined lands result in non-native grasslands or shrub lands. The Forestry Reclamation Approach (FRA), which emphasizes non-native vegetation removal, soil decompaction, planting of native trees and shrubs, and, in some cases, wetland creation represents an alternative to grassland-based reclamation that may promote forest-associated wildlife on legacy surface mines. We used automated recording units to evaluate the response of anurans to created wetlands and the FRA in Kentucky and West Virginia, USA. We used …

Law Librarianship And Legal Information Science In The Age Of Genai, Paul D. Callister

Faculty Works

This article examines the relationship between law librarianship and legal information science in the age of generative AI (GenAI), arguing that closer integration between the two is essential to navigating a rapidly evolving legal information landscape. It contends that law librarianship—long grounded in stable classification systems and cognitive authority—must adopt the analytical methods of legal information science to remain effective in the digital era. Together, these fields can reinforce the rule of law by improving the organization, retrieval, and stability of legal information. The article identifies emerging subfields of legal information science that support this integration and develops several concepts …

The Impact Of Regional Fishery Management Organization Structure On Collaborative Performance, Evelyn Roozee, Owen Temby, Gordon M. Hickey

School of Earth, Environmental, & Marine Sciences Faculty Publications

Collaboration is integral to understand, plan, coordinate, and implement management measures for fisheries that cross international borders. Regional Fishery Management Organizations (RFMOs) are the main arenas for countries to collaborate and make decisions for transboundary fisheries, but these organizations have generally failed to prevent the depletion of some of the world's most valuable fish stocks. It is unclear how the structure and functioning of RFMOs can improve collaborative performance to better manage transboundary fish stocks. Using fuzzy-set qualitative comparative analysis, our study analyzes 10 RFMOs to identify the combination of six organizational conditions associated with high and low collaborative performance. …

Deep Crustal Boundaries As Fluid Conduits: A Geochemical Investigation Of Mvt Mineralization In Kentucky And Beyond, Dairian Boddy M. Boddy

Theses and Dissertations--Earth and Environmental Sciences

Critical minerals are vital to the United States economy and national security, yet their supply chains are at risk. Common minerals in Mississippi Valley-type (MVT) deposits, such as sphalerite, galena, fluorite, and barite, host critical metals such as barium, gallium, germanium, and zinc, which are essential for energy technologies. An investigation of three MVT mineral districts in Kentucky elucidated previously unrecognized systematics, genetic relationships, and sources of ore components using stable and radiogenic isotope geochemistry, particularly from galena, sphalerite, barite, and gangue minerals (e.g., carbonates). The localization and dominant type of mineralization in each district are potentially influenced by deep …

Large Aerosol Particles Favor Haze Conditions Through Limitations On Water Budget And Activation Kinetics, Hamed F. Sadi, Ernie Lewis, Kadja Flore Gali, Fan Yang, Jesse Anderson, Suryadev Pratap Singh, Jae Min Yeom, Will Cantrell, Raymond Shaw

Michigan Tech Publications

Experiments in the Pi Convection‐Cloud Chamber conducted by systematically changing the diameter of injected dry aerosol particles while holding the temperature difference constant demonstrate that dry diameter strongly influences the onset of haze‐dominated conditions. Two factors contribute: the system becomes water‐limited, resulting in reduction of supersaturation by growing aerosol particles to the activation diameter; and the activation process becomes kinetically limited. Dry aerosol diameter exerts a strong influence on activation time, with a power‐law exponent of 9/2. Kinetically limited activation occurs when the ratio of the activation and droplet residence times is greater than unity. The findings demonstrate that a …

Data-Driven Methodologies For Mapping Cultural Heritage: The Case Of The National Coal Heritage Area, West Virginia, Usa, Hossain Mohammad Nahyan

Graduate Theses, Dissertations, and Problem Reports (ETD)

The objective of this dissertation was to develop a comprehensive, data-driven spatial framework for characterizing the complex cultural landscape of the National Coal Heritage Area (NCHA) in West Virginia. By transitioning away from traditional, heuristic spatial mapping, this research integrates advanced spatial statistics, machine learning, and GIS-based methodologies to objectively quantify the physical, visual, and cultural dimensions of the post-mining environment. The research is structured around three interconnected empirical studies, each addressing a specific scale of the Landscape Character Assessment (LCA) framework to support heritage conservation and sustainable spatial planning. The first paper focused on landform classification, developing an automated …

Paleo-Environmental Change In Deer Lagoon, Whidbey Island Interpreted From Diatoms And Lithology, Lourdes Garcia

All Master's Theses

Puget Sound is a densely populated, tectonically active area that can be affected by earthquakes from local crustal faults and the Cascadia subduction zone capable of producing abrupt coseismic subsidence. Tidal wetlands are particularly sensitive to abrupt changes because they are depositional environments that reside at sea-level and their lithology and ecological communities are strongly controlled by elevation within the tidal frame. As a result, coseismic subsidence can disrupt established environmental gradients and leave distinguishable signatures preserved within the stratigraphy, like tidal mud directly over peat deposits. These preserved records provide an opportunity to reconstruct past earthquakes and associated relative …

The Geomorphology And Hydrogeology Of Pre-Restoration West Fork Teanaway River, Wa, Usa, Shana M. Egan

All Master's Theses

The West Fork Teanaway (WFT) River in Kittitas County, WA is an entrenched bedrock river channel with disturbed floodplain geomorphology and degraded riparian ecology. Two stream restoration approaches, “stage 0” valley bottom reset and engineered logjam installation, will be installed at the WFT in summer 2026 by collaborators at the Washington State Department of Fish and Wildlife and Mid-Columbia Fisheries Enhancement Group. The objective of this study was to constrain the pre-restoration geomorphic and hydrologic conditions of the WFT. The WFT has an unconsolidated floodplain aquifer of predominantly coarse-grained fluvial deposits. Monitoring of groundwater and surface water levels began in …

Understanding The Cost Of Catastrophe: Wildfire Suppression Costs Drivers By Fire Size Class, Stephanie Overla

All Master's Theses

While most wildfires burn less than 100 acres, the western United States experiences much larger fires annually, placing increasing pressure on suppression resources. Changes in weather patterns, fuel composition, and the spatial complexity of human development have rapidly altered historic fire regimes, increasing both the frequency of large wildfires and the challenges of managing them. This study compares two wildfire classes—Fires of Unusual Size (FOUS, >90,000 acres with at least one rapid growth event), and Large Fires (LF, 25,000–90,000 acres), —to identify differences in how size- and growth-based fire classes influence wildfire suppression costs. Suppression cost data for 60 …

Using Grounded Iceberg Wake Patterns To Interpret Catastrophic Flood Events In Southcentral Alaska, Jana K. Macinnis

All Master's Theses

Catastrophic flood events such as landslide tsunamis and jökulhlaups in glaciated areas can transport and strand icebergs, which obstruct the flow of floodwaters and leave a unique and recognizable grounded iceberg wake pattern in the sediment surface. Grounded iceberg wake patterns (GIWs) were identified at the two study areas in Southcentral Alaska; the outwash plain of a 1967 landslide tsunami at the Grewingk Glacier and proglacial lake, and the Matanuska River valley which experienced an unrecorded jökulhlaup in recent geological times. From these sites, 110 GIWs were identified through visual interpretation of lidar imagery and characterized by measuring their geometry, …

Pre-Eruptive Timescales Via Olivine Diffusion Chronometry For Lava And Tephra Of The Schreibers Meadow Cinder Cone Eruption, Mount Baker (Kulshan), Wa, Sabrina Ansari

All Master's Theses

Mount Baker is a very-high threat Cascade volcano and is located near densely populated areas in northern Washington, putting many at risk if an eruption were to occur. Schreibers Meadow cinder cone is located on the southern flank of Mount Baker and produced the Sulphur Creek (SC) tephra and lava 9.8 ka. Previous work on the SC eruption used petrology and geochemistry to reconstruct the pre-eruptive magmatic architecture beneath Mount Baker Volcanic Field, including olivine-hosted melt inclusions to determine crystallization pressures, as well as plagioclase- and clinopyroxene-derived diffusion timescales to determine magma storage timescales of several months and recharge-to-eruption timescales …