Physical Sciences and Mathematics Commons^™

Optical Coherence Tomography Harmonization With Anatomy-Guided Latent Metric Schrödinger Bridges, Shuwen Wei, Blake E. Dewey, Samuel W. Remedios, Bruno Jedynak, Shimeng Wang, Peter Calabresi, Shiv Saidha, Aaron Carass, Multiple Additional Authors

Mathematics and Statistics Faculty Publications and Presentations

Medical image harmonization aims to reduce the differences in appearance caused by scanner hardware variations to allow for consistent and reliable comparisons across devices. Harmonization based on paired images from different devices has limited applicability in real-world clinical settings. On the other hand, unpaired harmonization typically does not guarantee anatomy consistency, which is problematic because anatomical information preservation is paramount. The Schrödinger bridge framework has achieved state-of-the-art style transfer performance with natural images by matching distributions of unpaired images, but this approach can also introduce anatomy changes when applied to medical images. We show that such changes occur because the …

Recontextualizing Engagement With Data Visualizations In The Context Of The Socio-Ecological, Eva Thanheiser, Laurie Rubel, Beth Herbel-Eisenmann, Courtney Koestler

Mathematics and Statistics Faculty Publications and Presentations

We explore how data visualizations (DVs) are representational tools that can be used to narrate certain aspects of a context but silence others. Using multiple DVs allows for contrasting the DVs and likely provides opportunities for critical reading and exploring the entanglement of political and ecological dimensions of an issue. We start by integrating two sets of practices, Notice, Wonder, Feel, Act and Reimagine (NW-FAR) (Kahn, et al., 2022) and critical graph reading, Framing, Formatting, Narrating (FFN) (Rubel, et al., 2021) towards taking a socio-political stance and supporting students to read data visualizations and develop critical data literacy. We look …

Osa-Diff: An Origin Sampling Based Adversarial Attack Using Diffusion Models, Shayan Jalalipour, Banafsheh Rekabdar

Computer Science Faculty Publications and Presentations

Diffusion models are becoming an increasingly popular emerging technology, however their use in adversarial attacks remains a scarcely explored topic. We show that diffusion models can be used to create end-to-end hidden adversarial perturbations with high rate of success, and propose a novel diffusion based adversarial attack that allows for substantially faster training time (through improved convergence on high quality images) and with substantially less computational overhead than typical diffusion model training

Polynomial-Time Constant-Approximation For Fair Sum-Of-Radii Clustering, Sina Nezhad, Sayan Bandyapadhyay, Tianzhi Chen

Computer Science Faculty Publications and Presentations

In a seminal work, Chierichetti et al. [20] introduced the (t,k)-fair clustering problem: Given a set of red points and a set of blue points in a metric space, a clustering is called fair if the number of red points in each cluster is at most t times and at least 1/t times the number of blue points in that cluster. The goal is to compute a fair clustering with at most k clusters that optimizes certain objective function. Considering this problem, they designed a polynomial-time O(1)- and O(t)-approximation for the k-center and the k-median objective, respectively. Recently, Carta et …

Retrieval-Augmented Feature Generation For Domain-Specific Classification, Xinhao Zhang, Jinghan Zhang, Fengran Mo, Dakshak Keerthi Chandra, Yu-Zhong Chen, Fei Xie, Kunpeng Liu

Computer Science Faculty Publications and Presentations

Feature generation can significantly enhance learning outcomes, particularly for tasks with limited data. An effective way to improve feature generation is to expand the current feature space using existing features and enriching the informational content. However, generating new, interpretable features usually requires domain-specific knowledge on top of the existing features. In this paper, we introduce a Retrieval-Augmented Feature Generation method, RAFG, to generate useful and explainable features specific to domain classification tasks. To increase the interpretability of the generated features, we conduct knowledge retrieval among the existing features in the domain to identify potential feature associations. These associations are expected …

Summed Series Involving 1F2 Hypergeometric Functions, Jack C. Straton

Physics Faculty Publications and Presentations

Summation of infinite series has played a significant role in a broad range of problems in the physical sciences and is of interest in a purely mathematical context. In a prior paper, we found that the Fourier–Legendre series of a Bessel function of the first kind J_N(kx) and modified Bessel functions of the first kind I_N(kx) lead to an infinite set of series involving ₁F₂ hypergeometric functions (extracted therefrom) that could be summed, having values that are inverse powers of the eight primes 1/ ( 2ⁱ 3^j 5^{k …}

Efficient Visual Data Processing Approaches To Improve Resource Utilization, Yeganeh Jalalpour

Dissertations and Theses

With continuous advancements in technology, the volume of visual data being captured, distributed, and consumed across various applications is rapidly increasing. Enhancing the efficiency of visual data processing can improve resource consumption, making the storage, transmission, and use of this growing visual content more effective.

Image and video data constitute a significant share of internet traffic, making video compression a critical factor in enhancing overall data throughput by improving the video compression ratio. Capturing, transferring, and storing raw video data is challenging due to the substantial resources required for both storage and computation. Video compression, however, can significantly mitigate these …

Tag-Based Security In C: Writing And Specifying Flexible Protection, Sean Noble Anderson

Dissertations and Theses

The C language is ubiquitous and insecure. Tag-based security policies offer a flexible toolkit for runtime protection, including policies that mitigate the effects of undetected programming bugs and those that enforce security properties of the program logic. But tag policies can be difficult to define, and the protection that they offer can be difficult to specify and to prove.

This dissertation builds from an assembly-level specification of stack safety, encompassing the essential control-flow structure of C and other high level languages, to a C source-level policy definition framework called Tagged C. Tagged C includes a variant C semantics parameterized by …

Investigating Student Expectations, Buy-In, And Engagement In Lower Division Undergraduate Chemistry Labs, Elizabeth Blanche Vaughan

Dissertations and Theses

Laboratory courses constitute an integral aspect of chemistry education at the undergraduate level. Despite their prominence, a growing number of researchers have begun to think more critically about the value of laboratory learning experiences. As pedagogical decisions should be based on evidence, it is necessary for chemistry education researchers and practitioners to investigate the claim that teaching laboratories are a valuable part of science education. Therefore, the aim of this dissertation was to address one small section of this gap in the literature by obtaining a more robust understanding of students' expectations, buy-in, and engagement in lower division, undergraduate, chemistry …

Aquatic Plant Threats To The Columbia River, Jacob Rose, Gabriel Campbell

Center for Lakes and Reservoirs Publications and Presentations

These presentation slides provide an overview of some of the invasive aquatic plants that pose an emerging threat to Oregon waterways. It contains botanical notes and high-quality photographs of approximately nine different plant species. Additional slides emphasize the importance of early detection and rapid response, as well as existing resources for invasive species outreach. This presentation was given orally at the Oregon Department of Agriculture's Interagency Noxious Weed Symposium to an audience of natural resource practitioners.

Emerging Aquatic Plant Threats To Oregon Waterways, Jacob Rose, Gabriel Campbell

Center for Lakes and Reservoirs Publications and Presentations

This brief presentation provides an overview some of two invasive aquatic plants that pose a threat to the Columbia River, where it borders Oregon and Washington. Flowering rush (Butomus umbellatus) and fragrant waterlily (Nymphaea odorata) threaten aquatic habitats up and down the Columbia River. Staff from the Center for Lakes & Reservoirs promoted a quick, picture-based key for flowering rush and lookalikes. This presentation was given orally at the Oregon Department of Agriculture's Interagency Noxious Weed Symposium to an audience of natural resource practitioners.

Recovery Of Black Carbon Concentrations In Burned Forests In Wyoming, Usa, Monica Vanesa Zapata Villegas

Dissertations and Theses

Burned forests that remain standing following fire release light-absorbing particles (LAPs), including black carbon (BC), into winter snowpacks, reducing snow surface albedo and accelerating snowmelt timing for decades postfire. Although the role of LAPs in seasonal snow has been extensively studied, the spatiotemporal variability of LAPs' contributions to snowmelt relative to time-since-fire and burn severity remains unknown. This study aimed to quantify the spatiotemporal variability of forest fire effects on LAPs in snow and associated snow albedo in the Triple Divide region of western Wyoming, headwaters of the Colorado, Columbia, and Missouri rivers. Using geochemical analysis and radiative transfer modeling, …

Landslide Mapping, Characterization, And Hazard Assessment With 3d Slope Stability Modeling In White Bluffs, Washington State, Anna Tsitsivas

Dissertations and Theses

Slope failures shape the landscape by moving unstable material downslope and, in doing so, become a great hazard to all those in their path. Understanding the mechanisms that control landslide location, timing, size, type, and runout - and therefore hazards - requires a deep understanding of the local geology, stratigraphy, and groundwater conditions. Along White Bluffs, in south-central Washington, landslides of several failure styles have likely been triggered by an increased water table in recent decades, threatening both farmland behind the bluffs and habitat below. This study focuses on characterizing potential groundwater sources and determining controls on spatial and temporal …

Increased Thermal Stability And Retained Antibacterial Properties In A Sulbactam And Amantadine Salt: Towards Effective Antibacterial-Antiviral Combination Therapies, Josephine Bicknell, Ivan Bondarenko, Alice Colatrella, Elani J. Cabrera-Vega, Jesus Daniel Loya, Delbert S. Botes, Jay L. Mellies, Gonzalo Campillo-Alvarado

Chemistry Faculty Publications and Presentations

A clinically relevant multidrug solid comprising sulbactam (β-lactamase inhibitor) and amantadine (antiviral) displays enhanced thermal stability and sustained antibacterial activity compared to starting materials.

We describe the formation of a multidrug salt comprising sulbactam (SUL, β-lactamase inhibitor) and amantadine (AMNH, antiviral). Physicochemical investigation of the SUL·AMNH salt revealed enhanced thermal stability compared to pristine starting materials. In vitro studies found that salt formation in SUL·AMNH does not disrupt antibacterial activity against model organisms Escherichia coli and Staphylococcus epidermidis. To our knowledge, we show the first β-lactamase inhibitor-antiviral salt where both components have been approved by the U.S. Food and Drug …

Sustainability Assessment Of Photovoltaic Cells In Cross-Functional Applications, Achyuth Ravilla

Dissertations and Theses

Achieving the G7 countries' net-zero emissions target by 2050 requires integrating photovoltaic (PV) systems into diverse cross-functional applications that support sustainable energy transitions across multiple sectors. This dissertation explores the economic and environmental sustainability of three such applications: agrivoltaics, lower-dimensional materials in perovskite solar cells, and PV-electrochemical water-splitting technologies for hydrogen production. Employing life cycle assessment (LCA) and techno-economic analysis (TEA), we address the knowledge gap in comprehensive evaluations of PV-integrated solutions.

The first chapter assesses agrivoltaic systems (AVS), which combine PV systems with agriculture to mitigate land-use conflicts while enhancing food and energy production. Findings indicate that AVS designs, …

Applying Positive Unlabeled Learning Techniques And Using The Kullback-Leibler Divergence To Improve Geothermal Surveying Assessments, Martín Thomas Rodriguez

Dissertations and Theses

As we face the current climate crisis, the discovery of geothermal energy resources has the potential to greatly reduce our dependence on fossil fuels worldwide. However, the development of any new energy infrastructure is expensive and depends on the willingness of energy agencies and developers to make initial investments based on calculated risk measures. One such measure, called geothermal favorability, is the likelihood that a site has conditions favorable for geothermal systems containing recoverable energy potential. Its prediction from existing geophysical datasets proves to be a nontrivial task. The prediction of geothermal favorability can be framed as a binary classification …

Aars Online: A Collaborative Database On The Structure, Function, And Evolution Of The Aminoacyl-Trna Synthetases, Jordan Douglas, Haissi Cui, John J. Perona, Oscar Vargas-Rodriguez, Henna Tyynismaa, Claudia Alvarez Carreno, Jiqiang Ling, Lluis Ribas De Pouplana, Xiang-Lei Yang, Multiple Additional Authors

Chemistry Faculty Publications and Presentations

The aminoacyl-tRNA synthetases (aaRS) are a large group of enzymes that implement the genetic code in all known biological systems. They attach amino acids to their cognate tRNAs, moonlight in various translational and non-translational activities beyond aminoacylation, and are linked to many genetic disorders. The aaRS have a subtle ontology characterized by structural and functional idiosyncrasies that vary from organism to organism, and protein to protein. Across the tree of life, the 22 coded amino acids are handled by 16 evolutionary families of Class I aaRS and 21 families of Class II aaRS. We introduce AARS Online, an interactive Wikipedia-like …

Landscaping Impacts On Urban Soil Development, Fry Lundgren

University Honors Theses

Urban soils can play a key role in flood mitigation, water filtration, and supporting urban plant communities, however many are highly disturbed due to development and management practices. Although full recovery will take time (centuries), in the short term managing soils in ways that conserve organic matter inputs and promote nutrient cycling can support important soil functions and likely promote long term development. To understand how landscaping impact soil development on PSU campus, organic matter content, moisture content, and respiration rates were measured in soils from four area types with different long term weed management strategies (mulch- M; sustained plant …

How Does Herbicide Resistance Change Farmer’S Weed Management Decisions? Evidence From The Roundup Ready Experiment, Huichun Sun, Terrance Hurley, George B. Frisvold, Katherine Dentzman, David Ervin, Wesley Everman, Jeffrey Gunsolus, Jason Norsworthy, Micheal Owen

Environmental Science and Management Faculty Publications and Presentations

Adoption of diverse weed management practices is viewed as essential for slowing the spread of herbicide-resistant (HR) weeds. Yet, adoption of diverse tactics has remained low, while there has been explosive growth of resistant weeds. This study analyzes U.S.-farm-level data to identify factors affecting adoption of diverse weed management practices. This study uses directed acyclic graphs (DAGs) to consider how practice adoption is influenced by different causal pathways between farmer and farm characteristics and farmer awareness of and concern over HR weeds. This study then uses multiple regression analysis to estimate the direct and indirect pathways that influence practice adoption. …

Predicting Cloud-To-Ground Lightning In The Western United States From The Large-Scale Environment Using Explainable Neural Networks, Dmitri A. Kalashnikov, Frances V. Davenport, Zachary M. Labe, Paul C. Loikith, John T. Abatzoglou, Deepti Singh

Geography Faculty Publications and Presentations

Lightning is a major source of wildfire ignition in the western United States (WUS). We build and train convolutional neural networks (CNNs) to predict the occurrence of cloud-to-ground (CG) lightning across the WUS during June-September from the spatial patterns of seven large-scale meteorological variables from reanalysis (1995-2022). Individually trained CNN models at each 1° × 1° grid cell ( = 285 CNNs) show high skill at predicting CG lightning days across the WUS (median AUC = 0.8) and perform best in parts of the interior Southwest where summertime CG lightning is most common. Further, interannual correlation between observed and predicted …

Mean Field Control Of Droplet Dynamics With High-Order Finite-Element Computations, Guosheng Fu, Hangjie Ji, Will Pazner, Wuchen Li

Mathematics and Statistics Faculty Publications and Presentations

Liquid droplet dynamics are widely used in biological and engineering applications, which contain complex interfacial instabilities and pattern formation such as droplet merging, splitting, and transport. This paper studies a class of mean field control formulations for these droplet dynamics, which can be used to control and manipulate droplets in applications. We first formulate the droplet dynamics as gradient flows of free energies in modified optimal transport metrics with nonlinear mobilities. We then design an optimal control problem for these gradient flows. As an example, a lubrication equation for a thin volatile liquid film laden with an active suspension is …

Inefficiencies In Water Supply And Perceptions Of Water Use In Peri-Urban And Rural Water Supply Systems: Case Study In Cali And Restrepo, Colombia, Diana Carolina Callejas Moncaleano, Saket Pande, Melissa Haeffner, Juan Pablo Rodríguez Sánchez, Luuk Rietveld

Environmental Science and Management Faculty Publications and Presentations

Introduction:

Water scarcity is a significant global challenge that frequently manifests as inadequate water supply for domestic purposes. However, domestic water insecurity can occur even in regions where water is naturally abundant. Despite Colombia’s plentiful surface water resources, rural and peri-urban communities often experience limited access to water. Existing water supply systems are frequently susceptible to poor maintenance, particularly in remote areas where much of the infrastructure remains outdated. Consequently, water is often lost through leaks or unintentional non-domestic use. Although a regulatory framework for water usage exists, it does not consistently translate into effective implementation.

Methodology:

Based on an …

Automated Verification Of Compiler Transformations, Yanzhao Wang

Dissertations and Theses

The ever-growing complexity of software and its target hardware makes it increasingly challenging to develop reliable compilers that preserve the semantics of source code during compilation. Traditional testing methods often lack sufficient test coverage and fail to identify subtle errors and undefined behaviors that can lead to compiler malfunctions. Furthermore, while formal compiler certification ensures semantic preservation through theorem proving, the inherent complexity of this process makes re-certification after each compiler revision substantially labor-intensive. This often significantly hinders the improvement of compilers.

This research aims to bridge the gap between increasing compiler complexity and the limited scalability of formal verification …

Investigating The Learning Goals And Expectations Of Laboratory Coordinators, Graduate Teaching Assistants, And Students In General And Organic Chemistry Laboratory Courses, Elizabeth Blanche Vaughan, A. Montoya-Cowan, Christine Kim, Alexandra Stephens, Osie Hamilton, Jack Barbera

Chemistry Faculty Publications and Presentations

As chemistry education researchers and practitioners continue to investigate and improve undergraduate laboratory courses, it is necessary to consider the perspectives held by each of the stakeholders who are directly involved in these courses, including laboratory coordinators, graduate teaching assistants, and students. This study sought to qualitatively investigate the learning goals and expectations held by laboratory coordinators, graduate teaching assistants (GTAs), and students for general and organic chemistry laboratory courses at a single institution. This was completed through the collection and analysis of semistructured interview data from laboratory coordinators and GTAs and open-ended written responses from students. Results indicated that …

Polymorphism Control Of Polyethylene Terephthalate (Pet) Degradation Product Via Mechanochemistry Leads To Accelerated Microbial Degradation, Deepika Shingwekar, Nicholas Lutz, Delbert S. Botes, Elani J. Cabrera-Vega, Gonzalo Campillo-Alvarado, Jay L. Mellies, Jesus Daniel Loya

Chemistry Faculty Publications and Presentations

Here, we optimized a chemo-microbial degradation of polyethylene terephthalate. Developed a path to mechanochemically interconvert between BHET polymorphs and established that BHET polymorphism influences bacterial biodegradation rate.

On The Improved Convergence Of Lifted Distributional Gauss Curvature From Regge Elements, Jay Gopalakrishnan, Michael Neunteufel, Joachim Schöberl, Max Wardetzky

Mathematics and Statistics Faculty Publications and Presentations

Although Regge finite element functions are not continuous, useful generalizations of nonlinear derivatives like the curvature, can be defined using them. This paper is devoted to studying the convergence of the finite element lifting of a generalized (distributional) Gauss curvature defined using a metric tensor approximation in the Regge finite element space. Specifically, we investigate the interplay between the polynomial degree of the curvature lifting by Lagrange elements and the degree of the metric tensor in the Regge finite element space. Previously, a superconvergence result, where convergence rate of one order higher than expected, was obtained when the approximate metric …

A Finite-Horizon Approach To Active Level Set Estimation, Phillip Kearns, Bruno Jedynak, John Lipor

Mathematics and Statistics Faculty Publications and Presentations

We consider the problem of active learning for level set estimation (LSE), where the goal is to localize all regions where a function of interest lies above/below a given threshold as quickly as possible. We present a finitehorizon search procedure to perform LSE in one dimension while optimally balancing both the final estimation error and the distance traveled during active learning for a fixed number of samples. A tuning parameter is used to trade off between the estimation accuracy and distance traveled. We show that the resulting optimization problem can be solved in closed form and that the resulting policy …

Investigating Students' Expectations And Engagement In General And Organic Chemistry Laboratory Courses, Elizabeth B. Vaughan, Saraswathi Tummuru, Jack Barbera

Chemistry Faculty Publications and Presentations

Students’ expectations for their laboratory coursework are theorized to have an impact on their learning experiences and behaviors, such as engagement. Before students’ expectations and engagement can be explored in different types of undergraduate chemistry laboratory courses, appropriate measures of these constructs must be identified, and evidence of validity and reliability for the data collected with these instruments must be investigated. This study collected evidence related to response process validity, internal structure validity, and single administration reliability for version 2 of the Meaningful Learning in the Laboratory Instrument (MLLIv2) and a measure of student engagement in the undergraduate chemistry laboratory. …

Properties Of Generalized Polyhedral Convex Multifunctions, Ngoc Luan Nguyen, Mau Nam Nguyen, Dong Yen Nguyen

Mathematics and Statistics Faculty Publications and Presentations

This paper presents a study of generalized polyhedral convexity under basic operations on multifunctions. We address the preservation of generalized polyhedral convexity under sums and compositions of multifunctions, the domains and ranges of generalized polyhedral convex multifunctions, and the direct and inverse images of sets under such mappings. Then we explore the class of optimal value functions defined by a generalized polyhedral convex objective function and a generalized polyhedral convex constrained mapping. The new results provide a framework for representing the relative interior of the graph of a generalized polyhedral convex multifunction in terms of the relative interiors of its …

Altitude-Driven Variations In Chrysophycean Stomatocyst Assemblages: Implications For Climate Reconstructions In The Three Parallel Rivers Of Yunnan Protected Area, China, Yanling Li, Qi Liu, Yangdong Pan, Wanting Pang

Environmental Science and Management Faculty Publications and Presentations

The Three Parallel Rivers of Yunnan Protected Area (TPRYPA) is in the core area of the Hengduan Mountains, characterized by paralleling alternately high mountains and canyons that led to significant vertical temperature variation. Developing a climate transfer function for this region is crucial for both biodiversity protection and enhancing our understanding of feedback mechanisms between low-latitude and high-altitude areas in the context of global climate change. We investigated the chrysophycean stomatocyst assemblages from surface sediments of 46 high mountain lakes (altitude: 3244 to 5043 m) in the TPRYPA to assess the suitability of cysts in prediction of climate variability in …