Digital Commons Network^™

Evaluating Methods For Assessing Interpretability Of Deep Neural Networks (Dnns), Emily Barnes, James Hutson

Faculty Scholarship

The interpretability of deep neural networks (DNNs) is a critical focus in artificial intelligence (AI) and machine learning (ML), particularly as these models are increasingly deployed in high-stakes applications such as healthcare, finance, and autonomous systems. In the context of these technologies, interpretability refers to the extent to which a human can understand the cause of a decision made by a model. This article evaluates various methods for assessing the interpretability of DNNs, recognizing the significant challenges posed by their complex and opaque nature. The review encompasses both quantitative metrics and qualitative evaluations, aiming to identify effective strategies that enhance …

Predicting Rheology Of Uv-Curable Nanoparticle Ink Components And Compositions For Inkjet Additive Manufacturing, Cameron D. Lutz

Master's Theses

Inkjet additive manufacturing is the next step toward ubiquitous manufacturing by enabling multi-material printing that can exhibit various mechanical, electronic, and thermal properties. These characteristics are realized in the careful formulation of the inks and their functional materials, but there are many constraints that need to be satisfied to allow optimal jetting performance and build quality when used in an inkjet 3-D printer. Previous research has addressed the desirable rheology characteristics to enable stable drop formation and how the metallic nanoparticles affect the viscosity of inks. The contending goals of increasing nanoparticle-loading to improve material deposition rates while trying to …

Catalytic Role Of Histidine-114 In The Hydrolytic Dehalogenation Of Chlorothalonil By Pseudomonas Sp. Ctn-3, Grayson Gerlich, Callie Miller, Xinhang Yang, Brian Bennett, Judith Klein-Seetharaman, Richard C. Holz

Physics Faculty Research and Publications

Chlorothalonil (2,4,5,6-tetrachloroisophthalonitrile; TPN) is an environmentally persistent fungicide that sees heavy use in the USA and is highly toxic to aquatic species and birds, as well as a probable human carcinogen. The chlorothalonil dehalogenase from Pseudomonas sp. CTN-3 (Chd, UniProtKB C9EBR5) degrades TPN to its less toxic 4-OH-TPN analog making it an exciting candidate for the development of a bioremediation process for TPN; however, little is currently known about its catalytic mechanism. Therefore, an active site residue histidine-114 (His114) which forms a hydrogen bond with the Zn(II)-bound water/hydroxide and has been suggested to be the active site acid/base, was substituted …

General Chemistry Ii: Chem 2134, Subha Pratihar

ATU Faculty OER Books and Materials

No abstract provided.

Unconventional Computing With Photonic Oscillator Networks, Mostafa Honari Latifpour

Dissertations, Theses, and Capstone Projects

The ever-increasing demand for data processing and the challenges in scaling traditional computing architectures are driving intensive research into alternative computing paradigms. Optical computing has garnered renewed attention since the 2010s, driven by its potential to accelerate specialized computational tasks such as combinatorial optimization and neural networks.

Coherent light sources including lasers and parametric oscillators have been around for decades and become indispensable tools in modern technology, but these photonic oscillators are also nonlinear dynamical systems that can exhibit emergent, complex phenomena, especially when coupled in arrays. These nonlinear optical systems have recently been shown to be capable of doing …

Moral Responsibility And Other Visceral Attitudes Of Western Michigan University Students Toward Food Waste, Quinn Heiser

Masters Theses

Despite the large number of people that go hungry on a regular basis in America, food waste remains a looming issue, globally and nationally. Both American college students and the universities themselves contribute a large portion to the national food waste totals. A dichotomy that is especially curious is the difference between students who live on-campus and whose main source of meals is the dining centers, versus students who live off campus and rely mainly on groceries to make meals independently. However, food waste has seldom been studied in the context of the fact that college is a major transition …

Radiogenomics-Based Risk Prediction Of Glioblastoma Multiforme With Clinical Relevance, Xiaohua Qian, Hua Tan, Xiaona Liu, Weiling Zhao, Michael D Chan, Pora Kim, Xiaobo Zhou

Faculty, Staff and Student Publications

Glioblastoma multiforme (GBM)is the most common and aggressive primary brain tumor. Although temozolomide (TMZ)-based radiochemotherapy improves overall GBM patients' survival, it also increases the frequency of false positive post-treatment magnetic resonance imaging (MRI) assessments for tumor progression. Pseudo-progression (PsP) is a treatment-related reaction with an increased contrast-enhancing lesion size at the tumor site or resection margins miming tumor recurrence on MRI. The accurate and reliable prognostication of GBM progression is urgently needed in the clinical management of GBM patients. Clinical data analysis indicates that the patients with PsP had superior overall and progression-free survival rates. In this study, we aimed …

Matrix Approximation And Image Compression, Isabella R. Padavana

Master's Theses

This thesis concerns the mathematics and application of various methods for approximating matrices, with a particular eye towards the role that such methods play in image compression. An image is stored as a matrix of values with each entry containing a value recording the intensity of a corresponding pixel, so image compression is essentially equivalent to matrix approximation. First, we look at the singular value decomposition, one of the central tools for analyzing a matrix. We show that, in a sense, the singular value decomposition is the best low-rank approximation of any matrix. However, the singular value decomposition has some …

A Microgenetic Learning Analysis Of Contextuality In Reasoning About Exponential Modeling, Elahe Allahyari

Dissertations

This work explores the complex cognitive processes students engage in when addressing contextual tasks requiring linear and exponential models. Grounded within Piagetian constructivism and the Knowledge in Pieces (KiP) epistemological perspective (diSessa, 1993, 2018), this empirical study in a clinical setting develops a Microgenetic Learning Analysis (MLA) of the reasoning of 14 students from an Algebra II course. It reveals the critical role of cognitive disequilibrium as an essential cognitive state for conceptual development and the process of reorganizing knowledge systems. The study uncovers the fluctuations in students’ reasoning patterns and the significant impact on students’ reasoning patterns of task-specific …

(R2074) A Comparative Study Of Two Novel Analytical Methods For Solving Time-Fractional Coupled Boussinesq-Burger Equation, Jyoti U. Yadav, Twinkle R. Singh

Applications and Applied Mathematics: An International Journal (AAM)

In this paper, a comparative study between two different methods for solving nonlinear timefractional coupled Boussinesq-Burger equation is conducted. The techniques are denoted as the Natural Transform Decomposition Method (NTDM) and the Variational Iteration Transform Method (VITM). To showcase the efficacy and precision of the proposed approaches, a pair of different numerical examples are presented. The outcomes garnered indicate that both methods exhibit robustness and efficiency, yielding approximations of heightened accuracy and the solutions in a closed form. Nevertheless, the VITM boasts a distinct advantage over the NTDM by addressing nonlinear predicaments without recourse to the application of Adomian polynomials. …

Aromatic-Carbonyl Interactions As An Emerging Type Of Non-Covalent Interactions, Chaowei Yin, Hebo Ye, Yu Hai, Hanxun Zou, Lei You

Faculty, Staff and Student Publications

Aromatic-carbonyl (Ar···C═O) interactions, attractive interactions between the arene plane and the carbon atom of carbonyl, are in the infancy as one type of new supramolecular bonding forces. Here the study and functionalization of aromatic-carbonyl interactions in solution is reported. A combination of aromatic-carbonyl interactions and dynamic covalent chemistry provided a versatile avenue. The stabilizing role and mechanism of arene-aldehyde/imine interactions are elucidated through crystal structures, NMR studies, and computational evidence. The movement of imine exchange equilibria further allowed the quantification of the interplay between arene-aldehyde/imine interactions and dynamic imine chemistry, with solvent effects offering another handle and matching the electrostatic …

Associations Between Longer Leukocyte Telomere Length And Increased Lung Cancer Risk Among Never Smokers In Urban China, Jason Y Y Wong, Xiao-Ou Shu, Wei Hu, Batel Blechter, Jianxin Shi, Kevin Wang, Richard Cawthon, Qiuyin Cai, Gong Yang, Mohammad L Rahman, Bu-Tian Ji, Yutang Gao, Wei Zheng, Nathaniel Rothman, Qing Lan

Faculty, Staff and Student Publications

BACKGROUND: The complex relationship between measured leukocyte telomere length (LTL), genetically predicted LTL (gTL), and carcinogenesis is exemplified by lung cancer. We previously reported associations between longer pre-diagnostic LTL, gTL, and increased lung cancer risk among European and East Asian populations. However, we had limited statistical power to examine the associations among never smokers by gender and histology.

METHODS: To investigate further, we conducted nested case-control analyses on an expanded sample of never smokers from the prospective Shanghai Women's Health Studies (798 cases and 792 controls) and Shanghai Men's Health Studies (161 cases and 162 controls). We broke the case-control …

Advances In The Integration Of Microalgal Communities For Biomonitoring Of Metal Pollution In Aquatic Ecosystems Of Sub-Saharan Africa, Mary Mulenga, Concillia Monde, Todd Johnson, Kennedy O Ouma, Stephen Syampungani

Faculty, Staff and Student Publications

This review elucidated the recent advances in integrating microalgal communities in monitoring metal pollution in aquatic ecosystems of sub-Saharan Africa (SSA). It also highlighted the potential of incorporating microalgae as bioindicators in emerging technologies, identified research gaps, and suggested directions for further research in biomonitoring of metal pollution. Reputable online scholarly databases were used to identify research articles published between January 2000 and June 2023 for synthesis. Results indicated that microalgae were integrated either individually or combined with other bioindicators, mainly macroinvertebrates, macrophytes, and fish, alongside physicochemical monitoring. There was a significantly low level of integration (< 1%) of microalgae for biomonitoring aquatic metal pollution in SSA compared to other geographical regions. Microalgal communities were employed to assess compliance (76%), in diagnosis (38%), and as early-warning systems (38%) of aquatic ecological health status. About 14% of biomonitoring studies integrated microalgal eDNA, while other technologies, such as remote sensing, artificial intelligence, and biosensors, are yet to be significantly incorporated. Nevertheless, there is potential for the aforementioned emerging technologies for monitoring aquatic metal pollution in SSA. Future monitoring in the region should also consider the standardisation and synchronisation of integrative biomonitoring and embrace the "Citizen Science" concept at national and regional scales.

Snpaimer: R Package For Evaluating Ancestry Informative Marker Contributions In Non-Model Population Diagnostics, Kim L. Vertacnik, Oksana V. Vernygora, Julian R. Dupuis

Entomology Faculty Publications

Motivation: Single nucleotide polymorphism (SNP) markers are increasingly popular for population genomics and inferring ancestry for individuals of unknown origin. Because large SNP datasets are impractical for rapid and routine analysis, diagnostics rely on panels of highly informative markers. Strategies exist for selecting these markers, however, resources for efficiently evaluating their performance are limited for non-model systems.

Results: snpAIMeR is a user-friendly R package that evaluates the efficacy of genomic markers for the cluster assignment of unknown individuals. It is intended to help minimize panel size and genotyping effort by determining the informativeness of candidate diagnostic markers. Provided genotype data …

(R2070) Poisson-Exponentiated Weibull Distribution: Properties, Applications And Extension, Alphonsa George, Dais George

Applications and Applied Mathematics: An International Journal (AAM)

In this article, we introduce a new member of the Poisson-X family namely, the Poisson-exponentiated Weibull distribution. The statistical as well as the distributional properties of the new distribution are studied, and the performance of the maximum likelihood method of estimation is verified by a simulation study. The flexibility of the distribution is illustrated by a real data set. We develop and study a reliability test plan for the acceptance or rejection of a lot of products submitted for inspection when their lifetimes follow the new distribution. A real data example is also given to illustrate the feasibility of the …

(R2071) Global Stability Analysis Of Chikv Dynamics Model With Adaptive Immunity And Distributed Time Delays, Taofeek O. Alade, Samson Olaniyi, Hassan A. Idris, Yaqoob Al Rahbi, Mohammad Alnegga

Applications and Applied Mathematics: An International Journal (AAM)

The application of mathematical biology and dynamical systems has proven to be an effective approach for studying viral infection models. To contribute to this research, our paper proposes a new CHIKV model that takes into account an adaptive immune response and distributed time delays, which accurately reflects the time lag between initial viral contacts and the production of new active CHIKV particles. By analyzing the model’s qualitative behavior, we establish a biological threshold number that can predict whether CHIKV will be cleared from or persist in the body. We demonstrate the global stability of both CHIKV-present and CHIKV-free steady states …

Lead Along Arid Route 66: Concentration, Fate, Surface Transport, And Awareness, Dominic Joel Ombati

Loma Linda University Electronic Theses, Dissertations & Projects

Fate and transport of lead (Pb) are well studied in humid, high precipitation environments. Few studies have compared or addressed fate of lead (Pb) in arid, low precipitation areas where the soil binding capacity may differ from classic studies. The goal of this study is to identify the control of fate and transport in the arid section of Route 66 by determining the concentration, chemical forms, and surface transport mechanism of lead (Pb) along the arid section of Route 66. Understanding the fate and transport of lead (Pb) in different environments is key in the environmental mitigation of lead (Pb) …

Santa Maria Climate Action Plan Recommendations: Building Energy And Transportation, Thomas Zimmerman, Elena Blewett

City and Regional Planning

The Santa Maria Climate Action Plan Recommendations addresses GHG emissions reduction for the largest sectors in the City of Santa Maria- Building Energy and Transportation. The project includes GHG forecasts and reduction targets from the City’s Draft 2020 Community-Wide Greenhouse Gas Inventory Report. The reduction targets are met through a series of actionable measures to help the City meet aggressive reduction targets by 2030 and 2045.

Using Bayesian Multispecies Models To Evaluate Fish And Invertebrate Detection Probability And Distribution In The Hypersaline Bahia Grande Tidal Basin, Roy M. Ulibarri, Catherine M. Eckert, David Hicks, David Montagne, Brandon Jones, David R. Stewart

School of Earth, Environmental, & Marine Sciences Faculty Publications

Objective

In 2000, the Laguna Atascosa National Wildlife Refuge acquired the Bahia Grande (Texas) management unit, a space that had lain barren and arid for 70 years. A large cooperative partnership launched a restoration project to replenish the basin and recover its original tidal hydrology. In 2005, the construction of a pilot channel successfully restored water throughout the basin, and plans to eventually widen the channel were developed. Our study aims to evaluate an estuarine habitat restoration by assessing ecological drivers and the impacts on species diversity.

Methods

We evaluated species richness, detection/occupancy rates, and species–habitat relationships, and we estimated …

Moss Biomonitoring Of Lead Emissions From Hillsboro Airport, Daria Kolpakov

University Honors Theses

The objective of this experiment was to use biomonitoring as a method to determine lead concentration levels around Hillsboro Airport in Hillsboro, Oregon. Twenty-two samples were collected within a 2 km radius around Hillsboro Airport using a randomized sampling strategy. The concentrations of lead within the samples were determined using ICP-MS. The average lead concentration was (2.8 ± 5.0) mg/kg with a peak value of 21.6 mg/kg 0.57 km from Hillsboro Airport. As the average lead concentration was substantially skewed, Hillsboro Airport is likely to be the source of the lead increase.

Grazing Annual Pastures – Using Feed On Offer (Foo) As A Guide, Department Of Primary Industries And Regional Development, Western Australia

Animal production and livestock factsheets

Grazing management in winter and spring in South West Western Australia (SW WA) can manipulate the quality, quantity and composition of pasture. These pasture changes can increase livestock feed efficiency and productivity, reduce insect populations and improve pasture persistence. Seasonal grazing based on feed on offer (FOO) is described here to maximise stocking rate and pasture production.

The Department of Primary Industries and Regional Development recommends using feed measurements and feed budgeting to increase productivity and reduce livestock health risks.

Boosting Winter Pasture Growth, Department Of Primary Industries And Regional Development, Western Australia

Grains and other field crops factsheets

Applying gibberellic acid or nitrogen fertiliser to pasture in winter can increase dry matter production of grasses and broadleaf weeds and help reduce feed shortages in winter.

The Cultivation Of Ulva Lactuca In Jambiani, Zanzibar: A Case Study, Jazmine R. Compton

Anthós

This case study explores the feasibility of Ulva lactuca cultivation in Jambiani, Zanzibar, Tanzania. The seaweed farming industry in Zanzibar is facing challenges related to climate change that have resulted in increased rates of crop failure and decreased production. Cultivation of the green algae Ulva lactuca has been suggested as a potential solution due to its tolerance to extreme environmental conditions. In collaboration with Marine Cultures, this project has tested different cultivation methods typically used for red algae (Rhodophyta) species. Experimental plots of Ulva lactuca were established in Jambiani, Zanzibar using the floating line and off- bottom methods. At the …

Poster: Profiling Event Vision Processing On Edge Devices, Ila Nitin Gokarn, Archan Misra

Research Collection School Of Computing and Information Systems

As RGB camera resolutions and frame-rates improve, their increased energy requirements make it challenging to deploy fast, efficient, and low-power applications on edge devices. Newer classes of sensors, such as the biologically inspired neuromorphic event-based camera, capture only changes in light intensity per-pixel to achieve operational superiority in sensing latency (O(μs)), energy consumption (O(mW)), high dynamic range (140dB), and task accuracy such as in object tracking, over traditional RGB camera streams. However, highly dynamic scenes can yield an event rate of up to 12MEvents/second, the processing of which could overwhelm …

Community Discovery Over Attributed Graphs, Yudong Niu

Dissertations and Theses Collection (Open Access)

Community discovery, as a fundamental problem in graph mining, finds applications in various domains such as biological analysis, system optimization and fraud detection. Although many efforts have been made to address community discovery based on graph topology, few works have been devoted to community discovery over attributed graphs, where graphs are equipped with attribute information such as node and edge types. Thus, this thesis is devoted to designing innovative solutions that can utilize the attribute information together with graph topology for community discovery. In particular, we study novel problems with efficient algorithms for both homogeneous and heterogeneous attributed graphs and …

Udbrnet: A Novel Uncertainty Driven Boundary Refined Network For Organ At Risk Segmentation, Riad Hassan, M. Rubaiyat Hossain Mondal, Sheikh Iqbal Ahamed

Computer Science Faculty Research and Publications

Organ segmentation has become a preliminary task for computer-aided intervention, diagnosis, radiation therapy, and critical robotic surgery. Automatic organ segmentation from medical images is a challenging task due to the inconsistent shape and size of different organs. Besides this, low contrast at the edges of organs due to similar types of tissue confuses the network’s ability to segment the contour of organs properly. In this paper, we propose a novel convolution neural network based uncertainty-driven boundary-refined segmentation network (UDBRNet) that segments the organs from CT images. The CT images are segmented first and produce multiple segmentation masks from multi-line segmentation …

Hydrological Analysis Of Post-Fire Responses Within The Little Creek Watershed Of Swanton Pacific Ranch, Alexander Jeffrey Wiens

Master's Theses

Climate change and a growing wildland-urban interface are associated with an increase in the number and severity of wildfires. While severe wildfires do cause a costly and dangerous impact on the environment and the public, their after-effects comprise important subjects of study. In post-fire hydrologic studies, the reduced infiltration and plant cover that results from wildfires can commonly be associated with increased peakflows and erosion. Phenomena such as the flooding and debris flows in Montecito after the Thomas Fire in late 2017 can have important implications on infrastructure and human lives. Quantifying post-fire peak flows and flooding volumes has therefore …

Pain Points: Cluster Analysis In Chronic Pain Networks, Iris W. Ho

Master's Theses

Chronic pain is a pervasive health issue, affecting a significant portion of the population and posing complex challenges due to its diverse etiology and individualized impact. To address this complexity, there is a growing interest in grouping chronic pain patients based on their unique treatment needs. While various methodologies for patient grouping have emerged, leveraging graph-based approaches to produce and evaluate such groupings remains largely unexplored. Recent studies have shown promise in integrating knowledge graphs into exploring patient similarity across different biological domains, indicating potential avenues for research. Additionally, there is a growing interest in investigating patient similarity networks, highlighting …

Using Plankton Edna To Estimate Whale Abundances Off The California Coast: Data Integration And Statistical Modeling, Katherine Chan

Master's Theses

Understanding marine mammal populations and how they are affected by human activity and ocean conditions is vital, especially in tracking population declines and monitoring endangered species. However, tracking marine mammal populations and their distribution is challenging due to difficulties in observation and costs. Using surrounding plankton environmental DNA (eDNA) has the potential to provide an indirect measure of monitoring cetacean abundances based on ecological associations. This project aims to apply statistical methods to assess the relationship of visual abundances of common species of baleen whales with amplicon sequence variants (ASV) of plankton eDNA samples from the NOAA-CalCOFI Ocean Genomics (NCOG) …

Searching For The Hyperobject: Crystals As Transscalar Vehicles, Jay Costello

Masters Theses

When I touch the street outside my house, I'm touching Los Angeles—a contiguous vector of material bisecting a continent. A slab, a stone, dust and oil, a googolplex of tightly packed anisotropic particles... At nightfall, I sneak to the edge of the highway and break off a piece. 'What does it mean for a worm to be aware of the scale of the planet?' Bruno Latour's evocative questioning of scalar jumps prompts an existentialism that places me somewhere between the hyperlocal and the massively distributed. Like a cosmic traveler floating through the universe, I feel adrift. I look around, grasping …