Physical Sciences and Mathematics Commons^™

Variational Bayesian Inference For Functional Data Clustering And Survival Data Analysis, Chengqian Xian

Electronic Thesis and Dissertation Repository

Variational Bayesian inference is a method to approximate the posterior distribution under a Bayesian model analytically. As an alternative to Markov Chain Monte Carlo (MCMC) methods, variational inference (VI) produces an analytical solution to an approximation of the posterior but have a lower computational cost compared to MCMC methods. The main challenge of applying VI comes from deriving the equations used to update the approximated posterior parameters iteratively, especially when dealing with complex data. In this thesis, we apply the VI to the context of functional data clustering and survival data analysis. The main objective is to develop novel VI …

The Characterization And Electrochemistry Of Natural Uranium Dioxide Under Long-Term Disposal Conditions, Martin D. M. Badley

Electronic Thesis and Dissertation Repository

This thesis describes the studies performed on a number of natural uranium dioxide (UO₂) specimens to determine a range of reactivities. This work will support the safety case for the long-term disposal of spent nuclear fuel in Canada. Under relevant long-term disposal conditions, water radiolysis could produce oxidizing conditions at the surface of the fuel, potentially leading to fuel corrosion and the release of radionuclides into the groundwater. The rate of such a process would be determined by the radiation dose rate from the fuel and the reactivity of the fuel, which will be determined by its composition, …

Competition Effects In An Intraguild Predation Model, Nicholas A. Eekhof

Electronic Thesis and Dissertation Repository

In the biological world, many interactions exist between various species. These interactions generally consist of predator-prey relationships, competition between species and beneficial relationships. One observed phenomenon, termed the fear effect, occurs when one species reacts to an increased risk of predation by another species. The fear response causes the affected species to reproduce and forage for food less. In some cases, the fear response can be beneficial, while in other times it can be harmful. In this thesis, we consider a four compartment food-chain model in which there exists a top-level predator, a mesopredator and two types of prey who …

Host-Pathogen Co-Evolution With Various Transmission Modes Of Infection And Density-Dependent Dynamics, Bita Ghodsi

Electronic Thesis and Dissertation Repository

Pathogens can be transmitted both vertically (from the parent to the offspring) and horizontally. Here, I model the co-evolution of pathogens and their hosts allowing for vertical and horizontal transmission and density-dependent host population growth. My analysis uses evolutionary game theory. I use computational methods to find that increasing vertical transmission does not always result in more benign disease outcomes. Instead, it can lead to higher pathogen-induced mortality. Furthermore, more benign outcomes evolve more readily when horizontal transmission is more profitable for the pathogen, and overall virulence increases as horizontal transmission becomes more profitable. The results also indicate that vertical …

Understanding Protein Deep Learning Models Through Explainability, Zahra Fazel

Electronic Thesis and Dissertation Repository

This thesis investigates the application of Explainable Artificial Intelligence (XAI) techniques to deep learning models in the field of protein analysis, specifically targeting protein language models and protein interaction site prediction models. Despite the increasing adoption of these sophisticated deep learning models in bioinformatics, their intrinsic complexity often results in a black-box nature, obscuring the understanding of their decision-making processes.

This research represents a thorough effort to integrate explanation methods within this context. We analyze the resulting interpretations using biological-specific statistical tests to enhance the transparency and interpretability of the models. This work evaluates the efficacy of current XAI methods …

Osculating Curves, Sepideh Bahrami

Electronic Thesis and Dissertation Repository

Consider a complex analytic curve $X$ in $\mathbb{C}^2$, along with a specific point $p \in X$. The primary concern arises in approximating geometrically the curve $X$ precisely at the point $p$. Analogously, in introductory calculus, students learn to compute the tangent line to the graph of a function $y=f(x)$ at a given point $p=(x_*,f(x_*))$ by utilizing the derivative of $f$ at $x_*$.

For analytical convenience, we assume a local representation of the curve $X$ using a power series expansion. This representation centers the point $p$ at the origin $(0,0) \in \mathbb{C}^2$. Thus, our mathematical input becomes a Taylor series:

\[ …

Impact Of Energy Allocation On Fish's Age And Weight At Maturation By Mathematical Models, Siyi Zhang

Electronic Thesis and Dissertation Repository

The age and weight at maturation are crucial traits in an organism’s life cycle, influencing its growth, survival, and reproduction. We propose a biphasic energy allocation model, distinguishing pre-maturity and post-maturity, to study the mechanisms of maturation and estimate the age and weight at maturation. This model is parameterized for female lake whitefish (Coregonus clupeaformis). We compare different functions involved in the model, estimate parameters, and do sensitivity analysis. Our results indicate that (i) weight at maturation is positively related to the fraction of energy allocated to growth which, by data fitting, is almost a constant; (ii) age …

Approximation Algorithms For High Multiplicity Strip Packing, Thief Orienteering, And K-Median, Andrew Bloch-Hansen

Electronic Thesis and Dissertation Repository

This thesis investigates three research objectives on three different problems: (1) algorithm design for problems in which the input can be grouped into a small number of classes, demonstrated on the high multiplicity strip packing problem; (2) algorithm design for problems with multiple interdependent sub-problems, demonstrated on the thief orienteering problem; and (3) algorithm design using neural networks with few layers, demonstrated on the k-median problem.

(1) The two-dimensional strip packing problem consists of packing in a rectangular strip of width $1$ and minimum height a set of $n$ rectangles, where each rectangle has width $0 < w \leq 1$ and height $0 < h \leq h_{max}$. We consider the high-multiplicity version of the problem in which there are only $K$ different types of rectangles. For the case when $K = 3$, we give an algorithm that produces solutions requiring at most height $\frac{3}{2}h_{max} + \epsilon$ plus the height of an optimal solution, where $\epsilon$ is any positive constant. For the case when $K = 4$, we give an algorithm yielding solutions of height at most $\frac{7}{3}h_{max} + \epsilon$ plus the height of an optimal solution. For the case when $K > 3$, we give an …

The Fundamental Groupoid In Discrete Homotopy Theory, Udit Ajit Mavinkurve

Electronic Thesis and Dissertation Repository

Discrete homotopy theory is a homotopy theory designed for studying graphs and for detecting combinatorial, rather than topological, “holes”. Central to this theory are the discrete homotopy groups, defined using maps out of grids of suitable dimensions. Of these, the discrete fundamental group in particular has found applications in various areas of mathematics, including matroid theory, subspace arrangements, and topological data analysis.

In this thesis, we introduce the discrete fundamental groupoid, a multi-object generalization of the discrete fundamental group, and use it as a starting point to develop some robust computational techniques. A new notion of covering graphs allows us …

Mercury Exposure, Fuel Stores And Torpor Use In Silver Haired Bats, Melina Kuerschner

Electronic Thesis and Dissertation Repository

Methylmercury (MeHg) is an environmental contaminant that has a high biomagnification potential with potent neurotoxic effects. Insectivorous bats may be readily exposed to MeHg through their diet. To test the effect of exposure on torpor and body composition in silver-haired bats (Lasionycteris noctivagans), I measured total mercury (THg, combination of inorganic and methylmercury) through fur samples and quantitative magnetic resonance analysis, temperature sensitive radio tags, and respirometry data from these bats to quantify body composition and torpor use. THg levels varied 20-fold with heavier and fatter bats having higher levels, suggesting that individuals that routinely eat more accumulate …

Predictive Models Of Polymer Composites: A Thesis, Navid Afrasiabian

Electronic Thesis and Dissertation Repository

Predictive models are a powerful tool to understand and improve physical systems. Predictive models not only can be used to improve current materials, but they also gain fundamental understanding of the underlying processes. There are numerous theoretical and numerical models introduced in the field of polymer composites and nanocomposites. Different methods best describe a system at a specific time and length scale. In this thesis, I utilize Coarse-grained Molecular Dynamics (CGMD), Multi-PhaseField (MPF), and Lattice-Boltzmann (LB) methods to study different aspect of polymer composites and nanocomposites.

Starting at the nanoscale, we study the dispersion and orientation patterns of nanorod-polymer systems …

Multi-Species Toxicity Testing Of Iprnhc: A Candidate For Organic Coating Enhancements, Maryam Khalilvand Nahid

Electronic Thesis and Dissertation Repository

Corrosion is a natural process affecting the longevity and integrity of metals. N-Heterocyclic carbenes (NHCs) are robust organic compounds that can form strong σ-bonds with metal atoms, allowing for the formation of monolayers on the metal surface. This property makes NHCs promising for coating metals. However, their long-term effects on the aquatic environment are not well understood. The present study investigated the ecotoxicity of 1,3-diisopropyl-1H-benzoimidazolium bicarbonate (iPrNHC NCO₃^-), a candidate for organic coating enhancements, on various species of aquatic organisms. The results showed that high concentrations of iPrNHC significantly increased mortality rates in zebrafish embryos, planarians, Daphnia, …

Investigating The Stability Of Different Sizes Of Gold Nanoparticles In Physiological Environments And Different Gold Nanoclusters In Water., Narges Hajighasemi

Electronic Thesis and Dissertation Repository

Gold nanoparticles (AuNPs) have become promising candidates for various biomedical applications due to their unique physicochemical properties and biocompatibility. Nevertheless, the efficacy of AuNPs in these applications highly relies on their stability and ability to maintain their desired properties within the complex environment of the human body. This thesis investigates the stability and aggregation behavior of citrate-coated AuNPs in in-vitro physiological environments and nitrogen heterocyclic carbene (NHC)-coated gold nanoclusters (AuNCs) in water over time. Analytical techniques such as electrophoretic mobility, dynamic light scattering, and inductively coupled plasma mass spectrometry were employed. It was shown that cell media (in contrast to …

Container Migration: A Perfomance Evaluation Between Migrror And Pre-Copy, Xinwen Liang

Electronic Thesis and Dissertation Repository

The concept of migration and checkpoint/restore has been a very important topic in research for many types of applications including any distributed systems/applications or single massive systems/applications; and low latency vehicular use cases, augmented reality(AR) and virtual reality(VR) applications. Migrating a service requires that the state of the service is preserved. This requires checkpointing the state and restoring it on a different server in multiple rounds to avoid a total loss of all data in case of a failure, fault or error. There are many different types of migration techniques utilized such as cold migration, pre-copy migration, post-copy migration.

Compared …

Monotone Functions On General Measure Spaces, Alejandro Santacruz Hidalgo

Electronic Thesis and Dissertation Repository

Given a measure space and a totally ordered collection of measurable sets, called an ordered core, the notion of a core decreasing function is introduced and used to generalize monotone functions to general measure spaces. The least core decreasing majorant construction, the level function construction, and the greatest core decreasing minorant, already known for functions on the real line, are extended to this general setting. A functional description of these constructions is provided and is shown to be closely related to the pre-order relation of functions induced by integrals over the ordered core.

For an ordered core, the down space …

Analytic Properties Of Quantum States On Manifolds, Manimugdha Saikia

Electronic Thesis and Dissertation Repository

The principal objective of this study is to investigate how the Kahler geometry of a classical phase space influences the quantum information aspects of the quantum Hilbert space obtained from geometric quantization and vice versa. We associated states with subsets of a product of two integral Kahler manifolds using a quantum line bundle in a particular manner. We proved that the states associated this way are separable when the subset is a finite union of products. We presented an asymptotic result for the average entropy over all the pure states on the Hilbert space H⁰(M₁,L_{1 …}

Investigating The Effect Of Bentonite Clay Compaction Density On The Corrosion Of Copper Materials, Claire Samantha Tully

Electronic Thesis and Dissertation Repository

As per international consensus on the best practice for managing used nuclear fuel (UNF), the Nuclear Waste Management Organization (NWMO) plan to isolate and contain UNF within a multiple-barrier system, underground in a deep geological repository (DGR). In the proposed design, used fuel bundles will be sealed in copper-coated carbon steel used fuel containers (UFCs), encased in blocks of highly compacted bentonite clay, and emplaced ~500-800 m (depending on host rock geology) below ground. Any gaps between the rock walls and the compacted bentonite blocks will be filled with a bentonite gap fill material (GFM).

The compacted bentonite material serves …

Exploring The Chemistry Of Bis(Azido)Phosphine Chalcogenides And The Pursuit Of Isolable Phosphinidene Chalcogenides, John Lortie

Electronic Thesis and Dissertation Repository

The study of low-coordinate species and the pursuit of interesting bonding motifs has revealed new reactivity modes for main-group compounds, akin to transition metals, in the past two decades. An underexplored class of two-coordinate phosphorus compound is a phosphinidene sulfide, which has yet to be isolated in the solid-state with an accompanying crystal structure. This dissertation explores strategies towards the synthesis and reactivity of low-coordinate phosphinidene chalcogenide species, and related compounds supported by strongly pi-donating or weakly pi-donating environments. While the primary synthetic targets remained elusive, significant discoveries were made towards new methods of preparing electron rich phosphines, and the …

Leveraging Intersubject Representational Similarity Analysis To Explore Individual Differences In Early Life Adversity And Cortico-Amygdala Connectivity In A Preadolescent Sample, Amira Hmidan

Electronic Thesis and Dissertation Repository

Preadolescence is a critical developmental phase characterized by changes in the functional connectivity (FC) between the cortex and amygdala, which are essential for emotional processing and regulation. Early life adversity (ELA), such as exposure to childhood maltreatment, familial dysfunction, and poverty, is associated with negative physical and mental health outcomes (Felitti et al., 1998). Emerging research indicates that disturbances in cortico-amygdala FC could act as a mechanism linking ELA to various mental health issues; however, most focus on adult populations and overlook individual differences. Here, intersubject representational similarity analysis (IS-RSA) was leveraged to explore how individual variations in ELA relate …

Knowledge-Grounded Natural Language Understanding Of Biomedical And Clinical Literature, Xindi Wang

Electronic Thesis and Dissertation Repository

Natural Language Understanding (NLU) resides at the intersection of artificial intelligence, linguistics, and computer science, with the goal of empowering machines to comprehend and interpret human languages in a way that is both significant and contextually pertinent. The intrinsic complexity of human language, marked by its subtleties, cultural variances, and dependence on context, poses a significant challenge to NLU. The real world is a vast repository of knowledge that encompasses not only facts but also complex relationships, dynamic concepts, and cultural subtleties. This external knowledge represents the context that is often implicitly assumed in human communication. For machines to fully …

Mixstm: Adapting The Structural Topic Model For A Quantitative Analysis Of Focus Group Data, Pascale A. Nevins

Electronic Thesis and Dissertation Repository

The Structural Topic Model (STM) incorporates external information about expected document-topic proportions to enhance the model. Motivated by focus groups, whose transcripts represent text data inherently grouped by session, we propose three extensions to the STM: 1) mean document-topic proportion estimation using a regression with random effects; 2) partitioned estimation of group-specific topic covariance matrices; and 3) a post hoc mixed effects regression on topic prevalence which incorporates latent variable uncertainty into the coefficient estimates. We explore the utility of these modifications through simulated examples and apply them to focus group transcripts from a pan-Canadian study on homelessness. The new …

An Exploration Of Causal Cognition In Large Language Models, Vicky Chang

Electronic Thesis and Dissertation Repository

Causal cognition, how beings perceive and reason about cause and effect, is crucial not only for survival and adaptation in biological entities but also for the development of causal artificial intelligence. Large language models (LLMs) have recently taken center stage due to their remarkable capabilities, demonstrating human-like reasoning in their generative responses. This thesis explores how LLMs perform on causal reasoning questions and how modifying information in the prompt affect their reasoning. Using 1392 causal inference questions from the CLADDER dataset, LLM responses were assessed for accuracy. With simple prompting, LLMs performed more accurately on intervention queries compared to association …

Framework For Bug Inducing Commit Prediction Using Quality Metrics, Alireza Tavakkoli Barzoki

Electronic Thesis and Dissertation Repository

This thesis relates to the topic of software defect prediction within the broader area of continuous software engineering. The approach presented in this thesis is employing source code and process metrics obtained for each commit, and is examining as to whether specific patterns, as the system moves from one commit to another, can predict an impending bug inducing commit. The thesis utilizes the SonarQube Technical Debt open source data which provides source code metrics and process metrics for each commit in 22 medium to large scale open source Apache projects.

Central to this research is the novel utilization of commits …

Quantifying Resting-State Functional Connectivity In Critically Brain-Injured Patients: A Graph-Theoretical Approach With Fnirs, Ira Gupta

Electronic Thesis and Dissertation Repository

Assessment of consciousness in behaviourally unresponsive patients with critical brain injuries continues to be a challenge. There remains a need for robust tools that can accurately characterize preserved cortical function and predict patient outcomes. In the present study, functional near-infrared spectroscopy is employed in conjunction with graph theory and machine learning to quantify resting-state functional connectivity in 16 acutely brain-injured patients and 23 healthy controls. Results revealed significant channel-level differences between the groups for three graph metrics, including degree, clustering coefficient, and local efficiency. Further investigation using machine learning algorithms revealed that these metrics can be used to distinguish between …

The Application Of Elastic Distance In Astrophysical Time Series, Xiyang Zhang

Electronic Thesis and Dissertation Repository

Elastic distances, e.g. dynamic time warping (DTW), evaluate the similarity between query and reference sequences by dynamic programming. The 1-Nearest-Neighbor predictor with DTW is one benchmark in time series classification. However, DTW is less efficient in astronomical time series because of ignorance of the information in time stamps and its dependence on the shape and magnitude between query and reference sequences. We apply two elastic distances which integrate the information in the time domain, time warp editing distance (TWED) and Skorohod distance, which is calculated by using Fre ́chet distance, to three astronomical datasets to compare with DTW and Euclidean …

Investigating Co2 Adsorption Behavior In Metal-Organic Frameworks By Solid-State Nmr, Yan Ham Ng

Electronic Thesis and Dissertation Repository

With increasing demands in controlling carbon dioxide emissions, metal-organic frameworks (MOFs) are considered as promising candidates for CO₂ capture due to their large CO₂ adsorption capacity. In this study, the adsorption behavior of CO₂ molecules in [Zn₂(TRZ)₂(NH₂-BDC)] (TRZ=1,2,4-triazolate, NH₂-BDC=2-amino-1,4-benzenedicarboxylic acid), and CALF-20 are studied. Moreover, water is ubiquitous in the atmosphere and could have a negative impact on the MOF’s gas adsorption. Therefore, understanding the behavior and dynamics of water and CO₂ in MOFs is of fundamental importance. Solid-state nuclear magnetic resonance (SSNMR) is a powerful technique which …

Planetary Exploration Via Fully Automatic Topological Structure Extraction Using Adaptive Resonance, Jonathan Kissi

Electronic Thesis and Dissertation Repository

Renewed interest in Solar System exploration, along with ongoing improvements in computing, robotics and instrumentation technologies, have reinforced the case for remote science acquisition systems development in space exploration. Testing systems and procedures that allow for autonomously collected science has been the focus of analogue field deployments and mission planning for some time, with such systems becoming more relevant as missions increase in complexity and ambition. The introduction of lidar and laser scanning-type instruments into the geological and planetary sciences has proven popular, and, just as with the established image and photogrammetric methods, has found widespread use in several research …

Electrosprayed Serine Octamer Magic Number Cluster: Formation Via Gas Phase Assembly And Collision-Induced Dissociation, Vida Alinezhad

Electronic Thesis and Dissertation Repository

Magic number clusters refer to ion species that exhibit unusually high intensities in electrospray ionization (ESI) mass spectrometry (MS) experiments. The serine octamer cluster [Ser₈+H]⁺ is of special interest since its formation mechanism and structure remain controversial, although a recently proposed model in the literature represents a possible candidate structure. Nonetheless, the formation mechanism of [Ser₈+H]⁺ remains unexplored. Some hypotheses suggest that it may pre-exist in bulk solution, or that [Ser₈+H]⁺ can be a collision-induced dissociation (CID) product of large clusters formed in evaporating ESI droplets. We used ESI-MS, mobile proton …

Black Tio2 Nts And Zno-Tio2 Nts Heterostructure: Synthesis, Characterization, And Synchrotron-Based Spectroscopy Studies, Lu Yao

Electronic Thesis and Dissertation Repository

The one-dimensional (1D) TiO₂ nanotubes (NTs), and their derivatives have been extensively studied due to their potential use in water-splitting, solar cells, and lithium-ion batteries. Since TiO₂ has a large band gap (~3.2 eV for anatase), there has been a search for higher photocatalytic efficiency by shifting the band gap into the visible range. This thesis presents a study of black TiO₂ NTs and ZnO-TiO₂ heterostructures using synchrotron-based X-ray spectroscopy and X-ray diffraction techniques. It involves the transformation from as-prepared TiO₂ NTs to black TiO₂ NTs via an electrochemical reduction method. ZnO-TiO₂ NT …

The Black-To-White Hole Transition, Farshid Soltani

Electronic Thesis and Dissertation Repository

Classically, an isolated black hole is a stable gravitational object. If however semiclassical effects are taken into account, an isolated black hole can be shown to slowly radiate its mass away in a process called evaporation. At the end of the evaporation process, when the size of the horizon becomes Planckian, the quantum nature of the gravitational field can no longer be neglected and the dynamics of the horizon is governed by quantum gravity. The main objective of this thesis is the systematic investigation of a tentative scenario for the “end of the life” of a black hole: the black-to-white …