VictorJuiz/thesis huggingface dataset:
Statistical Computing With Graphics Processing Units

This thesis consists of two main projects and a third project which is provided in the appendix. The contribution of the first project, is a tool set for parallel random number gen- eration on GPUs in R, namely, the clrng package. This package is currently the only R package that provides facilities for generating random numbers in parallel on a GPU. It enables reproducible research by setting random initial seeds for streams on GPU and CPU. The random number generator in clrng guarantees independent parallel samples even when R is used interactively in an ad-hoc manner, with sessions being interrupted and restored. This package can be easily incorporated in other R packages, allowing developers to develop other types of random number generators or accelerate suitable computations in statistical applications. The contribution of the second project, is a methodology and software for creating profile likelihoods for parameters in Gaussian spatial models with Mat ́ern family of correlation functions, including anisotropic models. This methodology adopts a novel reparametrization for generation of representative points, and is implemented in the software gpuLik, which uses GPUs for parallel profile likelihoods computation. Our work has shown how GPU’s enable likelihood-based inference for Gaussian spatial models without requiring approximations to the variance matrix, even for moderately large datasets. The third project provided in the Appendix is dedicated to evaluating the impact of the COVID-19 pandemic on online public interest in various cancers (breast, colon, lung, prostate, and thyroid). A cross-sectional retrospective study was conducted utilizing Google Trends aggregate anonymous online search data from Canada. Welch’s Two Sample t-tests were performed and Benjamini-Hochberg procedure was used to correct for multiple comparisons.

Keywords: clRNG library
clrng package
GPU parallel computing
likelihood-based confidence intervals
linear geostatistical models
profile likelihood
Advisor: Brown, Patrick
On the Role of Resource Epistemology and Epistemic Tensions as Explainers of Fisheries Management Outcomes

The aggregate status and trends of marine capture fisheries and the ecosystems which support fisheries production have deteriorated significantly since the end of World War II. These declines have material impacts for human health and well-being, as fisheries make important contributions to employment, economic activity, food security, and cultural and social practices around the world. Fisheries research not only seeks to identify biomass declines in commercial fisheries and their supporting ecosystems, but also to explain declines, identify root causes, and identify potential solutions to improve outcomes for resources and resource users. This dissertation contributes to the broader effort seeking to understand the causes of unsustainable outcomes for fisheries resources by examining the influence of resource epistemology on resource decision-making. The dissertation uses a case study of northern cod (Gadus morhua) in the Northwest Atlantic Ocean to examine how epistemic tensions influence (1) the governance of species recovery, (2) decision-making in the context of the precautionary approach to fisheries management, and (3) the uptake of knowledge co-production processes in fisheries management. The dissertation borrows from the findings of the case study to inform a literature review which outlines the potential that climate change could undermine resource policy efficacy by creating or exacerbating epistemic tensions between stakeholders. This work views the epistemic orientations embedded in governance structures as key sources of tension between stakeholders, which influence resource decision-making and, in turn, resource outcomes.

Keywords: co-production
environmental governance
epistimology
fisheries management
precautionary approach
resource management
Advisor: Klenk, Nicole
Educational Currency: Teacher-Parents, Privilege, and Schools Choice in Ontario

Neoliberal school choice policies continue to expand across the globe. Supporters claim that the school system’s failings can be solved by moving away from a one-size-fits-all, geographically allocated body, and towards a more diversified, individualized market. At the forefront of this movement are choice advocates who insist that it is more equitable to provide families with the opportunity to decide where their children will learn and that school markets are more socially responsive. However, these sentiments are not undisputed. The following study is built on the opposing position – that current school choice policies are discriminatory and unjust. I challenge the notion that markets enhance equity by investigating the complex process of how schools are selected. Because neoliberal, market methods are rooted in competition, I emphasize that the practice of school choice is yet another opportunity in which families experience uneven amounts of advantage. But, while many agree that school choice policies privilege certain parents more than others, little is known about what this privilege looks like, how it is attained, and how it is used during the selection process. In this study, I attempt to understand the intricacy of school market privilege by studying teacher-parents, a subgroup of the population who possess it. The experiences of teacher-parents provided insight into how privilege may be differently retained, acquired, and used in school choice. This is the story of how twenty-three public school teachers navigate the marketed school system in Ontario, Canada. In this study, participants share their insider experience and demonstrate how their unique combinations of cultural, social, and economic capital allowed them to collect and spend (use) educational currency (EC) as they choose schools for their own children. The data not only reaffirms that certain populations possess unique amounts of educational currency and provides insight into what exactly EC is; it also unveils that choice can have a concerning tendency to shape a more racially, ethnically, and economically segregated system. This information has become even more relevant since the as the Covid-19 global pandemic has created novel concerns and options including various forms of online and distance learning. Word count: 348. Keywords: school choice, privilege, educational currency

Keywords: choice
education
equity
markets
neoliberal
school
Advisor: Ryan, James
Curriculum Governance in the Professions: A Comparative and Sociological Analysis of Engineering Accreditation

Professional education operates in a tension between its two key institutional homes – universities and professional bodies. Curriculum governance – the structures and processes for making decisions about the curriculum – is embedded in higher education but influenced by professional accreditation. This multiple paper thesis explores the implications of a worldwide shift in engineering towards outcomes-based accreditation. The study is framed by a comparative case study methodology, and empirical data is drawn from 78 interviews across the United Kingdom, Australia, Singapore, and South Africa. All four countries are signatory to the Washington Accord, a mutual recognition agreement that has been influential in helping to spread outcomes-based accreditation.This study is theoretically grounded in Bernstein’s pedagogic device, from the sociology of education, and regime theory, from international relations. At a global level, the key findings are that the Washington Accord has evolved into an explicit regime that shapes the behaviour of its 20+ signatories, as well as countries thinking about applying. From a power perspective, the regime disproportionately benefits its founding members, while newer signatories are scrutinized before being admitted. From a cognitivist perspective, the regime is under threat from a subtle shift in its purpose, from mobility to quality assurance. Drawing on the pedagogic device, the thesis finds meaningful differences across countries in the structure of the ‘recontextualizing field’ – comprised of the official field which sets accreditation policy, and the pedagogic field which interprets and implements the policy. Four archetypes, based on the four countries, are shown to explain some of the differences in uptake of outcomes-based accreditation. Within the ‘field of reproduction’, curriculum governance structures are shown to differ according to the type of university. Research-intensive universities are less invested in accreditation, more decentralized, and centrally control the curriculum less. Teaching-intensive universities depend on accreditation for legitimacy and invest more in a centralized approach to curriculum governance. Overall, this study highlights the importance of power differences between old and new signatories, between research-intensive and teaching-intensive universities, and between central faculties and their departments. These tensions represent an important area of research within professional education at large.

Keywords: accreditation
curriculum
engineering
governance
professions
Advisor: Sa, Creso
Accelerating the Discovery of Materials for Energy Capture and Energy Storage Using Quantum Chemistry and Machine Learning

In order to reduce the global dependence on fossil fuels it is critical that we develop new materials to efficiently capture and store energy. The enormous size of the material space poses a formidable challenge to the discovery of energy materials. In this thesis, I develop machine learning (ML) approaches and search algorithms that enable accelerated discovery of energy materials. First, I develop a material representation that enables relaxed crystal properties prediction from unrelaxed crystal structures using ML. The results show that the approach accelerates the discovery of mixed halide perovskites by a factor of 105 over conventional computational screening approaches based on Density Functional Theory (DFT). I apply the method to two material discovery problems: the search for photovoltaic materials with small bandgaps; and UV and IR light-emitting materials. Next, I generalize the above-mentioned approach to tackle one of the main criticisms of ML-based approaches: their black-box nature i.e., lack of interpretability. I do this by training accurate ML models that can predict energy above hull, bandgaps, and the nature of bandgaps among different material classes using unrelaxed crystal structures. With the combination of statistical techniques and simpler supervised learning methods, I develop a method to extract scientific insights from trained ML models and use these generated insights to design new, stable UV light emitting materials and direct bandgap semiconductors. Finally, I develop a method to efficiently search the chemical space. The proposed search method efficiently identifies the material with the desirable set of properties an order of magnitude faster than genetic algorithms and bayesian optimizations. Applying this to the discovery of oxygen evolution reaction (OER) catalysts, I predict several previously unreported promising candidates that are then validated in the lab. The best candidate Ru0.58Cr0.25Mn0.08Sb0.07O2 shows a mass activity 8 times higher than the current state-of-art, RuO2, and maintains performance for 180 hours while operating at 10mA/cm2 in acidic 0.5M H2SO4 electrolyte. The studies in this thesis introduce and demonstrate the application of data-driven approaches to accelerate the discovery of energy materials through the development of generalizable ML models, interpretability analysis and efficient search algorithms.

Keywords: density functional theory
electrocatalysis
light emission
machine learning
photovoltaics
quantum chemistry
Advisor: Sargent, Edward H
Absence in Nyāya and Mīmāṃsā

I examine competing views from Nyāya and Mīmāṃsā philosophers about the epistemology of absence, which asks how we learn that an object or property is absent. In particular, I examine Nyāya defenses of, and Mīmāṃsā challenges to, perceptualism, according to which we learn that an object or property is absent (abhāva) by perceiving (pratyakṣa) its absence. In the first chapter, I introduce cases of past absence (prāṅnāstitāsthala), purported counterexamples to perceptualism which involve agents learning in retrospect that an object or property was absent. I identify two groups of views about these cases: recollection views, according to which cases of past absence involve agents recalling negative information; and recollection failure views, according to which cases of past absence involve agents failing to recall positive information. I reconstruct two recollection views: a Bhāṭṭa view belonging to Uṃveka, and a Nyāya view belonging to Jayanta and Bhāsarvajña. I then examine Śālikanātha and Sucarita’s critiques of recollection views. In the second chapter, I examine recollection failure views. I introduce the Bhāṭṭa philosopher Pārthasārathi's view, following which I reconstruct the Nyāya philosopher Gaṅgeśa's critiques. Gaṅgeśa defends a similar view to Pārthasārathi's that mends its difficulties and secures a perceptualist explanation of past absence. According to Gaṅgeśa, agents learn that a recollectable (smaraṇārha) object or property was absent by inferring its past absence from failing to recall (asmaraṇa) that object or property. In the third chapter, I examine the Nyāya philosopher Raghunātha's attack on a condition according to which we are always aware of an absence as an absence of its counterpositive (pratiyogin), or its corresponding absent object or property. Gaṅgeśa defends this condition, showing that it is supported by a plausible thesis about the epistemology of relational properties and motivates the Nyāya defence of absence as irreducible to a positive. But Raghunātha identifies cases in which the condition fails. Finally, I provide a translation of, and commentary on, a selection from the Pramāṇapārāyaṇa by the Prābhākara philosopher Śālikanātha. I argue that he defends a reductionist metaphysics according to which absence reduces to an awareness-event (buddhi), and knowledge of absence thereby reduces to self-knowledge.

Advisor: Ganeri, Jonardon
Tethered Magnetic Serial Robots for Minimally Invasive Neurosurgery

The high-speed, non-ionizing, wireless power transfer capabilities of low-frequency magnetic fields make them an attractive option for actuating devices on the nanometer scale up to the centimeter scale, enabling a new suite of minimally-invasive techniques for a wide variety of medical procedures. There is a significant demand for smaller, more manoeuvrable, surgical robot tools to reduce the invasiveness of neurosurgical procedures. A magnetic approach to surgical robots could enable smaller tools, but no viable magnetic robot approach exists. Existing magnetic approaches to surgical tasks involve either untethered agents, serial arms with bulky surface-mount transmission units, or highly-underactuated continuum bodies. Surgical tasks, especially in delicate regions such as the brain, require precisely controlled trajectories and applied forces: they require fully-actuated robots.In this thesis, rigid-link serial robots with embedded magnets in each link are designed to achieve high forces and ensure full actuation over their configuration space. A novel analytical model was derived from a combination of magnetostatics and rigid-link serial robot dynamics to determine the equivalent actuator torques at the joints of the serial robot for a given actuating field, as well as the effective torsion-spring-like behaviour induced by interactions between the magnets in the serial robot. From this analytical model, a performance metric and novel design methodology was developed to improve the actuation performance and tailor the magnetic torsion-spring behaviour in the robot by adjusting the orientation and position of the embedded magnetic material. Several 3 mm - 4 mm diameter rigid-link robot prototypes were developed using this methodology, and their performance was evaluated according to key design criteria for microneurosurgical tasks. The tools can be operated open loop or closed loop with computer vision feedback, achieving step response rise times of less than 1 second and maximum output forces of up to 181 mN. By enabling smaller tools without a need for transmission components, more space is left in the trocar (surgical insertion point) for other systems, such as lighting, irrigation, or integrated sensing. Magnetic serial robots could thus enable a new class of multifunctional surgical tools.

Keywords: Magnetic actuation
Minimally invasive surgery (MIS)
Robot surgery
Advisor: Diller, Eric D
Life and Love Under Criminalization: The Experiences of People Living with HIV in Canada

Through in-depth qualitative interviews with 75 people living with HIV (PLWH), this dissertation examines the impact of HIV criminalization upon the lives of PLWH in Ontario, Canada, particularly in terms of HIV stigma, sexual and romantic relationships, and community, as well as the unique challenges the law creates for marginalized groups, specifically women living with HIV (WLWH) and racialized people living with HIV (RPLWH). The first paper of this dissertation examines how HIV criminalization impacts the lives of WLWH and the HIV stigma they experience. Key themes that emerge from the accounts of women in the study include how the law facilitates social exploitation, the impact of the law upon sexual and romantic relationships, and their treatment by the criminal justice system. The women in the study experience criminalization through the lens of motherhood – regardless of whether they have children. The second paper of this dissertation focuses on the experiences of Indigenous, Black, and other racialized people living with HIV who participated in the study, as they navigate disclosure, relationships, and life under HIV criminalization. RPLWH in the study report the experience of high amounts of HIV stigma in their communities. RPLWH employ various strategies to navigate the law and the high levels of perceived community stigma. These include keeping their HIV status hidden, having firm boundaries between and within communities, abstaining from relationships, leaving the country to have sex, avoiding HIV networks, and self-non-disclosure. Drawing upon the full sample, the third paper of this dissertation examines the impact of HIV criminalization upon the sexual and romantic relationships of PLWH, as well as the strategies they employ to navigate and protect themselves from the law. Key themes include concern with the law’s impact on dating desires and practices, the power imbalance that the law enables with serodiscordant partners, the privacy implications of being investigated or charged, as well as their potential treatment by both police and media. PLWH use various navigation strategies to protect themselves from the law including staying in relationships, celibacy, serosorting, anonymous and casual sex, leaving the jurisdiction, universal disclosure, non-disclosure, and disclosure documentation.

Keywords: HIV Criminalization
People Living with HIV
Racialized People Living with HIV
Romantic Relationships
Sexual Relationships
Women Living with HIV
Advisor: Green, Adam I
Dielectric Properties of Minerals and Ores and the Application of Microwaves for Assisted Comminution and Ore Sorting

Upon exposure to microwave radiation, most valuable minerals heat very well, while in general, gangue minerals do not. This selective heating leads to differential thermal expansion across phase boundaries and causes microfractures, which can improve liberation and reduce ore competency. During ore sorting, the heat signature is detected using infrared sensors to accept or reject valuable or gangue rock, respectively. A comprehensive literature review identified research gaps in the field of microwave-assisted comminution and ore sorting and found that developments have been limited by complexities associated with scaling up from bench- to pilot-scale. Dielectric properties were measured on key sulphide and silicate minerals and select ores at various frequencies and temperatures using the cavity perturbation technique. In combination with data from the literature, experimental data were used to ascertain which minerals could be defined as highly microwave-amenable phases (HMAPs). Bench-scale microwave heating experiments were completed on 42 ores. These data were then combined with the total wt.% HMAPs and the ore dielectric property data to create a database that can be used to predict the bench-scale heating behaviour of any ore based on the wt.% HMAPs. High-power microwave tests were done on select ores, which were subsequently ground using the SAGDesign test, and the degree of liberation of valuable minerals was obtained via QEMSCAN® (quantitative evaluation of minerals by scanning electron microscopy). Microwave treatment increased mineral liberation from most ores but reduced the competency of only a few ores. Massive sulphide ores could not be treated on the pilot-scale system given their very high conductivities, which caused severe arcing. A study on a Cu porphyry ore found that an upper boundary exists for the power density, above which the ore will experience excessive arcing. Bench-scale microwave infrared and conductivity sorting tests on a Cu-Ni ore found general agreement between rock conductivity and its overall sortability. Optimization tests were completed to determine the limitations of the pilot-scale system. Recommendations for high-power microwave treatment include microwave pulsing, quenching, and treatment of iron ores.

Keywords: comminution
liberation
microwaves
minerals
permittivities
sorting
Advisor: Bobicki, Erin R