Theses, Dissertations, and other Required Graduate Degree Essays

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This collection contains digitized SFU theses except for those theses submitted within the last 12 months. If you cannot find the thesis you are looking for please search Recently Submitted Theses as it may be a recently submitted thesis and thus not yet available in Summit.

Multilingual unsupervised word alignment models and their application

Date created: 
2021-03-05
Abstract: 

Word alignment is an essential task in natural language processing because of its critical role in training statistical machine translation (SMT) models, error analysis for neural machine translation (NMT), building bilingual lexicon, and annotation transfer. In this thesis, we explore models for word alignment, how they can be extended to incorporate linguistically-motivated alignment types, and how they can be neuralized in an end-to-end fashion. In addition to these methodological developments, we apply our word alignment models to cross-lingual part-of-speech projection. First, we present a new probabilistic model for word alignment where word alignments are associated with linguistically-motivated alignment types. We propose a novel task of joint prediction of word alignment and alignment types and propose novel semi-supervised learning algorithms for this task. We also solve a sub-task of predicting the alignment type given an aligned word pair. The proposed joint generative models (alignment-type-enhanced models) significantly outperform the models without alignment types in terms of word alignment and translation quality. Next, we present an unsupervised neural Hidden Markov Model for word alignment, where emission and transition probabilities are modeled using neural networks. The model is simpler in structure, allows for seamless integration of additional context, and can be used in an end-to-end neural network. Finally, we tackle the part-of-speech tagging task for the zero-resource scenario where no part-of-speech (POS) annotated training data is available. We present a cross-lingual projection approach where neural HMM aligners are used to obtain high quality word alignments between resource-poor and resource-rich languages. Moreover, high quality neural POS taggers are used to provide annotations for the resource-rich language side of the parallel data, as well as to train a tagger on the projected data. Our experimental results on truly low-resource languages show that our methods outperform their corresponding baselines.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Anoop Sarkar
Department: 
Applied Sciences: School of Computing Science
Thesis type: 
(Thesis) Ph.D.

Treatment wetlands for industrial wastewaters: A study of science, policy, and management

Date created: 
2020-07-16
Abstract: 

Bitumen extraction in Alberta’s oil sands region generates large volumes of oil sands process-affected waters (OSPW) that pose environmental and human health risks. Currently, few feasible options for managing these large and growing volumes of polluted waters exist. The primary objective of this research is to investigate the feasibility, effectiveness, and safety of treatment wetlands as a treatment option for the oil sands industry. To do this, a mechanistic model of the fate and toxicity of OSPW contaminants in treatments wetlands was developed and tested in field studies at the Kearl Treatment Wetland – a free water surface flow wetland in northern Alberta. Measuring concentrations of polycyclic aromatic hydrocarbons (PAHs) and naphthenic acids (NAs) in influent and effluent of the Kearl Treatment Wetland showed that the combined total mass of all detected PAHs and NA reduced by 54 to 83% and 7.5 to 69%, respectively, as a result of treatment. Concentrations of PAHs and NAs in the aqueous phase of the wetland were measured using polyethylene (PE) and Polar Organic Chemical Integrative Samplers (POCIS), respectively. The model is shown to be in good agreement with the experimental observations and required only minimal calibration. Application of the model shows that evapotranspiration is not likely to significantly contribute to the removal of OSPW contaminants. Chemical removal relies mainly on transformation in wetland rooting media due to high microbial activity in wetland biofilm. Higher rates of transformation result in greater removal efficiencies for most chemicals. However, highly hydrophobic substances experience low removal efficiencies and appear to be unaffected by changes in transformation rates in the wetland suggesting wetland treatment is not suitable for these substances. Treatment efficiency is sensitive to wetland surface area and flow rate of water through the wetland suggesting intentional wetland design and operation can improve treatment efficiency. Trade-offs in wetland design and operation can be informed by the model.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Frank Gobas
Department: 
Environment: School of Resource and Environmental Management
Thesis type: 
(Thesis) Ph.D.

Sovereign culture: Stó:lō cultural heritage and political activism in the twentieth century

Date created: 
2018-07-16
Abstract: 

Though scholars have often perceived of sovereignty in purely territorial and capital-p political terms, this is not a useful way to understand the concept when it comes to Indigenous nations. Both earlier and certainly throughout the twentieth century, Stó:lō communities of what is now south-western British Columbia saw no distinction between the political and cultural heritage practices that affirmed their sovereign relationships with Stó:lō Téméxw, a coalescence this dissertation refers to as “cultural sovereignty.” Stó:lō practices of cultural curation—the process of taking care of tangible and intangible heritage—were deeply connected to Stó:lō political organization and territorial management throughout the twentieth century. Additionally, Stó:lō cultural sovereignty during this period sometimes manifested as a gendered phenomenon, with women and men alternately enacting cultural sovereignty in distinct ways that corresponded to Stó:lō and sometimes settler gender ideologies. Stó:lō resistance to settler colonialism was not only a protest of land acquisition, it was also an attempt to protect Stó:lō cultural heritage from settler colonial appropriation. Moreover, this dissertation contends that the settler move to appropriate Stó:lō cultural heritage must be seen as part of the colonial project of dispossession. Reconciliation in Indigenous-settler relationships, then, must include not only discussions relating to restitution of land, but also of cultural heritage. In making these arguments, this dissertation contributes to scholarly conversations about Indigenous sovereignty, cultural heritage, and Stó:lō histories, and contributes to the fields of history, Indigenous studies, and museology. Its methodological approach comes from work in Indigenous research methodology, feminist oral history, and what is being called “new ethnohistory” or community-engaged methodology. The research process itself combined archival investigation, original oral history interviews, and field work. An intersectional feminist lens framed the analysis of that research. Chapters of this dissertation examine sequential eras during the twentieth century, focusing on particular case studies to analyze changes and continuities in historical examples of Stó:lō cultural sovereignty.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Mary-Ellen Kelm
Department: 
Arts & Social Sciences: Department of History
Thesis type: 
(Thesis) Ph.D.

Thermodynamic characterization of hypertrophic cardiomyopathy associated troponin C mutations

Author: 
Date created: 
2019-07-15
Abstract: 

Hypertrophic Cardiomyopathy (HCM) is the leading cause of sudden cardiac death in young adults under the age of 35; a devastating disease that is not yet well understood. To date, greater than 1000 HCM-associated mutations have been found in genes that encode mostly sarcomeric proteins. Familial Hypertrophic Cardiomyopathy (FHC) is the heritable form of HCM. The overlying phenotype of FHC is thought to be derived from an increase in calcium (Ca2+) sensitivity of contraction and impaired relaxation of the myocardium. Dilated Cardiomyopathy (DCM) associated mutations are thought to have the opposite functional effect. This study focuses on cardiac troponin C (cTnC) a component of the cardiac troponin complex where binding of Ca2+ acts as the regulatory switch, leading to a series of conformational changes that culminate in muscle contraction. This project explores Ca2+ binding by focusing on the proximal-most unit of the contractile apparatus. The interaction of Ca2+ with the regulatory domain of cTnC is studied through isothermal titration calorimetry in conjunction with Molecular Dynamics simulations to understand structural and functional changes in the N-terminal region of cTnC. Initially, we established a workflow by exploring the functional consequences of sequence variations in coordinating Ca2+ binding and the genetic control of paralog expression in response to environmental temperature change in zebrafish. We then focused on a series of FHC-associated mutations (A8V, L29Q, A31S, and C84Y), as well as an engineered Ca2+ sensitizing mutation (L48Q), and a DCM-associated mutation (Q50R). The effects of temperature in modulating the Ca2+-cTnC interaction was also studied in these mutants. We further explored the role of cellularly abundant magnesium (Mg2+) which also interacts with cTnC and may modulate the Ca2+ coordinating capabilities of this contractile protein. Lastly, the role of Mg2+ binding to the mutants of interest, under normal cellular condition and in energy depleted states was explored to better understand the etiology of FHC and provide biomedical and physiological insight into potential treatments for this disease.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Glen Tibbits
Department: 
Science: Department of Biomedical Physiology and Kinesiology
Thesis type: 
(Thesis) Ph.D.

Towards event analysis in time-series data: Asynchronous probabilistic models and learning from partial labels

Author: 
Date created: 
2021-03-10
Abstract: 

In this thesis, we contribute in two main directions: modeling asynchronous time-series data and learning from partial labelled data. We first propose novel probabilistic frameworks to improve flexibility and expressiveness of current approaches in modeling complex real-world asynchronous event sequence data. Second, we present a scalable approach to end-to-end learn a deep multi-label classifier with partial labels. To evaluate the effectiveness of our proposed frameworks, we focus on visual recognition application, however, our proposed frameworks are generic and can be used in modeling general settings of learning event sequences, and learning multi-label classifiers from partial labels. Visual recognition is a fundamental piece for achieving machine intelligence, and has a wide range of applications such as human activity analysis, autonomous driving, surveillance and security, health-care monitoring, etc. With a wide range of experiments, we show that our proposed approaches help to build more powerful and effective visual recognition frameworks.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Greg Mori
Department: 
Applied Sciences: School of Computing Science
Thesis type: 
(Thesis) Ph.D.

The allometry of oxygen supply and demand in the California Horn Shark, Heterodontus francisci

Author: 
Date created: 
2021-01-21
Abstract: 

The scaling relationship between metabolic rate and body mass is one of the most notable functional relationships in comparative physiology and macroecology. In aquatic ectotherms, the surface area of the gills is thought to be a major contributor to the allometric scaling patterns we see for metabolic rate, both within and across species. Here, I first examined the allometric relationship between oxygen supply (gill area) and consumption (metabolic rate) and found that the allometry of gill area was isometric and very similar to that of metabolic rate. Second, I tested the effects of three statistical analysis techniques for estimating maximum metabolic rate and found that a rolling regression model was the best candidate model across four fish species. Together, these results support the hypothesis that oxygen supply and demand are closely matched and suggest that a two-dimensional gill can overcome geometric constraints to increase at the same rate as the three-dimensional mass of an inactive organism. Additionally, they highlight the importance of statistical choices in producing comparable and reproducible estimates of metabolic rate across species.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Nicholas Dulvy
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) M.Sc.

Plants and presumptions: An assessment of the impact of plant macronutrient variation among hunter-gatherers on the recommendations of the Paleo Diet

Author: 
Date created: 
2021-03-02
Abstract: 

The Paleo Diet is a popular but controversial dietary regime that requires adherents to avoid domesticated plants and replicate the macronutrient distribution (i.e., the percentages of carbohydrates, protein, and fat) found in hunter-gatherer diets. In this thesis, I report a study in which I investigated an aspect of the Paleo Diet that has hitherto been overlooked – namely, its reliance on plant macronutrient values from a single country, Australia. First, I replicated the macronutrient consumption ratios reported in the study that underpins the Paleo Diet (Cordain et al. [2000] American Society for Clinical Nutrition 71, 682-692). I then examined the impact that an alternate set of plant values that Cordain et al. (2000) presented but did not use had on the macronutrient consumption ratios that Cordain et al.’s (2000) method yields. Next, I generated plant macronutrient values for a worldwide sample of ten recent hunter-gatherer societies, and statistically compared the new values to the ones Cordain et al. (2000) reported. Subsequently, I applied Cordain et al.’s (2000) method to the new plant macronutrient values with a view to generate new macronutrient consumption ratios. Thereafter, I statistically compared the new values to the values obtained by Cordain et al. (2000). The analyses revealed that there were some significant differences between the new plant macronutrient values and those that Cordain et al. (2000) created. The analyses also revealed that, in all cases, applying Cordain et al.’s (2000) method to the new macronutrient values produced macronutrient consumption ratios that differ significantly from those reported by Cordain et al. (2000). Together, the results of the analyses indicate that the Paleo Diet’s macronutrient consumption recommendations are dependent on Cordain et al.’s (2000) sample. As such, the recommendations of the Paleo Diet need to be revised or abandoned.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Mark Collard
Department: 
Environment: Department of Archaeology
Thesis type: 
(Thesis) M.A.

Increased risk of severe infections and mortality in patients with newly diagnosed systemic lupus erythematosus: A population-based study

Author: 
Date created: 
2021-01-25
Abstract: 

Systemic lupus erythematosus (SLE) is a chronic disease with a broad spectrum of clinical manifestations and infections are a leading cause of morbidity and premature mortality in patients with SLE. Findings from previous studies may be limited because of small sample sizes and using prevalent cohorts. To evaluate the risk of severe infection and infection-related mortality among patients with newly diagnosed SLE. We conducted an age- and gender- matched cohort study of all patients with incident SLE using administrative health data from British Columbia, Canada. Primary outcome was the first severe infection after SLE onset. Secondary outcomes were total number of severe infections and infection-related mortality. Multivariable Cox proportional hazard and Poisson models were used to evaluate the association of SLE with the outcomes, adjusting for confounders. The findings suggest SLE is associated with increased risks of first severe infection, a greater total number of severe infections and infection-related mortality.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Hui Xie
Department: 
Health Sciences: Faculty of Health Sciences
Thesis type: 
(Thesis) M.Sc.

Development of wearable, screen-printable conductive polymer biosensors on flexible and textile substrates

Author: 
Date created: 
2021-06-25
Abstract: 

Wearable biosensors have great potential for real-time diagnostics, but have been encumbered by costly fabrication processes, rigid materials, and inadequate sensitivity for physiological ranges. Sweat has hitherto been an understudied sample for measurement of components like pH and lactate, which can provide meaningful guidance for wound healing, eczema, and sports medicine applications. This thesis presents the development of a flexible, textile-based, screen-printed electrode system for biosensing applications. Furthermore, a flexible, pH-sensitive composite for textile substrates is developed by mixing polyaniline with dodecylbenzene sulfonic acid and textile screen-printing ink. The optimized composite’s pH response is compared to electropolymerized and drop-cast polyaniline sensors via open circuit potential measurements. A linear response is observed for all sensors between pH 3-10, with the composite demonstrating sufficient response time and a sensitivity better than -20 mV/pH, exceeding existing flexible screen-printed pH sensors. Investigations into a potentiometric, non-enzymatic lactate sensor using polyaminophenylboronic acid are also discussed.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Bonnie Gray
Department: 
Applied Sciences: School of Engineering Science
Thesis type: 
(Thesis) M.A.Sc.

The respiratory basis of metabolic rate and life histories

Author: 
Date created: 
2021-06-04
Abstract: 

Oxygen fuels aerobic metabolism and as such, plays an important role in the physiology, ecology, and evolution of organisms. Traits related to oxygen acquisition (respiratory surface area) and use (metabolic rate) or the balance of oxygen supply and demand (or its mismatch, termed ‘oxygen limitation’) have been proposed to underlie broad patterns such as the temperature-size rule and the geographic distributions of marine species. Moreover, traits related to oxygen acquisition and use form the central focus of seemingly disparate macroecological theories that aim to explain and predict the structure and dynamics of ecological systems and how these systems and their constituents will respond to a changing climate. While these existing theories and oxygen-related explanations offer a compelling story, the role of oxygen in shaping biological observations, responses, and patterns is hotly debated. Further, much work in this area is experimental in nature and typically focuses on a single species in laboratory settings. Broader scale, macroecological research stemming from meta-analysis and modeling is needed to understand the generality of patterns. To that end, this thesis takes a macroecological approach and examines the generality of the relationships among traits related to oxygen acquisition and use, ecology, and life histories. First, I reveal that respiratory surface area explains patterns of metabolic rate across the vertebrate tree of life. Second, I uncover that larger-bodied, active, pelagic sharks have greater gill surface areas (respiratory surface area in fishes) for a given size compared to their smaller-bodied, less active, benthic counterparts. Conversely, the rate at which gill surface area increases with body mass is the same for all species, regardless of activity level, habitat type, or maximum size. Third, I test a central prediction of the Gill Oxygen Limitation Theory and find that across fishes, growth and maximum size more strongly relate to activity level than gill surface area. Collectively, my thesis highlights the complexities of integrating data across scales and illustrates that oxygen acquisition and use is tightly correlated with activity level, but the relationships with life histories are less straightforward. This body of work builds on existing theory while empirically testing relationships among oxygen acquisition and use, ecological lifestyle, and the life histories among fishes and other vertebrates.

Document type: 
Thesis
File(s): 
Supervisor(s): 
Nicholas Dulvy
Department: 
Science: Biological Sciences Department
Thesis type: 
(Thesis) Ph.D.