VictorJuiz/thesis huggingface dataset:
Rethinking Clinical De-identification

The restricted availability of free-text clinical notes and embedding-models trained on clinical notes is a bottleneck in deploying machine learning in clinical settings. To ameliorate concerns regarding the confidentiality of patient data, researchers are developing methods which automatically remove sensitive personal information from notes. While these methods appear to perform exceedingly well, often with reported precision and recall well above 95%, automated approaches for de-identification are still not trusted by clinicians because there remains non-zero risk. In this work, we present fundamental limitations associated with current approaches to de-identification that cannot be solved by incremental improvements to model performance. These limitations stem from the fact that current approaches are all trained in a supervised manner. To address these limitations, this thesis proposes the first unsupervised approach to the de-identification on free-text clinical notes. The proposed algorithm replaces all tokens with other tokens pseudo-randomly sampled from trained embeddings and is most useful for tasks where humans are not required to read the de-identified notes (e.g., training word embeddings for public release, piloting the feasibility of end-to-end machine learning models). Our approach successfully side-steps the issues facing supervised approaches (e.g., having to decide what constitutes sensitive personal information). The second part of the thesis argues for an expansion to the scope of clinical de-identification. Whereas existing de-identification approaches focus solely on protecting patients’ identities, we argue that de-identification should also focus on protecting the identity of healthcare providers. First, we demonstrate that authorship attribution in clinical notes is a very easy task when compared to many traditional author attribution datasets. Despite the need for specialized and improved author obfuscation techniques, the data to develop such techniques is difficult to obtain due to privacy concerns; it is impractical to manually label paired sentences and difficult to crowd-source the task given data-sharing limitations. To enable the development of automated means of evaluating semantic relatedness, we developed a novel sentence-pair dataset ordered by semantic relatedness. This dataset can serve as a catalyst for future author obfuscation evaluation, and we draw insights from this dataset to better understand existing work.

Keywords: Clinical De-identification
Natural Language Processing
Advisor: Hirst, Graeme
Rudzicz, Frank
Brain Maturation and Sex Hormones duringA adolescence

The second decade of life is a critical period of transition: it involves a series of biological and psychosocial changes that are essential for learning and adaptation to adult life, as well as for the development of a healthy brain. The body of work presented in this doctoral thesis aims to investigate the maturation of the brain during puberty and the possible role of testosterone in shaping the brain; it extends what is known about the hormonal events during puberty. By integrating multi-modal datasets of brain structure and function and longitudinal data on pubertal testosterone, this thesis first revealed the relationship between pubertal testosterone and brain structure, which was modulated by the timing of the testosterone surge; an earlier peak in the change in testosterone levels predicted a stronger relationship. Then it revealed that the cumulative exposure to testosterone during puberty moderated the relationship between adult testosterone and brain response to faces. Using data acquired with functional magnetic resonance imaging (fMRI) in two large cohorts (the Avon Longitudinal Study of Parents and Children, IMAGEN) with the same face paradigm, we have also revealed robust canonical connectivity of the face network that was invariant across populations and developmental stages (i.e., from adolescence to young adulthood). When assessing this network at an individual level, connectivity profiles of individual participants deviated from the canonical one, with the magnitude of this deviation relating to the presence of psychopathology. Lastly, moving the focus from the brain to the body, we have clarified the nature of the relationship between testosterone and sex hormone-binding globulin (SHBG) and body mass index throughout puberty. Combining phenotypic and genetic data, our findings support a hypothesis that high SHBG leads to high total testosterone through a functional hypothalamic-pituitary-gonadal axis.Taken together, these findings indicate a possible organizational effect of pubertal hormones and suggest that consideration of the organizational effects of pubertal hormones is required to reveal the complex relationship between testosterone and social cognition later in life. In addition, we suggest that the relationship between testosterone and the brain may involve multiple biological and psychosocial factors.

Keywords: cerebral cortex
face processing
functional connectivity
puberty
sex hormone binding globulin
testosterone
Advisor: Paus, Tomas T
Issues that Influence Health during Pregnancy and the Postpartum Period: An International Concept Mapping Study

Background/Objectives: Pregnancy-related research has traditionally focused on the physical health of pregnant persons and their babies. This may be due to the lack of patient perspective in determining what issues affect their health during and after pregnancy and childbirth. The objective of my thesis was to identify issues that health-service users (HSUs, individuals with prior pregnancy experience) and healthcare professionals (HCPs) involved in their care, perceive to influence the health of pregnant persons and their babies, understand how these issues are prioritized by participant groups and identify actionable issues to inform pregnancy care, health policy and future research. Methods: I conducted a concept mapping study with HSUs and HCPs, which involved brainstorming sessions with HSUs and HCPs, data synthesis to condense the list of statements, sorting of items based on similarity, rating of items based on three scales (importance, preventability, recognizability), multidimensional scaling and hierarchical cluster analysis to produce concept maps, pattern matching graphs and go zones, and the interpretation of results with HSUs and HCPs Results: A total of 855 statements identified by 14 HSUs and 19 HCPs, were condensed to 85 unique statements, through several rounds of data synthesis. Participants from 10 high- and middle-income countries (29 HSUs and 33 HCPs) sorted and rated these statements into six clusters - maternal mental health, maternal mortality and physical morbidity, fetal/neonatal complications, unexpected peripartum events, health system challenges, and sociocultural factors. While participants agreed on issues that influence health, HSUs assigned greater importance to fetal/neonatal morbidity and maternal mental health and lower importance to health system issues, while HCPs assigned higher importance to maternal mortality and morbidity and lower importance to maternal mental health. Eleven actionable items were identified as priorities to address, to improve patients’ experiences with pregnancy care. Conclusion: The findings of my thesis demonstrate that HSUs and HCPs recognize that health during and after pregnancy is influenced by factors other than physical morbidity, but they differ in how they prioritize these issues. Addressing actionable items important to patients through multidisciplinary collaboration could improve health outcomes.

Advisor: D'Souza, Rohan D
The Development of Quayside: Planning Toronto’s Smart City

Smart cities are a growing area of scholarship, but they are understudied in the literature in urban planning. This case study of the Sidewalk Toronto/Quayside project offers insights into the smart city planning process and its actors. The public-private partnership between a tripartite government agency, Waterfront Toronto, and an Alphabet Inc. subsidiary, Sidewalk Labs, to plan one of the most significant urban smart city projects in North America, and its cancellation after two and a half years, provides an opportunity to study a smart city project that has not been undertaken anywhere else at this scale. My research examines the Sidewalk Toronto/Quayside smart city planning process through semi-structured interviews, participant observation, and discourse analysis. This dissertation is organized into a three-paper model, informed by three objectives: to contextualize the Quayside project within the history of waterfront regeneration in Toronto, to understand the origins and motivations underpinning the “co-creation” partnership between Waterfront Toronto and Sidewalk Labs, and to trace how the partnership shaped public engagement in the planning process. This research expands smart city planning literature by further illuminating the unique conditions and considerations of smart cities within established planning processes, including waterfront regeneration, partnership development, and participatory planning. Based on my research findings, I make three central arguments. The first is that Quayside represents both a repackaging of established entrepreneurial discourses on Toronto’s waterfront and a new phase of Toronto’s waterfront development in that the project was specifically designed to ensure the organizational longevity of Waterfront Toronto rather than to meet development objectives that were previously prioritized in the corporation’s work. Second, I argue that smart city planning processes are a fraught application for collaborative public-private partnership models given that these models depend on equity and mutual respect between partners, which is difficult to achieve in smart city partnerships where significant resource and knowledge asymmetries exist between large technology corporations and government agencies. Third, I argue that regardless of the scale and volume of public engagement opportunities, a smart city planning process cannot be citizen-centric if participation is directed and facilitated by a private smart city actor.

Keywords: Participatory Planning
Public-Private Partnerships
Smart Cities
Waterfront Regeneration
Advisor: Leslie, Deborah
Long-term Remote Sensing for Investigating Forest Change across a Suburbanizing Landscape

Forests, especially in urban and surrounding landscapes, are important natural resources that provide environmental, climatic, economic, social, health, and aesthetic benefits. It is thus important to continuously monitor these forests, which may grow, shrink, or be otherwise impacted by abrupt or gradual changes from many drivers. Long-term remote sensing time-series represent the only means by which the spatio-temporal dynamics of these forests can be consistently collected since the mid-1900s. Aerial photography provides the longest temporal coverage and can observe individual trees, but is limited in temporal density, in spectral coverage, and by differences in photograph technology through time. Landsat satellites with medium spatial resolution cannot observe individual trees but, with recent advances in sensor harmonization and time-series algorithms, can provide a consistent annual record of forest change since 1972. Combined with appropriate validation techniques and predictive modelling, Landsat holds potential for investigating changes in forest canopy cover over 50 years across landscapes that surpasses aerial photography. Both aerial photography and Landsat cover much of post-war suburbanization, when many rural-agricultural landscapes surrounding cities developed into suburban areas. However, few studies have utilized aerial photography time-series, and no studies have utilized Landsat’s full temporal record, for historical urban forest investigation and a better understanding of the suburbanization process. In this thesis, I demonstrate how long-term aerial photography and Landsat time-series can be built, validated, and analyzed to provide unique spatio-temporal results about forests and forest change across a suburbanizing landscape. With aerial photography, I capture tree density changes and drivers during the agriculture-suburban transition. With Landsat, I model a relationship with canopy cover for predictive mapping and explore connections with tree-rings as a form of temporal validation. I then build the longest-possible canopy cover time-series for investigating forest change across a heterogenous suburbanizing landscape and, more specifically, post-development residential canopy cover change in comparison with historical population demographics. These findings exemplify the power of long-term remote sensing for investigating different aspects of urban forest change, which have important research implications in urban forest and remote sensing time-series literature, and applied implications for municipal forest monitoring practices and knowledge acquisition for decision makers.

Keywords: Aerial photography
Landsat
Suburbanization
Time-series
Urban forests
Vegetation change
Advisor: He, Yuhong
Vital Bodies, Natural Cures: Moral Quests for Care in Kerala, South India

Based on long-term ethnographic fieldwork, this dissertation offers a semi-person-centered analysis of nature cure (prakr̥ti jīvanaṁ) caregiving in Kerala, South India. First promoted in India as part of M. K. Gandhi’s anti-colonial project, this medical tradition draws on the metaphor of vitality to frame the body as having a natural wisdom—a vital force—that works to restore health and balance. This dissertation examines care practices in homes, mobile health camps, and hospitals in order to canvass last-resort quests for cure, where patients become ‘self-doctors,’ taking their sickness as signs of alienation from plants and nonhuman animal life. Through mentorships with non-professionalized healers, patients aim to repair their ill bodies, revitalize the toxic environment, and respond to moral collapse. By foregrounding the ethical stakes of rehabilitation, this dissertation pushes against reducing the logic of health choices to the neoliberal realm of individual lives; instead, it engages a relational approach to care, asking how these actions intersect with larger social and political shifts. In doing so, this dissertation shows how healers and users co-construct ethical imaginaries of reviving local lifeways, in counterpoint to larger changes in failed care regimes, migrated kin networks, widening class, caste, and gender inequalities, and publicly mediated concerns of a toxic present. At the same time, this dissertation shows how even though naturopaths aspire to transcend enduring inequalities, the medical tradition remains embedded in a wider political context of communalist conflict. This dissertation braids together the pragmatic thought of William James with Gandhi’s philosophical explorations on health and self-determination, asking how their insights may guide us to better understand what freedom and care mean within and between the particulars of individual lives and the general strands of existence that weave through all lives. Together, their teachings help amplify how scientifically-unvalidated alternative medicines may be efficacious at the levels of moral personhood and temporally shaped intersubjective care. By examining how nature cure healers and users in Kerala engage a collectivized vision of wellness and self-care, the dissertation ethnographically brings into relief the ways that biomedicine does not in itself equate to effective rehabilitation.

Keywords: Care
Kerala
Medical anthropology
Naturopathy
Personhood
South India
Advisor: Lambek, Michael
Cody, Francis
A Performance Guide to George Enescu's Later Violin Works

Born in 1881 in Romania, George Enescu’s career combines the roles of composer, violinist, conductor, pianist, and pedagogue. Enescu’s multi-talented and multi-dimensional musicianship formed the basis for a complex compositional style. This reflects in his later two violin compositions, the Third Violin Sonata (opus 25) and the Suite Impressions d’enfance (opus 28). The complicated quality is achieved not only through the use of harmony but also in his approach to notation. The highly detailed markings include twenty different types of articulations, Enescu’s own system of dynamics, tempi changes, and performance instructions. Exploring the complexity of his music, addressing difficult performance issues, and building a performance guide are at the core of my research. Unlike his German-influenced First Violin Sonata and Fauré-influenced Second Violin Sonata, Enescu developed his own compositional language by infusing and creating Romanian folk music elements in his later violin works. The dense markings allow Enescu to express an expanded range of sonorities and nuances. However, differentiating these meticulous notations can be challenging, and a performance guide is much needed. My research offers guidance to performers in developing nuanced and colourful playing through a deeper understanding of Enescu’s music and its notation. The first chapter of the thesis outlines the purpose of the research, provides background on Enescu’s biography and compositional language and offers a literature review. The second chapter demonstrates complexities of notation and performance through close analysis of twenty-one recordings of the first seventeen bars of Ménétrier from Impressions d’enfance. The third chapter presents interviews with violinists Sherban Lupu and Axel Strauss, who have recorded both the Third Sonata and the Suite. The fourth chapter examines how specific dynamics that Enescu utilized fit in the commonly understood system of notating dynamic levels. The fifth chapter systematically explores the range of Enescu’s different articulations and offers guidance for violinists who wish to explore Enescu’s later violin works.

Keywords: articulation
detailed notation
dynamic
George Enescu
Impressions d'enfance
The Third Violin Sonata
Advisor: McClelland, Ryan
Elucidating Met Receptor Tyrosine Kinase Interactome to Identify Novel Regulators of Met Biology

Met receptor tyrosine kinase is a growth factor receptor implicated in multiple diseases, including cancers, whereby aberrantly activated Met underlies metastasis, survival, sustained proliferation and angiogenesis of tumor cells, and thus is a sought-out target in cancer drug discovery. However, despite its critical role, Met and its associated functions are considerably understudied, and this is further underlined by paucity of successful therapeutics and precision medicine approaches targeting Met-mediated oncogenicity. Given that protein-protein interactions (PPIs) govern protein function and are, since recently, considered to be druggable, novel knowledge and new therapeutic strategies can be uncovered by identifying and characterizing interacting partners of Met. Using the Mammalian Membrane Two-Hybrid (MaMTH) PPI mapping technology developed in our lab, this thesis takes a PPI mapping approach to enable study of Met to uncover novel regulators of Met biology. In this study, I have generated and characterized a MaMTH-compatible PPI mapping platform, which expresses inducible full-length Met, recapitulates known Met localization, and can detect previously known interactors of Met. Utilizing this platform, I have further mapped a targeted interactome of Met against SH2/PTB-domain containing proteins and FpClass-predicted putative interactors of Met, and identified thirty-two, including sixteen novel, interactors of Met. Non-small cell lung cancer (NSCLC)-focused functional characterization of one of the novel Met-interacting protein, B cell LiNKer (BLNK), reveal that BLNK is a positive regulator of Met signalling, and modulates surface localization and HGF-dependent trafficking of Met in NSCLC cell lines. Molecular studies in HEK293 models reveal that in the presence of BLNK, interaction between Met and its known interacting protein, GRB2 is increased, while the known constitutive interaction between BLNK and GRB2 is also increased in the presence of active Met. Finally, tumor phenotypical assays further uncover roles for BLNK in anchorage independent growth and chemotaxis of NSCLC cell lines. Cumulatively, my PhD thesis provides a PPI mapping platform for Met, targeted PPI map of Met, and describes a role for BLNK, a novel PPI of Met identified through this study, in regulating Met biology in NSCLC.

Keywords: Mammalian Membrane Two Hybrid
Met receptor tyrosine kinase
Non small cell lung cancer
Protein Protein Interactions
Signalling
Advisor: Stagljar, Igor IS
Three Essays on the Social Determinants of Labour Supply

This dissertation bridges empirical and theoretical insights from multiple disciplines to improve our understanding of individual labour supply decisions and, in turn, the optimal design of public policy. Chapter 1 examines the labour supply effects of the Working Income Tax Benefit (WITB) in Canada. An in-depth analysis of institutional details surrounding WITB reveals that low-income Canadians lack knowledge of the program. Consequently, WITB can be treated as a lump sum cash transfer rather than as an earnings subsidy. Using variation in WITB receipt both within and between individuals over time, results suggest that, contrary to the predictions of the standard labour-leisure choice model, WITB receipt had a robust, significant positive effect on the labour supply of single low-income workers. Chapter 2 investigates how the interaction of social norms and public childcare provisions impact maternal labour supply. Using data from the US, this chapter exploits exogenous increases in minimum school entry-age laws across states and time to measure how increasing the age at which children are eligible for public school impacts the labour supply of mothers. The results suggest that increasing the school starting age significantly decreases the labour supply of married mothers at the extensive margin and single mothers at the intensive margin. Additional analysis reveals that the negative labour supply effects are concentrated among mothers in states with progressive gender norms. Implications for public policy are discussed. Chapter 3 provides a critical evaluation of the assumption that work is a disutility, which underlies the standard model of labour supply used widely in economics, and in turn, public policymaking. The assumption implies that individuals supply labour to the market for the sole purpose of purchasing goods. This chapter reviews the work of William Stanley Jevons and Alfred Marshall, both of whom were critical in the development of the standard labour-leisure choice model, but of the opinion that work is not, in its entirety, a disutility. I then modify the standard model of labour supply to re-incorporate the positive utility of labour by making the marginal utility of leisure dependent on the amount of time spent working. The chapter concludes with a discussion of the implications of the intrinsic benefits of work for the design of public policy.

Advisor: Pohler, Dionne