VictorJuiz/thesis huggingface dataset:
Model Extraction in the Context of Audio Classifiers

Model extraction is the process of reverse-engineering the parameters of a machine learning model exposed through a query interface. Prior work on this class of attacks focuses on the vision domain for the most part. We demonstrate that subtle, yet crucial, distinctions between learning from audio and vision preclude us from directly applying existing model extraction attacks to audio. A key example is that the discriminative features learned by raw audio models appear to be more task-dependent. To extract audio models we thus need to carefully query the victim model to expose these task-specific or difficult-to-learn representations. To this end, we propose a simple task-dependent extraction approach using generative models to synthesize a diverse pool of candidate queries. Our experimentation shows this approach makes it possible to extract a victim model trained on LibriSpeech using a surrogate dataset, Voxceleb with a test accuracy of 76.51% given a budget of 3M queries. L'extraction de modèles correspond au processus visant à reconstruire par rétro-ingénierie les paramètres d'un modèle d'apprentissage automatique accessible via une interface de requête. Les travaux antérieurs menés sur cette classe d'attaques se sont concentrés pour la plupart sur le domaine de la vision. Nous démontrons l'existence de différences subtiles mais cruciales entre les domaines de l'audio et de la vision qui empêchent l'application des techniques existantes dans le cadre de l'audio. Un exemple marquant nous est donné par le fait que les caractéristiques discriminantes apprises par les modèles travaillant sur des données audio brutes semblent plus dépendantes de la tâche à résoudre qu'en vision. L'extraction de modèles d'audio nécessite ainsi l'utilisation de requêtes bien choisies qui exposent les représentations apprises. Dans ce but, nous proposons une approche d'extraction simple et dépendante de la tâche à résoudre qui utilise des modèles génératifs afin de synthétiser un ensemble divers de signaux candidats pour les requêtes. Nos expériences montrent que notre approche permet d'extraire un modèle cible entraîné sur LibriSpeech à l'aide d'un jeu de données de substitution, Voxceleb, avec une précision de 76,51 % et un budget de 3 millions de requêtes.

Keywords: Adversarial Machine Learning
Audio Processing
Computer Security
Machine Learning
Model Extraction
Advisor: Papernot, Nicolas
Enabling Skeletal Muscle Repair and Functional Recovery following Denervation-induced Injury Using Ultrasound Mediated Gene Delivery (UMGD)

Skeletal muscle is essential for mobility and its health relies upon innervation. Peripheral nerve injury denervates target skeletal muscle, causing immediate loss of function, atrophy, and development of fibrosis. Delayed re-innervation can result in permanent functional loss, leading to a myriad of physical, financial, social, and psychological burdens on affected individuals. Ultrasound-mediated Gene Delivery (UMGD) is a relatively novel technique that has been shown to provide localized and effective gene therapy in vivo. We hypothesize that UMGD of myogenic genes IGF-1, VEGF, and Ang-1 would sustain the mass and regenerative potential of denervated muscle awaiting reinnervation. After two weeks, UMGD of these genes mildly increased gross muscle weight, Type II fibre CSA, and vascularization compared to denervated muscle given no transgene. We have shown that UMGD is a viable model for targeted gene delivery to skeletal muscle through partial prevention of the atrophy and vascular loss induced by denervation injury.

Keywords: denervation
FAPs
gene therapy
micro bubbles
skeletal muscle
ultrasound
Advisor: Batt, Jane
Uncovering the Molecular Mechanism of Cholesterol Uptake in Class B Scavenger Receptor LIMP-2

Class B scavenger receptor proteins fulfill a variety of functions in immunity and homeostasis, including key roles in preventing heart disease, currently the leading cause of death worldwide. Recent evidence indicates that one class B receptor, LIMP-2, facilitates the uptake of cholesterol from bound lipoproteins to the lysosomal membrane and may therefore play a role in regulating cholesterol homeostasis. I hypothesize that uptake occurs through the large, predominantly hydrophobic cavity that spans the LIMP-2 ectodomain. To test this hypothesis, I perform extensive atomistic molecular dynamics simulations of cholesterol and LIMP-2 successively in solution, in a membrane mimetic, and using a novel reverse micelle approach to model a membrane and lipoprotein bound state. I demonstrate that cholesterol has an orientational preference in the LIMP-2 cavity and propose a novel ‘reversase’ mechanism of cholesterol uptake that I then sample using an enhanced-sampling algorithm. Our results indicate that the putative pathway includes a large side pocket which may enable cholesterol to flip within the protein, thereby facilitating its insertion into lipid membranes. Overall, our findings support the reversase mechanism of cholesterol uptake through LIMP-2 and raise the possibility that similar pathways for lipid uptake exist in other class B scavenger receptors, expanding our understanding of the molecular processes that mitigate heart disease risk.

Keywords: Computational biology
Molecular dynamics simulations
Advisor: Pomès, Régis
Being Academically At-risk and Building Capacity for Self-regulated Learning in University

University students who experience academic failure are at risk of becoming curbed by a pattern of failure in the absence of adequate self-regulatory processes. Repeated academic failures can result in academic probation or suspension, and the student is labeled academically at-risk (AAR). Adapted from Pintrich and Zusho’s (2007) model for student motivation and self-regulated learning (SRL) in the postsecondary classroom, this study proposes a model specific to the AAR student experience. Using existing literature on academically struggling student SRL and motivation, and psychometric analyses of an academic intervention’s assessment of the study habits and attitudes of AAR undergraduate students, this research investigates SRL within the AAR student experience, expands on the original model’s areas of SRL (cognition, behaviour, motivation and affect, and context), and demonstrates the intervention’s effect on AAR students’ SRL capacity. Future directions for AAR-specific SRL research, refinements to the model and assessments, and other implications are discussed.

Keywords: academic failure
academically at-risk
educational psychology
higher education
self-regulated learning
university
Advisor: Childs, Ruth
Investigating the Role of Onecut1 in Establishment of Cell- type-specific Enhancers during Mouse Motor Neuron Differentiation

Spinal motor neuron identity is established by three programming transcription factors (TFs): Ngn2, Isl1 and Lhx3. Isl1 and Lhx3 TFs bind to enhancers in nascent motor neurons regulating expression of many effector genes. In maturing motor neurons, Lhx3 downregulation results in relocation of Isl1 to Onecut1 TF bound enhancers. I characterized the role of Onecut1 in spinal motor neuron differentiation using CRISPR-Cas9 system to generate a Onecut1 mutant mouse embryonic stem (ES) cell line, followed by in-vitro differentiation of these ES cells into spinal motor neurons. Analysis for global gene expression changes revealed attenuated expression of a subset of motor neuron genes. Whereas, chromatin immunoprecipitation followed by next-generation sequencing (ChIP-seq) showed global redistribution of Isl1 binding and changes in enhancer activity in absence of Onecut1. Together, my analyses revealed association of Onecut1 with expression of a subset of neuronal genes via protein-protein interaction with Isl1 at motor neuron enhancers.

Keywords: ChIP-seq
Differentiation
Embryonic Stem cells
Genome wide
Spinal motor neurons
Transcription factors
Advisor: Rhee, Ho-sung HSR
Whole-genome Sequencing Approach to Characterize the Population Structure of Bacillus cereus at a Human Milk Bank

Stringent milk handling protocols including pasteurization are used at human milk banks serving critically-ill, preterm neonates. However, up to 30% of donated human milk is lost to contamination with the potentially neonatal pathogen Bacillus cereus, whose spores can resist pasteurization. Here, we used genomics to evaluate the population structure of a collection of B. cereus organisms recovered from pre- and post-pasteurized human milk donated to a human milk bank, from patients seeking care at that facility and from the hospital environment. Pangenome analysis revealed an unexpectedly high level of genetic diversity within the milk bank/hospital strain population. Phylogenetic analyses using core-genome polymorphisms did not permit identification of sources of human milk contamination by B. cereus. Genome-wide association studies revealed that variants of genes involved in sporulation are overrepresented among organisms recovered from post-pasteurized milk. The results may be used to improve milk banking protocols and research around the world.

Keywords: Bacillus cereus
Bioinformatics
Milk banking
Pangenome
Phylogenetics
Advisor: Fittipaldi, Nahuel V
Chelating Phosphorus and Nitrogen Donor Ligand Design for Catalytic Hydrogenation

The design of ligands for hydrogenation catalysts is a field that is constantly evolving, there are always improvements to be made in terms of activity, selectivity and cost. Chapter 2 focuses on synthesis, characterization and catalytic testing of a novel manganese complex with a known PNNP ligand for transfer hydrogenation. Chapter 3 highlights the attempted synthesis of a manganese catalyst with a PNP pincer ligand for ester hydrogenation. Chapter 4 describes two new secondary phosphine oxide ligands and their corresponding metal complexes. Three new Ru complexes with N-P(OH)-N donor ligands were synthesized and characterized. A paramagnetic nickel [Ni3(NPN)4] cluster was also reported and characterized. Finally, Chapter 5 highlights the use of the ligand acidity constant method to predict the acidity of molecular hydrogen-metal intermediates present in direct hydrogenation reactions. The catalytic cycles were discussed to highlight advancements in acid-tolerant catalysis as part of a literature review in progress.

Advisor: Morris, Robert H
VOCs in Toronto During the 2020 COVID-19 Lockdown and Potential Anthropogenic Isoprene and Monoterpenes

Volatile organic compounds can have either anthropogenic or biogenic sources. With the compositional shift of anthropogenic emissions towards volatile consumer products, it is becoming increasingly important to better understand the sources of VOCs in urban settings. In this work, the trends of VOCs in Toronto and various other Canadian locations are explored. Outdoor ambient VOC data were collected from the months of March to June in 2020 during the COVID-19 lockdown. Traffic-related data were analyzed to determine if there were changes in mixing ratios brought about by the change lockdown. Evidence for potential anthropogenic sources of isoprene and monoterpenes in Toronto is also explored. It was found that the lockdown brought about lower than normal mixing ratios of benzene and toluene. As well, from analysis of National Air Pollution Surveillance (NAPS) data, there is evidence to show that there are non-biogenic sources of monoterpenes in Toronto.

Keywords: air quality
atmospheric chemistry
environmental chemistry
monoterpenes
PTR-MS
VOC
Advisor: Abbatt , Jonathan
Chan, Arthur
Energetics of π-π Stacking Interactions: Implications in the Phase Separation of Intrinsically Disordered Proteins

π-π stacking interactions are found throughout the proteome and have been shown to play a role in the liquid-liquid phase separation of intrinsically disordered proteins; however, the structural and energetic properties of π-π interactions that drive intra- and intermolecular protein interactions are poorly understood. In this study, we investigate the pairwise interactions of sp2-hybridized groups within proteins through an analysis of the Protein Data Bank. Along with these statistical data, small-molecule representations of these groups are simulated using molecular dynamics, while quantum mechanical and molecular mechanical calculations are used to characterize the energies of π-π interactions across their conformational distributions. Molecular dynamics is further used to simulate the folding and unfolding equilibria of small peptides enriched in sp2 groups. Ultimately, this study provides a thorough quantification of the energetics of π-stacking contacts in proteins and evaluates the strengths and limitations of different computational methods in accurately modelling these interactions.

Advisor: Pomès, Régis
Assessing Bibliometrics for the Automation of Technology Readiness Level Assessments

Technology Readiness Levels (TRL) are used to assess technology maturity, an important factor in technology investment and onboarding decisions. Expertly assessed TRLs are time-consuming, financially demanding, and subject to bias. While quantitative TRL assessment tools have been suggested, their accuracy is yet to be confirmed. To address this, we explore an existing method that used prevailing bibliometric models of maturity to assess TRLs. We automated and replicated the method and investigated its reliability by estimating the TRLs of 23 technologies. We show that the results of the automated method do not agree with expertly assessed TRLs and we offer hypotheses as to why bibliometrics fail to provide accurate technology maturity estimates. We argue that the single indicator model commonly used to assess technology life cycle stages must be revised. Finally, we suggest machine learning and Natural Language Processing tools to replace outdated models of maturity and automate TRL assessments.

Keywords: Bibliometrics
Technology life cycle
Technology maturity assessment
Technology Readiness Levels
Advisor: Olechowski, Alison
Temporal Control over Biochemical Cues to Recapitulate Dynamic Tissues

Hydrogels are powerful materials that more accurately mimic the cellular microenvironment over static two-dimensional culture. Photochemical strategies enable dynamic complexity to be achieved within hydrogels to better mimic the extracellular matrix; However, many photochemical systems to pattern proteins are complicated by long reaction times to immobilize these proteins wherein the protein can lose activity to cells. As proof-of-concept, we demonstrate an elegant method where photo-caged proteins are immobilized in hydrogels and then directly photo-activated. Specifically, we immobilized streptavidin-ortho-nitrobenzyl-modified epidermal growth factor (EGF) to crosslinked hyaluronan hydrogels and cultured both EGF-responsive breast cancer and lung cancer cells therein. We used light to temporally uncage and control EGF activation, thereby inducing cell death in breast cancer cells and proliferation in lung cancer cells. These results show how temporal, photochemical protein activation influences cellular response and lays the foundation for further advances in manipulating the in vitro environment to control cellular response.

Keywords: Epidermal Growth Factor
Hyaluronic Acid
Hydrogels
Photoactivation
Photocaging
Advisor: Shoichet, Molly
The Impact of Cognitive and Physical Enrichment on Contextual Fear Memory Retention the Contribution of Oligodendrogenesis and Myelination

Memories are encoded in patterns of neural activity deemed “engrams” and are recalled when this network is reactivated. Physical and cognitive enrichment have been shown to increase neurogenesis and myelinogenesis which can alter the stability of the engram. We housed mice in both physical enrichment and a combination of physical plus cognitive enrichment and found that both caused forgetting of a contextual fear memory if housing occurred after conditioning, but improved memory recall if done beforehand. However, combining physical and cognitive enrichment caused a greater change in freezing behaviour relative to physical enrichment alone, only when housing was done after conditioning. Mice in which oligodendrogenesis was halted exhibited a trend of freezing less than mice with functioning oligodendrocytes regardless of enrichment, though this was not considered statistically significant. These results are consistent with the theory that enrichment exerts its effect on memory retention by altering engram stabilization during memory consolidation.

Keywords: Contextual Fear Conditioning
Enrichment
Memory
Myelin
Oligodendrogenesis
Advisor: Wheeler, Anne L
Cultivating Care: Backyard Hens and the Changing Geography of Human-Chicken Relations in Toronto

This project examines the changing geography of human-chicken relationships in Toronto, Ontario. Anchoring my project to themes of care and belonging, I first explore the city’s historical live animal debates through textual news media to highlight how arguments about the inhumane treatment and slaughter of urban chickens informed the expulsion of farm animals from residential and market spaces in the late-twentieth century. I then use contemporary media, documents, and semi-structured interviews with participants of the municipal pilot UrbanHensTO to consider how chickens are making a visible return to Toronto. My study shows that urban chicken-keeping is working in the city in transformative and subversive ways; it is allowing residents to cultivate a companionable ethic of care that brings the individuality, lifeworlds, joy, and suffering of chickens into focus. Importantly, these companionable backyard relations are challenging the ethical invisibility of farm animals while making chickens matter as more-than-producers and other-than-food.

Keywords: animal geographies
backyard chickens
care ethics
human-animal relations
Advisor: Wakefield, Sarah
Identifying Candidate Quality Indicators of Knowledge Translation Practice Tools that Support the Practice of Sustainability: A Scoping Review

Knowledge translation (KT) and implementation science (IS) aim to bridge the research gap between what we know (research evidence) and what we do (practice and policy) in health. KT practice tools (KT-PTs) provide methods guidance across a wide range of KT domains such as dissemination, implementation, sustainability, scalability, and IKT. There is limited evidence-based guidance to determine which KT-PTs are the most relevant for their needs and help assess the overall quality of KT-PTs. As a first step, a scoping review was conducted to identify candidate quality indicators of KT-PTs, focusing on the sustainability domain of KT. The scoping review was guided by the Joanna Briggs Institute methodology for scoping reviews. The review identified and characterized 35 KT-PTs. 17 candidate quality indicators were identified across four categories. Findings of this scoping review will guide next steps and future studies to develop and evaluate a quality assessment tool for KT-PTs.

Keywords: Implementation Science
Knowledge Transfer
Knowledge Translation
Advisor: Kastner, Monika
Deconstructing and Reconstructing Content and Language Integrated Learning (CLIL) in a Public System of Mexican Higher Education: An Autoethnography

This thesis explores how a dynamic CLIL project problematized “weak” and “strong” CLIL approaches and deficit discourse of learners and teachers in Mexican (language) education. The study draws from the researcher’s personal and professional challenges as an entry point to analyze language planning and policy in Mexican higher education and to interrogate dominant monolingual ideologies to open spaces for equity-based and inclusive language policy and practice.The study uses layered autoethnographic narratives that integrate experiences as a language educator, literature on CLIL, and primary and secondary sources of language planning and policy. The theoretical framework is grounded on the construct of problematization that derives from critical social theory. Ruiz´s language orientations (1984) guide the analysis of life stories, on-the-ground discourse and policy texts. The study concludes by envisioning a dynamic, critical and plurilingual approach to CLIL that builds on students’ and teachers’ diverse language repertoires and affirms their bi/plurilingual identities.

Keywords: Autoethnography
CLIL
Dynamic Bilingualism
Plurilingualism
Translanguaging
Advisor: Broad, Kathryn K
Rajendram, Shakina S
Partners in Life and Online Search: An Investigation on Older Couples’ Collaborative Information Behaviour

Online search is not always a solitary activity. While past research has investigated collaborative information seeking (“CIS”) among certain demographics, how older couples search online together has not been explored. To address this research gap, a qualitative research study is conducted using semi-structured interviews. Research data is analyzed using thematic analysis.Our analysis suggests that older couples engage in CIS for daily tasks, interests, and to fulfill curiosity. Our findings also suggest that older couples’ CIS is primarily a relationship maintenance behaviour. The trust, care and knowledge developed for each other during their lifelong relationship are essential to understand their communication, decision-making, and various strategies employed during their collaboration. Older couples’ relationship also appears to affect their technology adoption, as couples tend to share the same views about technology despite their individual differences. A few design considerations are recommended for systems aimed to facilitate older couples’ collaborative information seeking.

Keywords: Collaborative information seeking
Collaborative search
Human-Computer Interaction
Information behaviour
Technology for older adults
Advisor: Munteanu, Cosmin
Host Specificity of Pseudomonas syringae in Common Bean Plants (Phaseolus vulgaris)

Pseudomonas syringae is a phytopathogenic bacterial species with a wide host-range, encompassing numerous plants of agricultural importance. Here, I make use of machine learning and host-range testing to analyze the host specificity of P. syringae in common bean plants in order to understand the evolution of bean isolation. The first method that I used was to analyze gene content using random forest machine learning. The model identified type 3 secretion as an important predictor for determining if a P. syringae is able to grow on bean plants. AvrB is interesting since it elicits an immune response in soybean and common bean varieties, but this immune response can be prevented when HopF2 is present. I also designed a new method of bean infection with the goal of using it in order to screen the P. syringae species complex on bean plants, taking advantage of the seedborne nature of bean pathogens.

Keywords: Bean
Infection
Machine Learning
P. syringae
P. vulgaris
Advisor: Guttman, David S
Development of a Gelfoam-based Three-dimensional Culture System to Promote Type II Alveolar Epithelial Cell Maturation for Future Delivery in Cell Therapy

Introduction: Stem cell therapy holds promise for emphysema. However, this approach necessitates robust supplies of type II alveolar epithelial cells (AECIIs). AECII differentiation from induced pluripotent stem cells (iPSCs) presently limits maturation by overlooking matrix topography.Hypothesis: Three-dimensional biomimetic collagen sponges may enhance AECII maturation for in vivo cell delivery. Methods: Lung organoids were generated from iPSCs and differentiated to AECIIs on the Gelfoam. Differentiation status was compared to a standard Matrigel-based system. In a pilot study, Gelfoam delivery was assessed in a developed elastase-induced rat emphysema model. Results: Organoids differentiated into AECIIs on the Gelfoam sponge, with cultures potentially presenting a more mature and stable phenotype than Matrigel cultures. In vivo, Gelfoam composition and delivery technique requires further optimization. Conclusion: The Gelfoam was adapted for the development of a three-dimensional culture system for AECII differentiation, and may potentially serve as lung scaffolds for future cell therapy.

Advisor: Zhang, Haibo