VictorJuiz/thesis huggingface dataset:
A Multilinear (Tensor) Algebraic Framework for Computer Graphics, Computer Vision and Machine Learning

This thesis introduces a multilinear algebraic framework for computer graphics, computer vision, and machine learning, particularly for the fundamental purposes of image synthesis, analysis, and recognition. Natural images result from the multifactor interaction between the imaging process, the scene illumination, and the scene geometry. We assert that a principled mathematical approach to disentangling and explicitly representing these causal factors, which are essential to image formation, is through numerical multilinear algebra, the algebra of higher-order tensors. Our new image modeling framework is based on(i) a multilinear generalization of principal components analysis (PCA), (ii) a novel multilinear generalization of independent components analysis (ICA), and (iii) a multilinear projection for use in recognition that maps images to the multiple causal factor spaces associated with their formation. Multilinear PCA employs a tensor extension of the conventional matrix singular value decomposition (SVD), known as the M-mode SVD, while our multilinear ICA method involves an analogous M-mode ICA algorithm. As applications of our tensor framework, we tackle important problems in computer graphics, computer vision, and pattern recognition; in particular, (i) image-based rendering, specifically introducing the multilinear synthesis of images of textured surfaces under varying view and illumination conditions, a new technique that we call ``TensorTextures'', as well as (ii) the multilinear analysis and recognition of facial images under variable face shape, view, and illumination conditions, a new technique that we call ``TensorFaces''. In developing these applications, we introduce a multilinear image-based rendering algorithm and a multilinear appearance-based recognition algorithm. As a final, non-image-based application of our framework, we consider the analysis, synthesis and recognition of human motion data using multilinear methods, introducing a new technique that we call ``Human Motion Signatures''.

Keywords: multilinear algebra
tensor algebra
computer vision
computer graphics
machine learning
principal component analysis (PCA)
independent component analysis (ICA/BSS)
kernel component analysis (KPCA/KICA)
local linear embedding
multilinear principal component analysis (MPCA)
kernel multilinear independent component analysis (KMICA)
kernel multilinear principal component analysis (KMPCA)
multifactor LLE
M-mode SVD
M-mode PCA
M-mode ICA
multilinear projection
m-mode pseudo-inverse tensor
m-mode identity tensor
m-mode product genearlization
texture synthesis
face recognition
human motion analysis, recogntion and synthesis
human motion signatures
Advisor: Terzopoulos, Demetri
How Does Information Quality Affect Option Returns?

This study analyzes the impact of information quality on option returns. I find that firms with low-quality information have call option returns that are significantly lower than firms with high information quality. The findings hold in- and out-of-sample, over different time periods, and are robust to a battery of asset pricing tests. The results suggest that the risk caused by poor information quality has a powerful and non-diversifiable impact on the expected returns of option contracts. Further analysis shows that these results are important when examining the cross-sectional link between stock returns and information quality. Firms with low information quality and equity that is "option-like" have significantly lower future stock returns than firms with high information quality. If this option-like effect is not controlled for in empirical tests, the association between information quality and the cross-section of stock returns is often flat. This is especially true for accounting-based proxies of information quality.

Keywords: Information Quality
Asset Pricing
Advisor: Callen, Jeffrey
Accuracy of Ontario Health Administrative Databases in Identifying Patients with Rheumatoid Arthritis (RA)

Rheumatoid arthritis (RA) is a chronic, destructive, inflammatory arthritis that places significant burden on the individual and society. This thesis represents the most comprehensive effort to date to determine the accuracy of administrative data for detecting RA patients; and describes the development and validation of an administrative data algorithm to establish a province-wide RA database. Beginning with a systematic review to guide the conduct of this research, two independent, multicentre, retrospective chart abstraction studies were performed amongst two random samples of patients from rheumatology and primary care family physician practices, respectively. While a diagnosis by a rheumatologist remains the gold standard for establishing a RA diagnosis, the high prevalence of RA in rheumatology clinics can falsely elevate positive predictive values. It was therefore important we also perform a validation study in a primary care setting where prevalence of RA would more closely approximate that observed in the general population. The algorithm of [1 hospitalization RA code] OR [3 physician RA diagnosis codes (claims) with ≥1 by a specialist in a 2 year period)] demonstrated a high degree of accuracy in terms of minimizing both the number of false positives (moderately good PPV; 78%) and true negatives (high specificity: 100%). Moreover, this algorithm has excellent sensitivity at capturing contemporary RA patients under active rheumatology care (>96%). Application of this algorithm to Ontario health administrative data to establish the Ontario RA administrative Database (ORAD) identified 97,499 Ontarians with RA as of 2010, yielding a cumulative prevalence of (0.9%). Age/sex-standardized RA prevalence has doubled from 473 per 100,000 in 1996 to 784 per 100,000 in 2010, with approximately 50 new cases of RA emerging per 100,000 Ontarians each year. Our findings will inform future population-based research and will serve to improve arthritis surveillance activities across Canada and abroad.

Keywords: health administrative database
rheumatoid arthritis
Advisor: Bombardier, Claire
Detecting Prominent Patterns of Activity in Social Media

A large part of the Web, today, consists of online platforms that allow their users to generate digital content. They include online social networks, multimedia-sharing websites, blogging platforms, and online discussion boards, to name a few examples. Users of those platforms generate content in the form of digital items (e.g. documents, images, or videos), inspect content generated by others, and, finally, interact with each other (e.g. by commenting on each other's generated items). For the social process of information exchange they enable, such platforms are customarily referred to as `social media'. Activity on social media is largely spontaneous and uncoordinated, but it is not random; users choose the discussions they engage in and who they interact with, and their choices and actions reflect what they find important. In this thesis, we define and quantify notions of importance for items, users, and social connections between users, and, based on those definitions, propose efficient algorithms to detect important instances of social media activity. Our description of the algorithms is accompanied with experimental studies that showcase their performance on real datasets in terms of efficiency and effectiveness.

Keywords: social media
data mining
Advisor: Koudas, Nick
Design and Validation of a Comprehensive Simulation-enhanced Training Curriculum for a Complex Minimally Invasive Operation

Laparoscopic bariatric procedures are complex minimally invasive operations with a potential for substantial morbidity and mortality along the early part of a surgeon’s learning curve. Simulation-enhanced training can improve a surgeon's technical and non-technical performance and lessen the learning curves in the operating room. Unfortunately, despite the convincing evidence supporting the use of simulation in surgical education, there is still a gap in translation of knowledge and technical skills from the research environment into clinically relevant training curricula. The objective of this thesis was to design and validate a comprehensive simulationenhanced training curriculum that addressed cognitive knowledge, technical and non-technical skill in laparoscopic bariatric surgery. This objective was achieved using three experimental studies. The first study employed a modified Delphi methodology and an international panel of experts in surgical and medical education to develop a consensus-based framework for design, validation and implementation of simulation-enahnced training curricula in surgery. The second study used a modified Delphi methodology and an international panel of experienced bariatric surgeons to develop an objective scale for assessment of operative skill in laparoscopic gastric bypass procedure. This scale was feasible to use and had high inter-rater and test-retest reliability, as well as evidence of construct and concurrent validity. The third study used the previously developed consensus-based framework to design a comprehensive simulation-enhanced training curriculum for laparoscopic bariatric surgery. A prospective, single-blinded randomized controlled trial was used to compare the effectiveness of this curriculum in comparison to conventional surgery training. Surgery residents who were trained in this curriculum demonstrated superior technical skills, superior non-technical skills and enhanced safety in the operating room.

Keywords: Surgical education
Simulation-enhanced training
randomized controlled trial
bariatric surgery
Advisor: Grantcharov, Teodor
Discovery of a VEGF-A Responsive lincRNA in Human Endothelial Cells with Disease Relevance and Anti-angiogenic Therapeutic Potential in Glioblastoma Multiforme

Large intergenic RNAs (lincRNA) are involved in numerous cellular processes, including many relevant to normal development and cancer progression. In my doctoral research, we hypothesized that lncRNAs are functionally important to human endothelial biology, more specifically, to the process of human blood vessel formation or angiogenesis. To detect lincRNAs that are functionally important to human angiogenesis, a custom microarray was used to profile long noncoding transcripts in human vascular endothelium in two-dimensional versus three-dimensional pro-angiogenic cultures, with or without VEGF-A165. We identified a VEGF-A-responsive lincRNA near the VEGFR1 gene, which we termed lincRNA-VEGFR1 (LIVE1). Unbiased mRNA microarrays defined a number of potential target genes when LIVE1 was functionally disrupted using RNA interference. Importantly, knockdown and over-expression studies indicated that LIVE1 exerts transcriptional control over VEGFR1 as well as other VEGF receptors and direct angiogenesis in vitro. Furthermore, we found that LIVE1 is highly expressed in glioblastoma, and is enriched in glioma stem cell (GSC) fractions and neoplastic endothelial progenitor populations. In vivo knockdown of LIVE1 in a glioblastoma xenograft model decreased microvascular density, vascular perfusion, pericyte coverage, tumor volume and slowed tumour progression. Our results establish LIVE1 as a key mediator of angiogenesis and demonstrate the potential of lincRNA-based therapeutics.

Keywords: lincRNAs
Glioblastoma
Advisor: Marsden, Philip A.
Characterization of VPS16B, a Novel Protein Involved in Platelet α-granule Biogenesis

Platelets are small, anucleate cells that fulfill a central role in hemostasis through their ability to adhere to sites of vessel injury, where they change shape, secrete molecules, and aggregate to stop blood leakages. Their secretory organelles - alpha (α)-granules, dense (δ)-granules and lysosomes - are critical in mediating the formation of a hemostatic plug, and interference with their biogenesis leads to bleeding disorders. Although several proteins are known to be required for δ-granule development, less is known about α-granule biogenesis. Studies in our laboratory have identified the only proteins known to date to be relevant for α-granule biogenesis: the BEACH protein NBEAL2 and the Sec1/Munc18 protein VPS33B. Mutations in VPS33B have been associated with arthrogryposis, renal dysfunction, and cholestasis (ARC) syndrome. ARC platelets are pale and agranular in appearance, and display a complete absence of α-granule structures and contents. Using a yeast two-hybrid screen, mass spectrometry, co-immunoprecipitation, and bioinformatics studies, VPS16B was identified as a VPS33B-binding protein. Platelets from a patient with ARC syndrome containing mutations in C14orf133 encoding VPS16B recapitulate the phenotype observed in VPS33B-null platelets. Immunofluorescence microscopy of Dami cells stably expressing GFP-VPS16B revealed that similar to VPS33B, GFP-VPS16B co-localized with markers of the trans-Golgi network, late endosomes and α-granules. Depletion of VPS16B in platelet progenitor cells - human iii megakaryocytes - resulted in absent α-granules, though α-granule proteins were still synthesized. Taken together, these data identify VPS16B as a novel molecule required for platelet α-granule biogenesis.

Keywords: platelets
granules
VPS16B
VPS33B
Advisor: Kahr, Walter
Le « vécrire » dans l’œuvre romanesque de Marguerite Andersen

L’intérêt des romans de Marguerite Andersen repose sur les enjeux stratégiques des modalités génériques employées par l’auteure, ainsi que sur les mécanismes exploités par chaque narratrice dans le récit de son parcours identitaire. Nous proposons une approche théorique qui s’inspire de la thématique du « vécrire », néologisme emprunté au roman Salut Galarneau ! de Jacques Godbout. La narratrice du premier roman, De mémoire de femme, emploie le mot « vécrire » en réfléchissant à son projet d’écriture et si la narratrice exprime le même désir que le personnage de Jacques Godbout, celui d’entremêler la vie et l’écriture, il y a encore plus. Chez elle, « vécrire » est intimement lié à l’énonciation de la quête de sens de ses protagonistes féminins, un parcours narratif à visées éthiques et esthétiques. Il s’agit d’un processus complexe qui exige un cadre théorique à trois dimensions, alimenté d’écrits dans plusieurs domaines. La première dimension du cadre théorique porte sur la construction identitaire, la deuxième dimension, sur la dynamique mémorielle et figurative du « vivre » et de l’« écrire » et la troisième dimension, sur la question générique. La thèse comporte un premier chapitre consacré aux enjeux théoriques. Le deuxième analyse De mémoire de femme et sert en quelque sorte de matrice esthétique et didactique, car il révèle les éléments fondamentaux du « vécrire » qui traversent tout le corpus. Les troisième, quatrième et cinquième chapitres portent respectivement sur L’Homme-papier, La soupe et Parallèles. La quête scripturaire de chaque narratrice soulève des questions intéressantes quant à la confusion des sphères du référentiel et de l’imaginaire qui peut s’opérer selon la volonté de l’écrivaine – dans les termes de Jacques Godbout, par le mensonge – ou à d’autres moments, par le mécanisme du refoulement ou le jeu entre la mémoire et l’oubli. Dans la conclusion, nous abordons brièvement deux romans récents de Marguerite Andersen, pour dégager la cohérence de son projet d’écriture. Enfin, notre réflexion portera sur la façon dont ces textes participent au mouvement littéraire francophone, à l’écriture au féminin et à la littérature franco-ontarienne.

Keywords: Ontario
Canadian Literature in French
Identité
Autofiction
Franco-Ontarian Literature
Littérature canadienne en français
Littérature franco-ontarienne
Féminisme
Marguerite Andersen
Roman
Critique
20e et 21e siècle
Advisor: O'Neill-Karch, Mariel
How an Early Medieval Historian Worked: Methodology and Sources in Bede's Narrative of the Gregorian Mission to Kent

This dissertation examines the methods and sources employed by Bede in the construction of his account of the Gregorian mission, thereby providing an insight into how an early medieval historian worked. In Chapter 1, I begin by setting out the context for this study, through a discussion of previous compositional analyses of Bede’s works and the resulting interpretations of the nature and purpose of his library. Chapters 2-4 analyze the sources of the narrative of the Gregorian mission in the Historia ecclesiastica. Each of Bede’s statements is interrogated and its basis established, while the ways in which he used his material to frame the story in the light of his preconceptions and agendas are examined. Chapter 5 collects all the sources identified in the earlier Chapters and organizes them thematically, providing a clearer view of the material Bede was working from. This assessment is then extended in Chapter 6, where I reconstruct, where possible, those ‘lost’ sources used by Bede and consider how the information he used reached him. In this Chapter, I also examine the implications of Bede’s possession of certain ‘archival’ sources for our understanding of early Anglo-Saxon libraries, suggesting more pragmatic purposes for them, beyond those they have usually been credited with. The Chapter ends with an assessment of Bede’s primary sources for the account of the Gregorian mission and an examination of the reasons he possessed so few. Finally, in Chapter 7, I discuss those passages of Bede’s account of the ‘mission fathers’, whose origins were not able to be established in Chapters 2-4. Bede’s use of a set of proto-homiletic sources of a hagiographic nature, dedicated to the early bishops of Canterbury and the mission, emerges. The basic outlines of this collection are set out and the context for their composition described. Throughout, the dissertation is intended not only as end in itself, but as the basis for further investigation both of Bede’s methods and sources, and those of others. In particular, the provision of a more comprehensive awareness of Bede’s resources enables future work to dispense with the narrative Bede has superimposed on his evidence. This thus lays the foundations for re-writing, and not merely re-interpreting, the history of early Christian Kent on a firmer evidential basis than previously possible.

Keywords: Bede
Ecclesiastical History
Advisor: Murray, Alexander
PET Quantification for Assessing Tumour Response

Treatment response assessment in advanced head and neck cancer patients using Positron Emission Tomography (PET) has potential to provide significant clinical benefit. PET quantification methods can be either static or dynamic. The static approach is simple and is widely used. The simplified dynamic PET quantification method is a promising approach as it provides a reasonable trade-off between accuracy and clinical practicality. This method requires a blood sample which makes it not ideal since the PET quantification accuracy may be compromised due to small activity and volume of the blood sample. The implementation of image-based simplified dynamic PET quantification in head and neck cancer patients requires partial volume correction due to small vessel sizes and limitted PET spatial resolution. The objective of this thesis is to evaluate the accuracy of current PET quantification methods for response assessment in advanced head and neck cancer patients and to develop a novel and robust partial volume correction technique to improve PET quantification. First, the static PET quantification method using fixed size ROI is evaluated. Significant variation in response assessment was observed suggesting that static PET quantification using a fixed-size ROI should be approached with caution in heterogeneous tumours. Second, the accuracy of blood activity measurements and its effect on the accuracy of quantitative response assessment is evaluated. Significant inaccuracies in the blood sample based simplified dynamic PET quantification method are identified. The results support a need to develop an image-based simplified dynamic PET quantification method with partial volume correction. Finally, a novel partial volume correction technique was developed, validated, and its robustness was investigated. In comparison to previously published partial volume correction techniques, it performed better with noisy PET images and it was more robust for errors in PET-CT registration. The partial volume correction technique was also implemented and validated in sinogram space to provide additional advantages such as applicability to iterative reconstructions. The proposed partial volume correction technique enables the use of image-based simplified dynamic PET quantification in advanced head and neck cancer patients. Furthermore, the technique establishes a framework for future research to address the inherent low spatial resolution of PET.

Keywords: Medical Imaging
PET
Advisor: Caldwell, Curtis
New Insights into the Regulation of Intestinal Immunity by Nod1 and Nod2

Nod1 and Nod2 are intracellular pattern recognition receptors that detect specific moieties of peptidoglycan, a critical component of the bacterial cell wall, to initiate host innate immune responses. Importantly, mutations in the human NOD2 gene have been associated with increased risk to develop mucosal auto-inflammatory disorders such as Crohn’s Disease. However, how Nod1 and Nod2 mediate mucosal homeostasis still remains unclear. In Chapter 2, I determined that mice deficient for both Nod1 and Nod2 (Nod1-/-Nod2-/-) exhibited delayed induction of intestinal inflammation at early timepoints after infection with Citrobacter rodentium compared to wild-type mice, which correlated with compromised control of the pathogen at later timepoints. Notably, I determined that induction of the cytokines IL-17 and IL-22 in the cecal lamina propria (LP) was blunted in Nod1-/-Nod2-/- mice after infection with either C. rodentium or Salmonella enterica serovar Typhimurium. Importantly, I found that Th17 cells were the principal producers of IL-17 and IL-22 after infection. Due to the rapid kinetics of activation and the regulation by Nod1 and Nod2, I termed this early mucosal response the innate Th17 (iTh17) response. The iTh17 cells exhibited an effector memory phenotype and required priming from the enteric microbiota for full induction. Therefore, in Chapter 3, I next determined that major histocompatibility complex (MHC) class II expression in hematopoietic cells was required for the induction of LP Th17 responses after infection. Interestingly, I found that the percentage IL-17+CD8+ T cells was strongly upregulated when MHCII signaling was ablated, suggesting a dynamic compensatory mechanism of IL-17-producing T cell responses in the mucosa. In Chapter 4, I identified MDP(D-Glu2)-OCH3 as a synthetic Nod2 agonist that exhibited increased stimulatory ability of Nod2-dependent NF-B activation compared to MDP in an unbiased screen. Moreover, I determined that MDP(D-Glu2)-OCH3 induced more potent inflammatory responses both in vitro and in vivo and was a better adjuvant than MDP. Together, the data presented in this thesis expand our current understanding of the roles of Nod1 and Nod2 in the intestinal LP, the regulation of IL-17 producing T cells in the gut and the therapeutic potential of novel Nod2 agonists.

Keywords: Innate Immunity
Th17
Advisor: Girardin, Stephen