VictorJuiz/thesis huggingface dataset:
Missing Data Problems in Machine Learning

Learning, inference, and prediction in the presence of missing data are pervasive problems in machine learning and statistical data analysis. This thesis focuses on the problems of collaborative prediction with non-random missing data and classification with missing features. We begin by presenting and elaborating on the theory of missing data due to Little and Rubin. We place a particular emphasis on the missing at random assumption in the multivariate setting with arbitrary patterns of missing data. We derive inference and prediction methods in the presence of random missing data for a variety of probabilistic models including finite mixture models, Dirichlet process mixture models, and factor analysis. Based on this foundation, we develop several novel models and inference procedures for both the collaborative prediction problem and the problem of classification with missing features. We develop models and methods for collaborative prediction with non-random missing data by combining standard models for complete data with models of the missing data process. Using a novel recommender system data set and experimental protocol, we show that each proposed method achieves a substantial increase in rating prediction performance compared to models that assume missing ratings are missing at random. We describe several strategies for classification with missing features including the use of generative classifiers, and the combination of standard discriminative classifiers with single imputation, multiple imputation, classification in subspaces, and an approach based on modifying the classifier input representation to include response indicators. Results on real and synthetic data sets show that in some cases performance gains over baseline methods can be achieved by methods that do not learn a detailed model of the feature space.

Keywords: Computer Science
Artificial Intelligence
Machine Learning
Missing Data
Advisor: Zemel, Richard S.
TCDD Disrupts Gene Expression in the Developing Mouse Kidney

Dioxins such as the potent 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) are persistent environmental contaminants, exposure to which results in a number of toxic effects in several species. In mice, TCDD-induced hydronephrosis of the kidney is among the most sensitive of developmental abnormalities. It is widely accepted that the toxic effects of dioxins such as TCDD are mediated by the aryl hydrocarbon receptor (AHR), a ligand-activated transcription factor expressed in virtually all tissues. Though it is known that activation of the AHR during development is likely the first step in TCDD-induced hydronephrosis, genetic events occurring downstream of AHR activation remain to be elucidated. To this end, we investigated the effect of TCDD on gene expression during development of the mouse kidney through use of expression arrays. Our analysis indicates that TCDD alters the expression of genes involved in the developmentally-critical Wnt signaling pathway and genes involved in cell cycle and cell proliferation. Further investigation of the effect of TCDD on Wnt pathway gene expression using an mRNA expression time course and in situ hybridization to characterize localized mRNA changes suggests that TCDD inhibits canonical Wnt signaling in the developing kidney. Consistent with our expression array finding that TCDD downregulates genes involved in cell proliferation, we also report a decrease in cell proliferation that coincides with regions of the kidney where inhibitors of canonical Wnt signaling are induced in response to TCDD. TCDD-induced disruption of Wnt pathway gene expression is not limited to the kidney, and alteration of Wnt gene expression is tissue-specific with varying effects observed in the heart, lung, liver, skin, and brain. Preliminary evidence also indicates that exposure to TCDD during development can alter the expression of microRNAs predicted to target Wnt pathway genes, suggesting a new mechanism for TCDD-induced disruption of gene expression. Taken together, our findings suggest that TCDD may disrupt an important pathway that is critical to the normal development of several organs in numerous species.

Keywords: TCDD
Dioxin
Advisor: Grant, Denis M.
Harper, Patricia
Combinatorial Auctions for Truckload Transportation Procurement

The goal of this dissertation is to understand the market-based mechanisms that enable shippers to allocate lanes in an efficient way for truckload (TL) transportation procurement despite the self-interest of carriers. To understand the market-based mechanisms, we focus on proposing some novel models and mechanisms to enhance the use of combinatorial auction for TL transportation procurement. In this dissertation, our approach to gaining the understanding consists of three parts: 1. We develop a carrier optimal bid generation model for carriers (bidders) to discover the best sets of lanes to bid for at a given round. The optimal bid generation model simultaneously generates alternative tours and selects the most profitable package bid for the carrier under a myopic strategy, which has never been considered before. The simultaneous tour generation and selection significantly lessen the computational complexities of a carrier's optimization problem since it is unnecessary for the carrier to calculate the values for all possible packages. 2. We present an iterative combinatorial auction design that integrates the optimization problems for both the shipper and the bidders where the approximate dual prices derived from the result of a winner determination solution are used by the bidders in identifying profitable lanes. The auctions also allow the bidders to submit exclusive-OR (XOR) bids and are able to deal with some common business considerations. The extension of the concept of active bids enables this mechanism to effectively mitigate the exposure problem, the threshold problem, and the free-riding problem. Furthermore, both the shippers and the carriers are better off compared to multi-round auctions that do not integrate the shippers' and carriers' optimizations. 3. We extend a deterministic winner determination model to a two-stage stochastic winner determination model for TL transportation procurement under shipment volume uncertainty. We demonstrate that the value of the stochastic solution is always at least as good as one obtained by a deterministic model based on using expected shipment volumes. The sWDP model is to the best of our knowledge the first winner determination formulation of any kind that explicitly incorporates demand uncertainty.

Keywords: Combinatorial auctions
Truckload transportation
Procurement
Advisor: Kwon, Roy H.
Lee, Chi-Guhn
Age Differences in Recollection: The Roles of Support and Demand

Six experiments were conducted to examine the factors modulating the size of age differences in recollection. The research presented in the current thesis was guided by the notions of self-initiated processing and environmental support. Older and younger adults’ performance in recollection was measured by Jacoby’s (1990) process dissociation procedure (PDP); the age differences as a function of self-initiated processing demands of the task and the amount of support provided to the participants were assessed by manipulating the encoding (Experiments 2.1, 2.2, and 2.3) and retrieval (Experiments 3.1, 3.2, and 3.3) contexts. Experiments 2.1, 2.2, and 2.3 examined interactions of aging and encoding contexts. Recollection under baseline conditions (i.e. visually presented words) was contrasted with recollection of items encoded under contexts that are assumed to enhance memory. The results showed differential age-related patterns of benefits from encoding conditions: Presenting pictures with words benefited older adults more than younger adults; word generation benefited both groups equally; and presenting sound effects with visual words benefited younger more than older adults. Experiments 3.1, 3.2, and 3.3 investigated age-related changes in retrieval processes and their interactions with retrieval contexts. In each of the three experiments, some of the test lists were constructed so that participants had to recollect specific aspects of the encoding event to differentiate between the to-be-included and to-be-excluded items, whereas other test lists were constructed so that they only had to recollect general aspects. Older adults showed reduced levels of recollection than younger adults for the high-specificity test lists only (Experiment 3.1). Encoding manipulations improved (Experiment 3.2) or reduced (Experiment 3.3) recollection performance but the effects did not interact with test, whereas DA at retrieval (Experiment 3.3) in younger adults partly mimicked aging. In summary, the six experiments showed that older adults have greater difficulties in spontaneously carrying out distinctive and integrative processes at encoding, and in accessing specific information at retrieval compared to their younger counterparts. These age-related changes further interact with the processing demanded or afforded by the encoding and retrieval conditions.

Keywords: human memory
aging
controlled processes
context
Advisor: Craik, Fergus I. M.
Identification of Host and Parasite Factors Mediating the Pathogenesis of Severe and Cerebral Malaria

Severe manifestations of malaria, including cerebral malaria (CM) and respiratory distress, result in approximately three million deaths annually worldwide. Currently, relatively little is known about severe disease pathogenesis. The development and outcome of severe malaria is determined by host-pathogen interactions, a complex interface of genetics and immune responses. Hypothetically, a spectrum of genetic susceptibility and resistance to severe disease exists within the host population, and malaria infection results in diverse host and parasite responses that impact disease outcome. The aim of this study was to identify differential host and parasite responses in a murine model of severe malaria, Plasmodium berghei ANKA (PbA), in CM-susceptible and CM-resistant mice; and to analyze host genetics in patients with severe disease due to Plasmodium falciparum. In vivo, expression microarray analysis showed that, in malaria target organs, differential responses were related to immune response – primarily interferon and complement pathways – and apoptosis. Histopathological examination of the brain confirmed an increased prevalence of apoptosis in CM-susceptible mice. Further examination of the role of complement in CM-susceptibility determined that early complement 5 (C5) activation conferred susceptibility to CM, and that C5 deficiency conferred resistance, which could be recapitulated by antibody blockade of activated C5 or its receptor in susceptible mice. Additionally, single nucleotide polymorphism (SNP) studies identified that complement receptor 1 SNPs were associated with disease severity in patients with P. falciparum malaria. PbA parasites displayed a unique transcriptional signature in each tissue examined (brain, liver, spleen and lung), showed differential gene expression between CM-resistant and susceptible hosts, and were most prominent in lung tissue. Closer examination of lung involvement in PbA infection revealed that PbA-infected C57BL/6 mice develop acute lung injury (ALI), defined by disruption of the alveolar-capillary membrane barrier. ALI susceptibility did not correlate with CM susceptibility, but was influenced by peripheral parasite burden and CD36-mediated parasite sequestration in the lung. PbA provides a clinically relevant experimental model for CM and ALI, through which important disease mechanisms can be identified and modulated. Ideally, the use of such models aids in the discovery of disease biomarkers and novel therapeutic strategies, which may be applied to human severe and cerebral malaria.

Keywords: cerebral malaria
microarray
plasmodium falciparum
plasmodium berghei ANKA
severe malaria
acute lung injury
Advisor: Kain, Kevin C.
The "Problem" of Immigration and Contemporary Spanish Detective Fiction

“The Problem of Immigration and Contemporary Spanish Detective Fiction” examines the viability of the detective genre as a forum to dispute the commonly held perception of contemporary immigration to Spain as a problem. Focusing first on popular series of the Transition and Disenchantment periods that followed the death of Francisco Franco, I identify the detective novel, and in particular the hard-boiled variety on which the Spanish tradition is based, as an ideal space for discussions of otherness. In the 1990s, as large-scale immigration to Spain became an increasing reality, North Africans, Latin Americans, and Eastern Europeans joined minority groups already marginalised within Spain and became the focus of well-known authors such as Jorge Martínez Reverte, Arturo Pérez-Reverte, and Andreu Martín and relative newcomers Yolanda Soler Onís, José Javier Abasolo, Lorenzo Silva, and Antonio Lozano. All use the conventions of the detective genre––suspense, pursuit, intrigue––to address misconceptions about immigration and to reveal that the ultimate culprits in these stories are ill-willed traffickers, corrupt security agencies, and the widespread apathy of parts of the Spanish population and its government. Through the twists and turns of their storylines, these politically committed authors show that while immigrants may be forced to inhabit Spain’s underbelly, they are not single-handedly responsible for Spanish society’s perceived demise. My dissertation is informed by a multi-disciplinary approach that draws on media, cultural, socio-anthropological, and postcolonial studies. The connection between crime literature and the mass media is especially intriguing given the latter’s power of influence over the conceptualisation of immigration. The detective texts juxtapose the media of the post-modern electronic information age, which is by definition frontier-less, with a nation designing ever-stronger borders. While analysing the various borders that divide a national and global society in the entangled tale of immigration to Spain, and the discursive roles they play within the codified genre of crime fiction, I argue that these authors use the conventions of their medium to provide internal views of the process of immigration as an alternative to the voyeuristic daily reporting that otherwise threatens to desensitise the Spanish public to the topic altogether.

Keywords: Novela Negra
Immigration
Spanish Detective Fiction
Immigration in Spanish Mass Media
Novela Detectivesca
Arturo Pérez-Reverte
Juan Madrid
Manuel Quinto
Jorge Martínez Reverte
Yolanda Soler Onís
Lorenzo Silva
Antonio Lozano
José Javier Abasolo
Andreu Martín
Advisor: Davidson, Robert A.
The Labour Supply of Unpaid Caregivers in Canada

The Labour Supply of Unpaid Caregivers in Canada, Doctor of Philosophy (PhD), Meredith Lenore Lilly, Department of Health Policy, Management and Evaluation, University of Toronto, 2008. As medical care increasingly shifts from the hospital to the home, responsibility for care has also shifted from the state and paid care, to the family and unpaid care. Unpaid caregivers are family members and friends who provide homecare services to recipients in their place of residence without financial compensation, as a result of their close personal relationships. This research tests the multiple hypotheses that unpaid caregiving has an impact on (1) the probability of labour force participation (LFP); (2) hours of labour force work; and (3) earnings by caregivers in Canada. We analyzed the 1996 and 2002 General Social Surveys, applying multivariate probit, logistic, and OLS regression analyses to four equations: 1) the probability of labour force participation; 2) the hourly wage; 3) weekly hours of labour market work; and 4) the probability of being an unpaid caregiver. Results indicate that unpaid caregiving was negatively associated with labour force participation; however, the impact on hours of labour market work and wages was uncertain. Women and men caregivers were impacted differently: only caregiving men in 1996 had significantly lower wages than non-caregivers, and only women in 1996 worked significantly fewer hours in the labour market. When caregiving was defined broadly, only men in 1996 were significantly less likely to be employed than non-caregivers. Yet when we controlled for caregiving intensity in 2002, both male and female primary caregivers were much less likely to be in the labour force than non-caregivers, while secondary caregivers were no less likely to be employed than non-caregivers. We conclude that when caregiving responsibilities are relatively small, individuals seem able to balance both caregiving with employment. Yet when caregiving commitments become heavy, it becomes increasingly difficult to balance employment with caregiving. We make a number of policy recommendations ranging from improving caregiver access to financial supports, formal care and respite services, particularly for primary caregivers. We also encourage the development of workplace legislation and caregiver friendly workplaces for the majority of caregivers who remain in the labour market.

Keywords: home care
unpaid caregivers
health services research
labour force participation
regression
secondary data analysis
General Social Survey
Canada
labour supply
wages
hours of work
informal caregiving
health policy
systematic review
work life balance
family policy
gender
primary caregivers
Advisor: Coyte, Peter C.
The F-box protein FSN-1 Functions in an SCF-like Ubiquitin Ligase Complex to Regulate Synapse Formation

The chemical synapse is an asymmetric structure consisting of presynaptic and postsynaptic terminals in direct apposition to each other. Synapses function to mediate the transmission of signals between neurons and their targets. The formation of synapses is a tightly regulated process requiring the interaction of many genes and molecular pathways. I am interested in identifying genes and signaling pathways that are required for proper synapse formation. Using the GABAergic neuromuscular junctions of C. elegans as a model system, I have identified fsn-1 (F-box synaptic protein), a gene required for the control of synaptic growth. fsn-1 mutants exhibit a synaptic defect characterized by both synaptic over differentiation and under differentiation. FSN-1 is an F-box protein with a SPRY (SPla and RYanodine receptor) domain that functions cell-autonomously in neurons to regulate synaptic growth. I have shown that it functions in an E3 ubiquitin ligase-like complex with the RING-H2 finger protein RPM-1 (Regulator of presynaptic morphology), SKR-1 and Cullin. The composition of this complex is similar to SCF (Skp1, Cullin, F-box) E3 ubiquitin ligases. We hypothesize that this complex controls synapse formation by down regulating synapse promoting factors through an ubiquitin mediated process. We have identified two receptor tyrosine kinases that genetically interact with fsn-1, the Anaplastic Lymphoma Kinase homolog SCD-2 (Suppressor of Constitutive Dauer) and the C. elegans insulin receptor DAF-2 (abnormal DAuer Formation). Loss of function mutations in scd-2 or daf-2 partially suppress the synaptic differentiation defects of fsn-1 mutants, suggesting that they participate in signaling pathways whose activities are normally inhibited by FSN-1 during synapse formation. Unlike FSN-1 that functions in GABAergic neurons, I found that SCD-2 and DAF-2 have cell non-autonomous functions at GABAergic neuromuscular junctions. SCD-2 is required in the nervous system in the RID interneuron where it could modulate synapse formation through ligands present on the motoneuron cell surface. The DAF-2/insulin pathway functions in postsynaptic muscle cells to regulate FSN-1 dependent presynaptic growth likely through a retrograde or feedback mechanism. I propose a model where FSN-1 regulates synapse formation by attenuating signals that converge upon the presynaptic terminal to stimulate or inhibit synaptic growth.

Keywords: 0369
0306
Advisor: Zhen, Mei
Development of an On-line Planning and Delivery Technique for Radiotherapy of Spinal Metastases

The objective of this work is to develop an on-line planning and delivery technique for palliative radiotherapy of spinal metastases using a linear accelerator capable of cone-beam CT (CBCT) imaging. This technique integrates all preparation and delivery steps into a single session equivalent to an initial treatment session. The key technical challenges pertaining to the development and implementation of this novel treatment technique are related to CBCT image performance, efficient system integration, development of on-line planning tools and design of novel quality assurance (QA) phantoms and processes. Hardware and software image corrections were first implemented to make CBCT images suitable for target definition and planning. These corrections reduced CBCT non-uniformity and improved CBCT-number accuracy. The on-line treatment technique workflow and the integration of all the subsystems involved in the process were assessed on a customized spine phantom constructed for the study. The challenges related to the routine QA of the highly integrated on-line treatment technique were addressed with the construction and validation of an integral test phantom. This phantom, which contains point detectors (diodes) allows for real-time QA of the entire image guidance, planning and treatment process in terms of dose delivery accuracy. The integral test phantom was also effective for the QA of high-dose, high-precision spinal radiosurgery. Simulation of the on-line treatment technique on patient data showed that the planning step was the one of the most time consuming tasks due predominantly to manual target definition. A semi-automatic method for detection and identification of vertebrae on CBCT images was developed and validated to streamline vertebra segmentation and improve the on-line treatment efficiency. With a single patient setup at the treatment unit, patient motion during the on-line process represents the main source of geometric uncertainty for dose delivery. Spine intra-fraction motion was assessed on CBCT for a group of 49 patients treated with a palliative intent. The use of surface marker tracking as a surrogate for spine motion was also evaluated. Finally, the complete on-line planning and delivery technique was implemented in a research ethics board (REB) approved clinical study at the Princess Margaret Hospital and 7 patients have been successfully treated at the time of this report with this novel treatment approach.

Keywords: Bone metastases
Radiation oncology
Cone-beam CT imaging
Image processing
Dosimetry
Inftra-fraction motion
Advisor: Jaffray, David A.