VictorJuiz/thesis huggingface dataset:
Error Control for Network Coding
Keywords: network coding
error control
information-theoretic security
rank-metric codes
matrix channels

Network coding has emerged as a new paradigm for communication in networks, allowing packets to be algebraically combined at internal nodes, rather than simply routed or replicated. The very nature of packet-mixing, however, makes the system highly sensitive to error propagation. Classical error correction approaches are therefore insufficient to solve the problem, which calls for novel techniques and insights. The main portion of this work is devoted to the problem of error control assuming an adversarial or worst-case error model. We start by proposing a general coding theory for adversarial channels, whose aim is to characterize the correction capability of a code. We then specialize this theory to the cases of coherent and noncoherent network coding. For coherent network coding, we show that the correction capability is given by the rank metric, while for noncoherent network coding, it is given by a new metric, called the injection metric. For both cases, optimal or near-optimal coding schemes are proposed based on rank-metric codes. In addition, we show how existing decoding algorithms for rank-metric codes can be conveniently adapted to work over a network coding channel. We also present several speed improvements that make these algorithms the fastest known to date. The second part of this work investigates a probabilistic error model. Upper and lower bounds on capacity are obtained for any channel parameters, and asymptotic expressions are provided in the limit of long packet length and/or large field size. A simple coding scheme is presented that achieves capacity in both limiting cases. The scheme has fairly low decoding complexity and a probability of failure that decreases exponentially both in the packet length and in the field size in bits. Extensions of the scheme are provided for several variations of the channel. A final contribution of this work is to apply rank-metric codes to a closely related problem: securing a network coding system against an eavesdropper. We show that the maximum possible rate can be achieved with a coset coding scheme based on rank-metric codes. Unlike previous schemes, our scheme has the distinctive property of being universal: it can be applied on top of any communication network without requiring knowledge of or any modifications on the underlying network code. In addition, the scheme can be easily combined with a rank-metric-based error control scheme to provide both security and reliability.
Utility Indifference Pricing of Credit Instruments
Keywords: utility indifference pricing
credit instruments
risk aversion
model uncertainty
stochastic optimal control

While the market for credit instruments grew continuously in the decade before 2008, its liquidity has dried up significantly in the current crisis, and investors have become aware of the possible consequences of being exposed to credit risk. In this thesis we address these issues by pricing credit instruments using utility indifference pricing, a method that takes into account the investor's personal risk aversion and which is not affected by the lack of liquidity. Through stochastic optimal control methods, we use indifference pricing with exponential utility to determine corporate bond prices and CDS spreads. In the first part we examine how these quantities are affected by risk aversion under different models of default. The emphasis lies on a hybrid model, in which a regime switch of the reference entity is triggered by a creditworthiness index correlated to its stock price. The second part generalizes this setup by introducing uncertainty in the model parameters. Robust optimal control has been used independently in the literature to address model uncertainty for portfolio selection problems. Here, we incorporate this approach with utility indifference and derive some analytical and numerical results on how model uncertainty affects credit spreads.
Machine Learning in Computational Biology: Models of Alternative Splicing
Keywords: Machine Learning
Graphical Models
Computational Biology
Alternative Splicing

Alternative splicing, the process by which a single gene may code for similar but different proteins, is an important process in biology, linked to development, cellular differentiation, genetic diseases, and more. Genome-wide analysis of alternative splicing patterns and regulation has been recently made possible due to new high throughput techniques for monitoring gene expression and genomic sequencing. This thesis introduces two algorithms for alternative splicing analysis based on large microarray and genomic sequence data. The algorithms, based on generative probabilistic models that capture structure and patterns in the data, are used to study global properties of alternative splicing. In the first part of the thesis, a microarray platform for monitoring alternative splicing is introduced. A spatial noise removal algorithm that removes artifacts and improves data fidelity is presented. The GenASAP algorithm (generative model for alternative splicing array platform) models the non-linear process in which targeted molecules bind to a microarray’s probes and is used to predict patterns of alternative splicing. Two versions of GenASAP have been developed. The first uses variational approximation to infer the relative amounts of the targeted molecules, while the second incorporates a more accurate noise and generative model and utilizes Markov chain Monte Carlo (MCMC) sampling. GenASAP, the first method to provide quantitative predictions of alternative splicing patterns on large scale data sets, is shown to generate useful and precise predictions based on independent RT-PCR validation (a slow but more accurate approach to measuring cellular expression patterns). In the second part of the thesis, the results obtained by GenASAP are analysed to reveal jointly regulated genes. The sequences of the genes are examined for potential regulatory factors binding sites using a new motif finding algorithm designed for this purpose. The motif finding algorithm, called GenBITES (generative model for binding sites) uses a fully Bayesian generative model for sequences, and the MCMC approach used for inference in the model includes moves that can efficiently create or delete motifs, and extend or contract the width of existing motifs. GenBITES has been applied to several synthetic and real data sets, and is shown to be highly competitive at a task for which many algorithms already exist. Although developed to analyze alternative splicing data, GenBITES outperforms most reported results on a benchmark data set based on transcription data.
Mediators and Moderators in the Relative Deprivation – Crime/Counter-normative Actions Relationship
Keywords: Relative Deprivation
Crime
Counter-normative actions
mediators
moderators

Researchers have failed to specify when crime and counter-normative actions, as opposed to other responses may occur as a consequence of relative deprivation. To clarify this issue, a mediational model was developed that specified the causal processes leading from the recognition of deprivation to crime and counter-normative actions. This model hypothesizes that the recognition of deprivation (cognitive relative deprivation) leads to feelings associated with this recognition (affective relative deprivation) which in turn leads to crime and counter-normative actions. This model applies to both personal and group deprivation. In both cases, the feelings associated with deprivation include anger, resentment, dissatisfaction, and discontent. Data from a sample of 950 males between the ages of 16 to 30 supported the mediational model. Moderator variables were hypothesized to influence the causal processes in the mediational model, and were thus employed to specify the conditions under which the recognition of deprivation became more likely to lead to intense emotional reactions, and the conditions under which these emotional reactions became more likely to lead to crime and counter-normative actions. Personal deprivation was found to lead to stronger emotional responses if persons were pessimistic about their deprivation being relieved in the future, while at the group level, higher levels of optimism were related to stronger emotional responses. Both types of deprivation also lead to stronger emotional responses when persons believe that financial success and wealth are important. The emotive responses for both personal and group deprivation, in turn, were more likely to lead to crime and counter-normative actions if deprived persons had criminal peers. It was also found that the recognition of personal deprivation was more likely to lead to depression and lower self-esteem if people blamed themselves for their deprivation than if they did not. Persons who were not optimistic that their deprivation would be relieved in the future were more depressed than persons who were optimistic. Persons whose in-group was deprived were more likely to have lower self-esteem if they blamed the in-group for its deprivation than if they did not.
Family Matters: An Examination of the Association between Family Structure and Youth Injury
Keywords: youth injury
family structure

Injury is the leading cause of morbidity and mortality among Canadian youth. In order to develop successful prevention strategies for this major public health problem, it is necessary to determine injury risk factors. Despite reasons to believe that family structure (parents’ marital and living arrangements) may be associated with youth injury, this link has been largely overlooked in injury research. The objectives of this thesis were to determine whether family structure was associated with youth injury in a manner described by theory, after considering alternative explanations for the observed association and to explore how engaging in high risk behaviour mediated the impact of family structure on youth injury. The association was explored using cross-sectional and longitudinal data. This study was based on a representative, cross-sectional World Health Organization, Health Behaviour in School-aged Children (2006) survey of 9, 068 Canadian students, aged 11–15 years, from 186 schools. A sub-sample of 1, 885 Ontario students surveyed in 2006 and again in 2007 comprised the longitudinal sample. The associations were assessed using generalized estimating equations with classroom clusters and Poisson distribution, adjusting for identified potential confounders and examining mediation by high-risk behaviours. There were three main findings: 1) Family structure was associated with medically treated injury in females, after accounting for confounding. Results showed that females from non-intact families had slightly increased risk of any injury than those from intact families (PR=1.11; 95% CI: 1.04-1.19). However, they had a greater risk of non-sports (PR=1.30; 95% CI: 1.16-1.77) and severe, non-sports (PR=1.46; 95% CI: 1.12-1.91) injury. 2) Only a small portion of the association between family structure and injury was explained by engaging in high risk behaviour. 3) There was an inconsistent relationship between family structure and male non-sports injury (Canadian cross-sectional, PR=1.05; 95% CI: 0.94-1.16; Ontario longitudinal, PR=1.58; 95% CI: 1.20-2.07). The findings of this thesis call attention to the importance of non-intact family structures as a risk factor for youth injury. More research is needed to improve our understanding of the mechanisms through which family structure influences youths' risk of injury in order to guide policy development.
Enhancing Social Competence through a Group Intervention Program for Survivors of Childhood Brain Tumours
Keywords: pediatric brain tumours
intervention
social competence

Purpose: To examine the social competence of childhood brain tumour survivors in the context of a group social skills intervention program developed to address documented social deficits among this population and to expand outcomes obtained from a feasibility study, by: conceptualizing social competence as three separate but interrelated constructs including social adjustment, social performance, and social skills; incorporating a control group; eliciting teacher responses; and examining sense of self. Methods: Participants were 23 survivors (10 males; 13 females) aged 7 to 15 years and comprised an intervention (n=15) and control group (n=8). The intervention consisted of 8 2-hour weekly sessions focused on social skills including friendship making. At the level of social adjustment, intervention participants, controls, parents, and teachers (n=6) completed standardized measures of social adjustment including: social skills (SSRS, Gresham & Elliott, 1990); social functioning (Varni, 1999); and social problems (Achenbach, 2001). At the level of social performance, behavioural observations were conducted on intervention participants. At the level of social skills, intervention participants responded to the Social Problem-Solving Measure (SPSM; Vannatta, 1993). Survivors also completed standardized sense of self measures. Results: Outcomes related to social adjustment showed a significant increase from Time 1 to Time 2 for parent reported SSRS within and between groups. Significant improvements were also found for parent reported social problems between groups. Child reported social problems decreased within groups and a borderline effect was found between groups. Teachers reported improved SSRS scores form Time 1 to Time 2. For social performance, significant increases in frequency were found for maintaining facial attention and social conversations with peers over the course of the intervention. At the level of social skills, a borderline significant increase was found for quantity of strategies offered from Time 1 to Time 2. No significant findings were found for sense of self data. Conclusions: Improvements after intervention were noted at each level of social competence, but primarily at the level of social adjustment. Control group and teacher outcomes strengthen findings. This is the first study to explore varying levels of social competence and provides important insight into the source of survivors’ social deficits.
Learning Deep Generative Models
Keywords: computer science
probabilistic graphical models

Building intelligent systems that are capable of extracting high-level representations from high-dimensional sensory data lies at the core of solving many AI related tasks, including object recognition, speech perception, and language understanding. Theoretical and biological arguments strongly suggest that building such systems requires models with deep architectures that involve many layers of nonlinear processing. The aim of the thesis is to demonstrate that deep generative models that contain many layers of latent variables and millions of parameters can be learned efficiently, and that the learned high-level feature representations can be successfully applied in a wide spectrum of application domains, including visual object recognition, information retrieval, and classification and regression tasks. In addition, similar methods can be used for nonlinear dimensionality reduction.
The Significance of Choice in the Late Dorset Technology of Domestic Architecture
Keywords: Late Dorset
Domestic Architecture
Technology
Chaîne Opératoire
Palaeoeskimo
Arctic

This dissertation investigates the domestic architecture produced by the Late Dorset, an Arctic-adapted hunter-gatherer society which occupied much of the Eastern North American Arctic between circa 1500 B.P. and 500 B.P. Architecture, like any artefact class, is a dynamic and socially constructed technology that is produced, maintained, and transmitted by its practitioners. It is replicated via series of learned actions or techniques; patterns accordingly result from adherence to cultural standards while differences represent instances of technological divergence. Such departures are typically ignored or suppressed in closed systems, although they can be tolerated or even widely adopted in more flexible ones. In order to identify and explore patterning, a methodological strategy using the chaîne opératoire is adopted. This approach is invaluable because, when properly implemented, it links the static archaeological record with the dynamic architect-agents whose meaning-laden technical acts are visible archaeologically. Viewed through the lens of chaîne opératoire, I examine domestic architecture as a conduit for informing on Late Dorset structure and social organisation. As part of this investigation, a multi-scalar research design was implemented. The first analytical scale examined architecture across the Eastern Arctic to determine regional patterns of behavioural variability. Large-scale behavioural trends were recognised and demonstrated the range of behaviours enacted by Dorset architects as they designed, reproduced, and altered dwellings. The second stage of analysis focused on the micro-scale analysis of dwellings from three locations, each presented as fully contextualised case studies. Analysis at this level allowed for the investigation of how idiosyncratic behaviours and localised knowledge (reflecting an agent’s awareness of local conditions) was manifested and ‘fit’ within the overall technology. This strategy, which combined structure-specific analysis with purposefully broad regional patterning, suggests that Late Dorset architectural technology was comparatively open and flexible and that architects could adapt technological practise to suit local conditions and housing needs. This flexibility contrasts with other aspects of Late Dorset culture that appear more constrained and standardised.
'Forms Liberate': Reclaiming the Legal Philosophy of Lon L. Fuller
Keywords: legal philosophy
Lon Fuller

This thesis offers a reading of the legal philosophy of the mid-twentieth century legal scholar, Lon L. Fuller. By illuminating how Fuller’s vision of law gravitates constantly to the relationship between the form of law and the status of the legal subject as an agent, this reading provides a basis for revisiting the issues in dispute in his famous exchanges with the legal positivist philosopher, H.L.A. Hart. The thesis as a whole seeks to meet two main objectives. First, I seek to demonstrate how Fuller’s persistent concern for the way that the form of law instantiates respect for the legal subject lends his legal philosophy a coherence that has been insufficiently appreciated to this point. Second, I seek to elaborate the claim that once we appreciate the centrality of the relationship between legal form and agency to Fuller’s thought, we come to understand why he insisted that law can and should be distinguished from other modes of ordering, and why it must also be regarded as distinctively moral.
Temporal Changes in Reproduction, Competition, and Predation after Establishment of Introduced Populations of the greater European Pine Shoot Beetle, Tomicus Piniperda (L.) (Coleoptera: Curculionidae, Scolytinae)
Keywords: Tomicus piniperda
invasion ecology
forest entomology
scolytids

The establishment of exotic species in novel environments is a major environmental concern, however, few long-term studies have examined the effects of these species on their host environment and community, especially in forest ecosystems. The arrival and subsequent spread of the greater European pine shoot beetle, Tomicus piniperda (L.) (Coleoptera: Curculionidae, Scolytinae), into southern Ontario pine forests provided a natural experiment to assess biotic interactions between an exotic species and its new community over several years. Reproductive success of Tomicus piniperda colonies of various ages was studied between 2001 and 2004. The size and composition of competitor and natural enemy complexes present in these communities were also quantified over time. The impact of the natural enemy complexes on T. piniperda reproduction was assessed, Brood production (no. eggs and galleries/female) by T. piniperda populations rapidly approached those reported from its native range in Europe, with lower densities of parental adults. Thus, reproduction remained consistently above the replacement level for this beetle over all four years of study suggesting that these recently-introduced populations were growing rapidly and at a greater rate than in their country of origin. Tomicus piniperda successfully integrated into a large bark beetle community, and appeared to be capable of displacing native beetles to more marginal bark habitats, however, these competitors were not eliminated during the course of the study. The long-term effect of this marginalization on populations of native beetles is uncertain. Tomicus piniperda rapidly acquired natural enemies in the introduced areas, however, natural enemy-caused mortality did not show a regulating effect on its populations. It seems that intraspecific competition, rather than predation, regulates T. piniperda populations following introduction. The implications of these findings for the establishment and spread of exotic species in forest systems are examined, especially with reference to a prominent theory for success, the Enemy Release Hypothesis. In short, the Enemy Release Hypothesis is not applicable to an exotic species that is not regulated by natural enemies in its native range, and assessments of the Enemy Release Hypothesis should always include a determination of enemy regulation of the exotic in its native range.
Quantum Theory of Phonon-mediated Decoherence and Relaxation of Two-level Systems in a Structured Electromagnetic Reservoir
Keywords: Photonic Crystal
Quantum Dot

In this thesis we study the role of nonradiative degrees of freedom on quantum optical properties of mesoscopic quantum dots placed in the structured electromagnetic reservoir of a photonic crystal. We derive a quantum theory of the role of acoustic and optical phonons in modifying the optical absorption lineshape, polarization dynamics, and population dynamics of a two-level atom (quantum dot) in the ``colored" electromagnetic vacuum of a photonic band gap (PBG) material. This is based on a microscopic Hamiltonian describing both radiative and vibrational processes quantum mechanically. Phonon sidebands in an ordinary electromagnetic reservoir are recaptured in a simple model of optical phonons using a mean-field factorization of the atomic and lattice displacement operators. Our formalism is then used to treat the non-Markovian dynamics of the same system within the structured electromagnetic density of states of a photonic crystal. We elucidate the extent to which phonon-assisted decay limits the lifetime of a single photon-atom bound state and derive the modified spontaneous emission dynamics due to coupling to various phonon baths. We demonstrate that coherent interaction with undamped phonons can lead to enhanced lifetime of a photon-atom bound state in a PBG by (i) dephasing and reducing the transition electric dipole moment of the atom and (ii) reducing the quantum mechanical overlap of the state vectors of the excited and ground state (polaronic shift). This results in reduction of the steady-state atomic polarization but an increase in the fractionalized upper state population in the photon-atom bound state. We demonstrate, on the other hand, that the lifetime of the photon-atom bound state in a PBG is limited by the lifetime of phonons due to lattice anharmonicities (break-up of phonons into lower energy phonons) and purely nonradiative decay. We demonstrate how these additional damping effects limit the extent of the polaronic (Franck-Condon) shift of the atomic excited state. We also derive the modified polarization decay and dephasing rates in the presence of such damping. This leads to a microscopic, quantum theory of the optical absorption lineshapes. Our model and formalism provide a starting point for describing dephasing and relaxation in the presence of external coherent fields and multiple quantum dot interactions in electromagnetic reservoirs with radiative memory effects.