VictorJuiz/thesis huggingface dataset:
Collapsed variational inference for computational linguistics

Bayesian modelling is a natural fit for tasks in computational linguistics, since it can provide interpretable structures, useful prior controls, and coherent management of uncertainty. However, exact Bayesian inference is intractable for many models of practical interest. Developing both accurate and efficient approximate Bayesian inference algorithms remains a fundamental challenge, especially for the field of computational linguistics where datasets are large and growing and models consist of complex latent structures.
Collapsed variational inference (CVI) is an important milestone that combines the efficiency of variational inference (VI) and the accuracy of Markov chain Monte Carlo (MCMC) (Teh et al., 2006). However, its previous applications were limited to bag-of-words models whose hidden variables are conditionally independent given the parameters, whereas in computational linguistics, the hidden variable dependencies are crucial for modelling the underlying syntactic and semantic relations. To enlarge the application domain of CVI as well as to address the above Bayesian inference challenge, we investigate the applications of collapsed variational inference to computational linguistics.
In this thesis, our contributions are three-fold. First, we solve a number of inference challenges arising from the hidden variable dependencies and derive a set of new CVI algorithms for the two ubiquitous and foundational models in computational linguistics, namely hidden Markov models (HMMs) and probabilistic context free grammars. We also propose CVI for hierarchical Dirichlet process (HDP) HMMs that are Bayesian nonparametric extensions of HMMs.
Second, along the way we propose a set of novel algorithmic techniques, which are generally applicable to a wide variety of probabilistic graphical models in the conjugate exponential family and computational linguistic models using non-conjugate HDP constructions. Therefore, our work represents one step in bridging the gap between increasingly richer Bayesian models in computational linguistics and recent advances in approximate Bayesian inference.
Third, we empirically evaluate our proposed CVI algorithms and their stochastic versions in a range of computational linguistic tasks, such as part-of-speech induction, grammar induction and many others. Experimental results consistently demonstrate that, using our techniques for handling the hidden variable dependencies, the empirical advantages of both VI and MCMC can be combined in a much larger domain of CVI applications.

Advisor: Blunsom, P
What is the role of self-monitoring blood pressure in the management of hypertension?

Patient self-monitoring of blood pressure (SMBP) has shown promise in contributing towards improving ongoing management of hypertension, however it has yet to be fully integrated into guidelines or routine general practice in the UK.
The aims of this thesis were to investigate the role of SMBP in the management of hypertension to better understand: patient and clinician attitudes to SMBP; what behaviour change SMBP targets in patients to bring about better BP outcomes; to what extent SMBP is utilised as part of routine hypertension management in the UK; and to understand patient preferences for hypertension management in light of effective models of care.
A mixed methods approach was used including: systematic reviews of qualitative and quantitative evidence; semi-structured interviews with patients; a cross sectional survey; and a discrete choice experiment.
Self-monitoring was associated with better medication adherence, which could have significant impact at a population level given the high proportion of non-adherent hypertensive patients.
Use of SMBP should be seen as a continuum from being used solely to inform clinical decisions, through facilitating interaction between patients and clinicians, to empowering patients to be autonomous for example in self-management.
SMBP was most effective when patients had the knowledge and skills to make improvements in their lifestyle, and this has been shown in clinical trials and through qualitative investigation.
Clinicians recognise the potential benefits of SMBP, but are concerned that patients may become burdened. Clinicians should feel encouraged that patients are supportive of self-monitoring, but they must ensure that patients who wish to self-manage are equipped with the skills to do so. Lack of facility to make positive change may lead some patients to feeling disempowered and clinicians need to be cognisant of this fact.

Keywords: Self-monitoring
Advisor: McManus, R
Hinton, L
Rivero-Arias, O
The algebra of open and interconnected systems

Herein we develop category-theoretic tools for understanding network-style diagrammatic languages. The archetypal network-style diagrammatic language is that of electric circuits; other examples include signal flow graphs, Markov processes, automata, Petri nets, chemical reaction networks, and so on. The key feature is that the language is comprised of a number of components with multiple (input/output) terminals, each possibly labelled with some type, that may then be connected together along these terminals to form a larger network. The components form hyperedges between labelled vertices, and so a diagram in this language forms a hypergraph. We formalise the compositional structure by introducing the notion of a hypergraph category. Network-style diagrammatic languages and their semantics thus form hypergraph categories, and semantic interpretation gives a hypergraph functor.
The first part of this thesis develops the theory of hypergraph categories. In particular, we introduce the tools of decorated cospans and corelations. Decorated cospans allow straightforward construction of hypergraph categories from diagrammatic languages: the inputs, outputs, and their composition are modelled by the cospans, while the 'decorations' specify the components themselves. Not all hypergraph categories can be constructed, however, through decorated cospans. Decorated corelations are a more powerful version that permits construction of all hypergraph categories and hypergraph functors. These are often useful for constructing the semantic categories of diagrammatic languages and functors from diagrams to the semantics. To illustrate these principles, the second part of this thesis details applications to linear time-invariant dynamical systems and passive linear networks.

Advisor: Coecke, B
'Ludic passage': abstraction in post-war British literature 1945-1980

This thesis traces a line of literary experimentation in post-war British literature that was prompted by the aesthetic, philosophical and theoretical demands of abstraction. Spanning the period 1945 to 1980, it observes the ways in which certain aesthetic advancements initiated new forms of literary expression to posit a new genealogy of interdisciplinary practice in Britain. It is the first sustained chronological study to consider the ways in which a select number of British poets, authors and critics challenged the received views of their post-war moment in the discovery of the imaginative and idealizing potential of abstraction. At a time in which Britain became conscious of its evolving identity within an increasingly globalised context, this study accounts for the range of Continental and Transatlantic influences in order to more accurately locate the networks at play. Exploring the contributions made by individuals, such as Herbert Read, Ian Hamilton Finlay and Christine Brooke-Rose, as well as by groups of practitioners, such as the British concrete poetry movement, small press initiatives and Art & Language, this thesis offers a comprehensive account of the evolving status of abstraction across cultural, institutional and literary contexts. The discussions build a vision of an era that increasingly jettisons the predetermined critical lexicon of abstraction to generate works of a more pragmatic abstract inspiration: the spatial demands of concrete poetry, language as medium in the conceptual artwork, the absence of linear plot in the new novel.

Keywords: post-war
abstraction
literature
1945-1980
british
abstract
Advisor: Beasley, R
The dynamics of prenatal sex selection and excess female child mortality in contexts with son preference

This thesis examines demographic manifestations of son preference in three parts.Part I develops a simulation model that formalises the decision to practice prenatal sex selection through a "ready, willing and able" framework. The model is calibrated to South Korean and Indian sex ratio at birth (SRB) trajectories. Simulations reveal how SRB distortions in both countries have emerged despite declining son preference due to the rapid diusion of ultrasound combined with growing propensities to abort as a result of weakening norms for large families. Part II examines the potential role of big data to indirectly estimate the SRB at the subnational level in India. States with distorted SRBs tend to display a relatively high Google search activity for ultrasound. SRB "now-casts" generated using search volumes perform better than lagged variable models in high birth registration states. Part III examines the relationship between prenatal sex selection and postnatal excess female child mortality in two studies. The first applies lifetable techniques to decompose population changes in child sex ratios into a fertility component attributable to prenatal sex selection and a mortality component attributable to sex-differentials in postnatal survival. This study finds that although reductions in numbers of excess female deaths have accompanied increases in "missing" female births in all countries experiencing SRB distortions, excess female mortality has persisted in some but not in others. The second study uses birth histories of the Demographic and Health Surveys for six countries that have witnessed SRB distortions - India, Nepal, Pakistan, Azerbaijan, Armenia and Albania - to examine if differential mortality change by sex can be explained by the uptake of prenatal sex selection. This study finds that changes in prenatal sex selection only explain mortality change in India. Across all countries, although patterns of mortality disadvantage are concentrated amongst less educated mothers, prenatal sex selection is strongest among the better educated. Differential sorting into the two behaviours offers an explanation for why the effect for prenatal sex selection is generally weak.

Keywords: Son Preference
Missing women
Sex Ratios at Birth
Mortality
Sex Selection
Fertility
Excess female mortality
Asia
Advisor: Billari, F
Ancient history in British universities and public life 1715-1810

Over the eighteenth century, ancient history was increasingly read in English, appearing in new forms and interpretations. This reflected the development of history in universities as a subject not merely read, but taught. This teaching took on many forms: serving as a predecessor to other studies, building a knowledge base of case studies for 'higher' subjects, or (increasingly) an independent subject.
What ancient history was taught, how was it taught, why was it taught, and what did students go on to use it for? Ancient history as an independent subject had a limited role in the curriculum despite the foundation of Chairs of History in most universities. When it was taught as such, the focus was on explaining modern institutions via ancient comparisons; on the training of statesmen by classical examples; or, more rarely, on demonstrating a particular conception of social development. These uses of history could be seen across both national and subject boundaries. Whilst differences between universities are evident, evidence in the teaching of history suggests the absolute dichotomy between the English and Scottish systems has been overstated. The interesting case of Trinity College Dublin suggests common features across Britain in how “liberal education” was conceived of and how history fit into it.
The practical application of ancient history to the education of statesmen may be seen in the variety of ways it was used in political discourse. This is explored mainly in Parliament, the ultimate destination of the "statesmen" in whose training history was supposed to play a large part, via debates over questions of empire and imperial rights in the second half of the eighteenth century. Superior knowledge of ancient history constituted a rhetorical claim to the twin statuses of gentleman, being classically-educated, and statesman – showing understanding of historical context and precedent.

Keywords: british
reception studies
eighteenth-century
cultural history
universities
historiography
classical reception
Advisor: Young, B
The distribution and spread of emerging human infectious diseases

Despite many successes in the control of human infectious diseases they continue to pose a considerable risk to human health. The global distributions of pathogens are driven by ecological factors and the magnitude and extent of transmission are influenced by the dynamics of human behaviour.
Viruses such as chikungnunya virus, Zika virus, dengue virus, and Ebola virus have recently expanded geographically. However, prior to their expansion there was little quantitative evidence available to identify locations that may be susceptible to transmission and to evaluate the likelihood of virus introduction to such locations. In this thesis statistical modelling techniques were applied with the aim of understanding infectious disease ecology, determining the main drivers of disease occurrence, and predicting the magnitude and regional spread of an outbreak in real-time.
My results provide estimates of the populations now living in areas with possible transmission of chikungunya virus, show that the seasonal dynamics of Zika infection coupled with data on international travel, can better predict the arrival of the virus into new locations. Analyses of regional outbreaks of viruses including Ebola virus in West Africa and Yellow fever virus in Angola and the Democratic Republic Congo, show that patterns of human mobility strongly predict the real-time spread of disease. Further, I demonstrate that the impact of human movement varies considerably depending on the time of the outbreak (expanding versus declining phase) and the country of interest.
The results and conclusions of these studies are discussed in the context of improving our understanding of infectious disease dynamics and of informing public health policies, interventions, and control efforts.

Advisor: Hay, S
Smith, D
Multi-scale modelling and simulations into the mechanisms linking neuronal nitric oxide synthase and atrial fibrillation

Atrial fibrillation (AF) is the most common cardiac arrhythmia. Its incidence is projected to rise due to population ageing and increasing prevalence of associated risk factors. AF alters, or remodels, the affected atrial tissue, promoting future occurrences of itself and increasing resistance to treatment. Mechanisms underlying AF initiation and remodelling are not well understood. Recent experimental evidence indicates that decreased levels of the neuronal isoform of Nitric Oxide Synthase (nNOS) may be related to AF onset and precede remodelling. However, the potential mechanisms cannot be easily elucidated with experiments alone. Furthermore, experiments are complicated by inter-subject variability, which is particularly important in human studies due to the wide heterogeneity of the human population.
In this thesis, I use multi-scale modelling and simulations in synergy with experimental information to investigate mechanistic links between nNOS and AF at the level of ionic currents/cellular action potential/whole atria in human. First, I construct populations of models spanning experimentally-observed variability in human atrial myocytes under control conditions. Second, I use those populations of control models to identify key ionic mechanisms underpinning nNOS-mediated regulation of the cellular action potential in human atrial myocytes. I show that two of those currents – IKur and IK1 – play a key role in explaining the phenotypic shortening of the action potential observed under nNOS inhibition conditions and preceding AF-induced tissue remodelling. Finally, I build models of human whole atria and establish that this action potential shortening leads to the establishment of a vulnerable substrate, and hence is the main mechanism of pro-arrhythmia at this level. Overall, I provide a picture of nNOS-mediated mechanisms related to AF onset from ionic currents to the whole organ level.

Advisor: Bueno, A
Lopez, B
Casadei, B
Tropical stratosphere variability and extratropical teleconnections

The Quasi-Biennial Oscillation (QBO) is the dominant pattern of variability in the tropical stratosphere. Despite a well established theory regarding its generation in the atmosphere, the simulation in global climate models remains difficult. A set of metrics assessing the quality of model simulations is presented in this study. The QBO simulations in models submitted to the CMIP5 and CCMVal-2 intercomparison projects are characterised and compared to radiosonde observations and reanalysis datasets. Common model biases and their potential causes are addressed.
As the QBO has a long intrinsic period, knowing its influences on other parts of the climate system can be used to improve long range forecasts. These teleconnections of the QBO in observations are investigated using composite analysis, multilinear regression and a novel approach called causal effect networks (CEN). Findings from these analyses confirm previous results of the QBO modulating the stratospheric polar vortex and subsequently the North Atlantic Oscillation (NAO). They also suggest that it is important to take the equatorial zonal mean zonal wind vertical profile into account when studying teleconnections, rather than the more traditional method of using just one single level.
While QBO influences on the Northern Hemisphere winter polar vortex and the NAO are more clearly established, interactions within the tropics remain inconclusive. Regression analysis does not show a connection between the QBO and the MJO, whereas the CEN analysis does. Further studies are needed to understand the interaction mechanisms near the equator.
Finally, following the unprecedented disruption of the QBO cycle in the winter 2015/16, the event is described and a model analogue from the MPI-ESM-MR historical simulation is presented. Future implications are unclear, although model projections indicate more frequent QBO irregularities in a warming climate.

Keywords: QBO
Climate models
Holton-Tan effect
Stratosphere
Teleconnections
Advisor: Gray, L
Osprey, S
Investigating the function of microtubule-associated protein tau (MAPT) and its genetic association with Parkinson’s using human iPSC-derived dopamine neurons

Parkinson's disease (PD) primarily manifests as loss of motor control through the degeneration of nigrostriatal dopaminergic neurons. The microtubule-associated protein tau (MAPT) locus is highly genetically associated with PD, wherein the H1 haplotype confers disease risk and the H2 haplotype is protective. As this haplotype variation does not alter the amino acid sequence, disease risk may be conferred by altered gene expression, either of total MAPT or of specific isoforms, of which there are six in adult human brain. To investigate haplotype-specific control of MAPT expression in the neurons that die in PD, induced pluripotent stem cells (iPSCs) from H1/H2 heterozygous individuals were differentiated into dopaminergic neuronal cultures that expressed all six mature isoforms of MAPT after six months' maturation. A reporter construct using the human tyrosine hydroxylase locus was also generated to identify human dopaminergic neurons in mixed cultures. Haplotype-specific differences in the inclusion of exon 3 and total MAPT were observed in iPSC-derived dopaminergic neuronal cultures and a novel variant in MAPT intron 10 increased the inclusion of exon 10 by two-fold. RNA interference tools were generated to knockdown total MAPT or specific isoforms, wherein knockdown of the 4-repeat isoform of tau protein increased the velocity of axonal transport in iPSC-derived neurons. MAPT knockdown also reduced p62 levels, suggesting an impact of tau on macroautophagy, likely through altered axonal transport. These results demonstrate how variation at a disease susceptibility locus can alter gene expression, thereby impacting on neuronal function.

Keywords: Dopamine Neurons
iPSCs
Induced pluripotent stem cells
Tau
MAPT
Advisor: Wade-Martins, R
Caffrey, T
The responsibility of states for internationally wrongful acts committed within the framework of international organizations

This thesis investigates the often-voiced concern that the expanding activities of international organizations lead to an 'accountability gap' in the sense that if potentially harmful activities are carried out through an international organization, neither the organization nor its member States can effectively be held to account. Many international organizations are only beginning to establish procedural remedies through which the lawfulness of their activities can be reviewed. In the absence of a direct remedy against the organization, third parties often try to hold the member States responsible in relation to the organization's activities. This thesis investigates under what circumstances member States can be held responsible for wrongful conduct taken within the framework of an international organization. It deals comprehensively with the attribution of conduct in multilateral contexts, with complicity as a ground of member State responsibility, with reparation for injuries committed by multiple responsible parties and with the judicial enforcement of member State responsibility. In doing so, it demonstrates how with the transposition of the rules on international responsibility to the context of international organizations, certain rules of State responsibility, well-established in an exclusively inter-State context, have been opened up to fundamental questions. The separate legal personality of international organizations can in fact be seen as creating an 'institutional veil' which makes it more difficult to 'see through' and hold States responsible for their conduct qua members. This thesis argues that the possibility of holding member States responsible for unlawful conduct taken within the framework of international organizations not only counters the risk that States could use them as vehicles to carry out unlawful acts, but that it also serves as an incentive for member States to create better procedural remedies against their international organizations.

Advisor: Sarooshi, D