VictorJuiz/thesis huggingface dataset:
Computational dissection of schizotypy: differential contingency weighting

Schizotypy is a personality dimension related to psychotic experience, i.e., alteration of beliefs and sensory experiences, also is a liability for schizophrenia. In this dissertation I focus on schizotypy and its relationship with perceptual, learning, and agency. I employed computational models, and Contingency Learning Theory as a general framework, to develop novel behavioural tasks used to dissect cognitive features of schizotypy measured in the general population.
I studied the Jumping-to-Conclusions bias with a novel perceptual contingency task (Experiment 1). This task also tests the tendency to perceive associations between events. I found that people scoring high on schizotypy does not perceive associations easily, but they gather more sensory evidence to make correct decisions. In addition, I investigated whether schizotypy moderates how people use absent information to make judgments (Experiments 2 and 3). In an exploratory analysis, I found that high unusual experiences scores were negatively correlated with how people use the absence of events to judge event relatedness. Moreover, I developed a framework −behavioural paradigm and computational model− to study how two agents (one human and one artificial) interact and make judgments of control (Experiments 4 and 5). I used this task to study illusion of control and how people weight external and internal events as sources of control. I found that people scoring high in positive schizotypy have an enhanced illusion of control when estimating their control. Although, this result is dependent on participants not ‘interacting’ with another agent. I also found that unusual experiences in schizotypy negatively correlate with sensitivity to external controllers (or agents).
In summary, I found that weighting sensory evidence varies in relation to schizotypy. This was supported with my results showing a bias to gather more evidence, a weight reduction for absent information, an enhanced illusion of control when there is nothing else competing for the control, and a reduced sensitivity to perceived control from another agent. Together, my results indicate that high positive schizotypy is related to downweighting sensory evidence with a low saliency baseline (absence of target information, and other agents). Finally, I explored the differences in the concept of weight in computational modelling and I conclude that mathematically different models refer to a similar mechanism, a value multiplying a discrepancy learning signal.

Keywords: individual differences
computational modelling
contingency learning
schizotypy
psychopathology
learning theory
Advisor: Browning, M
Murphy, R
The demographic pathways of intergenerational transmission of educational attainment ----- the role of fertility and assortative mating in status reproduction

The intergenerational transmission of education examines to what extent has one generation's attainment determined the next generation's attainment. It is deemed an important indicator of social fluidity and inequality. This thesis explores the demographic pathways of intergenerational transmission, focusing on fertility and assortative mating. It includes four self-contained essays, two on fertility and two on assortative mating.
Chapter One brought the previous individual-level inquiries on the relationship between sibship size and educational attainment to the societal level. Using the case of China, findings show that fertility decline during its One Child Policy era brought modest improvement in the average educational attainment of the country. However, differential fertility rates by rural/urban residency have a marked impact on rural/urban educational inequality.
Chapter Two examined the role of fertility in three-generational transmission. It proposed a new moderator for the process: the fertility rates of the grandparents. Findings using data from the Panel Studies of Income Dynamics (PSID) show that having multiple children (i.e., multiple members in the parental generation) amplifies grandparents' influence on grandchildren's educational attainment.
Chapter Three examined the role of parents in adult children's marital sorting. It extends previous findings on first and new marriages from a life course perspective. Results using PSID data show divergent trends by gender. Parents' influence becomes less important for males but more vital for females over the life course.
Chapter Four examined the role of education homogamy in intergenerational reproduction. It brought the previous one-sided analysis, which focused on one parent only, to the couple level and proposed an approach that is the first to consider and distinguish two sources—resource combination and family milieu—that generate the difference between homogamy and heterogamy. Findings using PSID data demonstrate that these two sources affect couples' probability of having children and their children's educational attainment differently, and their influences change over cohorts.

Keywords: fertility
education
family demography
social reproduction
assortative mating
Advisor: Breen, R
Construction of gene coexpression networks and transcriptomic analysis for Rhizobium leguminosarum

Rhizobium leguminosarum is a soil bacteria which infects plants of the legume family such as peas, lentils, and beans. When associated with the plant, R. leguminosarum fixes atmospheric nitrogen (biological nitrogen fixation), producing ammonium that is assimilated by the plant, improving plant growth. This symbiotic relationship is very important for agriculture; increasing the knowledge of plant infection and nitrogen fixation processes might lead to a decrease in the use of chemical fertilisers.
In this thesis, I combine R. leguminosarum gene expression data from previous experiments to produce gene coexpression networks and increase the functional annotation of this bacterium. Gene coexpression networks are networks in which nodes represent genes and edges represent coexpression (i.e. two genes are connected if they have a similar expression pattern). Unfortunately, there is no standard method to generate gene coexpression networks from gene expression data. I introduce signed distance correlation as a measure of dependency between two variables and use it to generate self-consistent, unweighted and weighted, gene coexpression networks that are more stable and capture more biological information than those obtained from Pearson correlation or mutual information.
Subsequently, I present a pipeline that combines novel scores from gene coexpression network analysis in a principled way to identify the genes that are associated with certain growth conditions or highly coexpressed with a predefined set of genes of interest. This association can lead to putative functional annotation or to a prioritised list of genes for further study.
Lastly, I provide a detailed analysis of the transcriptome of R. leguminosarum. For this purpose, I generate different knock-out mutants lacking transcriptional regulators which are reported to be important in the nitrogen-fixing state of the bacteria and perform RNA-Seq experiments. I also carry out a preliminary study of the molecular signals that may affect the changes in gene expression between the free-living and the plant associated bacteria.

Keywords: Rhizobium leguminosarum
correlation
transcriptomics
nitrogen fixation
gene coexpression
networks
Advisor: Reinert, G
Poole, PS
Deane, C
Beguerisse Díaz, M
Economic diversification, entrepreneurship, and regime stability in Saudi Arabia and Nigeria

Why do political elites in resource-wealthy autocracies and hybrid regimes pursue regulatory liberalization at certain moments, but not others? Within academic debates over the beneficial or deleterious effects of resource wealth, scholars have used quantitative methods to evidence a resource curse through a positive relationship between oil rents and the regulation of private enterprise. This dissertation charts a departure from this received wisdom using a paired, qualitative comparison of the politics of corporate regulation within the largest oil producers in Africa and the Middle East—Nigeria and Saudi Arabia. Drawing from a broader array of legal and bureaucratic reforms, and considering their heterogeneous implementation, I demonstrate that oil rents have played a crucial role in facilitating the liberalization of business creation regulations in the 21st century. Without the necessary oil rents to placate diverse threats to regime stability, particularly during the 2014-2016 oil price downturn, liberalization was inhibited. I term this the rent-conditional reform (RCR) theory.
Before applying the RCR theory to the case countries, I explore the politics of corporate regulation within the two cases in historical perspective. Drawing from archival documents, this dissertation illustrates the distinct but parallel politicization of corporate regulation in the 20th century. While corporate regulation was politicized through the introduction of a Western-origin corporate code in Saudi Arabia in the 1930s, it was conversely politicized in Nigeria in the late 1980s through the first indigenous reform of the country’s corporate code. Moreover, I forge a theory of interest groups in Nigerian politics to explain the cross-class, cross regional collective action in the corporate regulatory reform and administration processes.
Employing interviews with political elites, entrepreneurs, and bureaucrats in Nigeria and Saudi Arabia, I build upon these historic analyses to apply the RCR theory to the two cases before, during, and after the 2014-16 oil downturn. Using process-tracing, I argue that crumbling elite cohesion during the downturn disincentivized corporate regulatory liberalization in Nigeria, while the threat of popular unrest in the wake of the Arab Spring provided a parallel disincentive in Saudi Arabia during the same period. Together, the distinct causal processes across the two cases illustrate the applicability of the rent-conditional reform theory across diverse contexts of natural resource rent volatility.

Keywords: resource curse
corporate law
Saudi Arabia
regime stability
Nigeria
entrepreneurship
autocracy
comparative politics
economic diversification
Advisor: Soares de Oliveira, R
Towards local property assessment of advanced manufactured microstructures: a case study in linear friction welded titanium

Recent developments in manufacturing technology have enabled a wealth of designs to be created and implemented in engineered products. These methods, empowered in part through data-driven approaches to materials processing, have optimised the structure of additive products and refined the processes for complex joining technologies. However, in doing so they radically change the material structure, often introducing strong local heterogeneity either by design or by consequence. A commensurate local understanding of the material and its behaviour at relevant length scales is necessary in order to ensure these parts live up to the stringent requirements in demanding or safety critical applications. Two methods are developed to contribute to this effort, with data-driven approaches to similarly accelerate the development cycles described above.
The effect of microstructure on the mechanical behaviour is investigated with these methods using a Ti-64 linear friction welded (LFW) joint as a case study. The LFW joint contains a highly varied microstructure, from the globular alpha and bimodal structures in the parent material on either side to the Widmänstatten structure found near the weld-line. The weld-line itself is known to be highly crystallographically textured, with a preference for the c axis to align with the transverse direction. The local static and dynamic material properties from the bulk microstructures to the refined and textured weld-line have been explored through nanoindentation and a novel mesoscale fatigue method. Local static properties are determined through correlated nano-indentation mapping and Electron Back Scatter Diffraction (EBSD), providing rapid structure property assessments.
Local fatigue properties are explored with a Bayesian Optimised data collection protocol and novel meso-scale ultrasonic fatigue test, permitting the efficient sampling of fatigue behaviour of weld-line material. These two methods provide new methods and datasets for assessing the properties of advanced manufactured materials, reflecting established knowledge and novel quantitative comparisons in the case study described.

Keywords: aerospace
fatigue
bayesian optimisation
advanced manufacturing
micromechanics
materials
titanium
mechanical
additive manufacturing
Advisor: Wilkinson, A
Gong, J
Essays on competitive and strategic bidding in multi-object auctions

This thesis addresses four important issues in multi-object auction markets, focusing on a theory of strategic bidding and corresponding empirical evidence, on questions of equilibrium existence with distributional preferences, and on the equivalence of market objectives.
The product-mix auction (PMA) designed by Paul Klemperer is used by the Bank of England to allocate loans to commercial banks at least monthly. If only a few bidders were thought to be participating, strategic behaviour may harm efficiency. I develop a theoretical model of strategic bidding in the PMA that enables the comparison with other auction formats commonly used for the sale of differentiated substitutes. While the theory predicts that the considered auctions perform (nearly) identically in bidder surplus, revenue, and efficiency, I also show contrasting empirical evidence. In a virtual lab experiment, the PMA achieves highest bidder surplus and efficiency. When bidders are symmetric, payoffs in the PMA are even between 90% and 156% higher and efficiency is 12% higher than in other auctions.
The product-mix auction was developed for substitute preferences, but similar concepts may be useful in markets with substitutes and complements. Extending the product-mix preferences and bidding language, I consider an even richer market with substitutes, complements, and distributional preferences. In this market, the seller can favour, e.g., a more concentrated allocation of products among buyers, or an even distribution of products. This type of preference, while common in many real world applications, is novel in the literature. I develop a graph-based bidding language and derive new results on the existence of competitive (Walrasian) equilibria, which can be computed via linear programming. The auction design I develop guarantees fair and transparent pricing.
In the context of substitutes, it is often practical for buyers to state their preferences with a budget. This may be spent on several products, while trade-offs between those products are stated as prices. Without budget constraints, it is known that revenue and welfare optimum may not coincide. We show, however, that with budget constraints, the market objectives of maximising revenue and maximising welfare result in the same, unique, market clearing prices and the same allocation. Our proof of this result also constructs an algorithm to identify these prices.

Keywords: auctions with budget constraints
Fisher markets
multi-unit auctions
strategic bidding
competitive equilibrium
experiment
Advisor: Klemperer, P
Optimal control and reinforcement learning for formula one lap simulation

Lap simulation in a Formula One context is a subclass of optimal control problems and describes the computation of optimal trajectories around racing circuits. The results of lap simulation are primarily used for vehicle setup and strategic racing decisions. The optimal lap problem is solved using two classes of algorithms. The first algorithm uses direct collocation to compute optimal trajectories and the second algorithm uses specially constructed reinforcement learning environments and generalised function approximation to compute desirable system inputs. Historically direct collocation methods were considered impractical for minimum lap time simulations, due to their high computational costs. The exponential increase in computational performance has enabled the practical application of these algorithms. These lap time simulations require a vehicle model, as well as a track discretisation. As an example for this, the classical bicycle model along with a curvilinear track model are introduced. To solve the resulting direct collocation problems, algorithms for non-linear optimisation problems are presented and performance critical aspects are discussed. The optimisation algorithm is accelerated by utilising highly parallel computer architectures, such as graphics processing units (GPUs). An analytical gradient approximation is presented to achieve approximations of projection systems which constitute one most performance critical components of the solution process. Mesh refinement algorithms are discussed and a novel mesh refinement heuristic based on optimal polynomial approximation in an L1 sense is discussed. The L1 approximation is improved by detecting singularities and using Clenshaw--Curtis quadrature on intermediary intervals. In Chapter 4 of this work, the lap time optimisation problem is reformulated as a reinforcement learning environments. For this, the relevant background literature on reinforcement learning is discussed and a translation of a training optimisation environment is constructed. Details of this environment are discussed in the form of reward signals, terminal conditions, and observation features. A series of learning models is discussed with increasing feature fidelity leading to an algorithm that can generalise well across representations of circuits from the 2022 Formula One calendar. This work expands on the current literature by providing novel, physically motivated, reinforcement learning environments for lap time optimisation tasks. The results of both approaches are combined by using strategy extraction to initialise the collocation optimisation algorithm and optimise the underlying mesh.

Keywords: autonomous vehicles
ppo
formula one
gpu compute
self driving
optimal control
reinforcement learning
torch
lap simulation
Advisor: Nakatsukasa, Y
Reisinger, C
Defending Henry VIII's royal supremacy in England and Ireland

This thesis offers new perspectives on the intellectual rationales employed to defend Henry VIII’s royal supremacy. It affirms that, far from being explicable merely by reference to the exigencies of politics, the supremacy was shaped by ideas about the nature of temporal authority over the Church, and it demonstrates the importance of securing ideological commitment to the supremacy.
The thesis addresses the intellectual case for the supremacy advanced by the English government, and especially by Thomas Cromwell, in the formative years of the 1530s, and the relationship between ideology and the institutional structures and functioning of the supremacy. The thesis also considers the application of the intellectual case for the supremacy to Ireland, although there the issues of Henry’s supremacy played out over a longer period, and are therefore pursued to the end of Edward VI’s reign.
There are three principal elements to the thesis.
The first concerns the role played by Cromwell in shaping the supremacy. It is argued that he initially promoted a parliamentary supremacy in accordance with his political philosophy, and manifested this by exercising the supremacy through statute. However, when Cromwell, as vicegerent, was endowed with extraordinary ecclesiastical powers, both the way in which the supremacy functioned, and the model of supremacy which he sanctioned in polemic, changed.
The second revises previous scholarly interpretations of Christopher St German’s proposals for the resolution of doctrinal issues by the king-in-Parliament, and argues that, ultimately, he repudiated his own theories.
The third proposes that the intellectual case for the supremacy was compromised in Ireland by political circumstances there and by policy decisions taken by the English government, and argues that a failure to convey an adequate intellectual justification for the supremacy to the people of Ireland is a factor helping to explain the Reformation’s rejection there.

Keywords: Religio-political history
Royal supremacy
Thomas Cromwell
ecclesiastical authority
ecclesiastical history
English history
Irish history
Tudor history
Irish Reformation
ecclesiastical government
history of ideas
Christopher St German
Advisor: MacCulloch, D
Gajda, A
Computational studies of lipopolysaccharide interactions with membrane transporters

Lipopolysaccharide (LPS) lipids compose the outer leaflet of the outer membrane in pathogenic Gram-negative bacteria and are chiefly responsible for host-immune responses. Therefore, the membrane proteins which interact with LPS as well as the transport system for LPS, the Lpt system, represents a class of extremely important drug targets. The focus of this thesis is to employ molecular dynamics studies to examine the effects of LPS binding upon the Lpt complex at every stage of the transportation process, validating and conferring recent mass spectrometry and cryo-electron microscopy (Cryo-EM) studies.
Molecular dynamics (MD) studies in this thesis reveal that LPS binds to other proteins found in the inner membrane in a similar manner to the transporter subcomplex LptB2FGC. Within the transporter itself, simulations of recently resolved Cryo-EM structure reveal that LPS shifts position to facilitate transportation across the periplasmic protein bridging complex. Binding energy calculations between the acyl chains of LPS and the bridging complex reveal a generally flat energetic landscape before reaching the terminal outer membrane subcomplex of the Lpt system, LptDE. Here, MD studies validate and explain hydrogen-deuterium exchange mass spectrometry results which capture the conformational changes required for LPS insertion into the outer membrane. With an increasing prevalence of antibiotic resistant pathogens, this thesis concerns characterising LPS interactions with its transport machinery suggesting means for developing antimicrobial therapeutics which target this essential system.

Keywords: LPS
Lpt complex
LptB2FGC
lipopolysaccharide
Native Mass spectrometry
molecular dynamics
HDX
Advisor: Stansfeld, P
Vivien Robinson, C