VictorJuiz/thesis huggingface dataset:
Derivative-free algorithms for nonlinear optimisation problems

Minimising a nonlinear function is a ubiquitous problem in applications, and standard algorithms need accurate evaluations of the function and its derivatives. However, if the function is black-box, expensive to evaluate, or noisy, it may be impractical or even impossible to obtain accurate derivatives, and we require derivative-free optimisation (DFO). Model-based DFO methods perform well in practice, taking many features from derivative-based methods, but can have lower performance for noisy problems and a high linear algebra cost. In this thesis, we aim to improve the flexibility, robustness and scalability of state-of-the-art methods for model-based DFO by designing, analysing, implementing and comprehensively testing three new algorithms for nonlinear optimisation, with a special focus on nonlinear least-squares problems (such as parameter fitting).
The first, DFO-LS, is designed for nonlinear least-squares problems, and is simpler than existing methods, constructing linear residual models with a flexible approach. DFO-LS can benefit from a reduced initialisation cost, and has improved scalability and runtime over existing methods without a performance penalty. DFO-LS also has features for noisy problems, including a novel multiple restarts mechanism, which are low cost in evaluations and linear algebra, giving DFO-LS better performance compared to existing techniques for handling noise.
We then introduce Py-BOBYQA, an extension of BOBYQA (Powell, 2009) with a similar multiple restarts mechanism to DFO-LS, amongst other new enhancements. It matches or outperforms BOBYQA and other state-of-the-art solvers on both smooth and noisy problems. We also propose a simple extension of Py-BOBYQA that may enable it to escape local minima and progress towards the global optima.
Lastly, we introduce, for large-scale nonlinear least-squares problems, DFBGN, the first model-based DFO method to optimise in low-dimensional subspaces at each iteration. DFBGN has lower linear algebra costs, improved runtime, and hence improved performance on large-scale problems than DFO-LS, as it can perform many more iterations within a reasonable runtime limit. It can also make progress under very small evaluation budgets, with a low runtime cost.

Keywords: derivative-free optimization
nonconvex optimization
trust region methods
Advisor: Cartis, C
Fiala, J
Marteau, B
Analytic conformal bootstrap at large spin

The conformal bootstrap is a powerful method to study conformal field theories, relying only on the existence and associativity of the OPE algebra, and has been used to provide both numeric and analytic constraints on a wide variety of theories. This thesis reviews the ideas of the lightcone bootstrap and large spin perturbation theory, and applies them to constrain the spectrum and algebra of several weakly coupled conformal field theories.
The first part studies the Gross-Neveu and Gross-Neveu-Yukawa models, whose spectrum and algebra are analyzed perturbatively in d = 2 + ε and d = 4 − ε dimensions, respectively. This is achieved by combining the method of twist conformal blocks with constraints from crossing symmetry of correlators of composite operators. Known results for the anomalous dimensions of nearly conserved currents are reproduced, and new results are found for the OPE coefficients and anomalous dimensions of a larger class of operators.
The second part studies the critical O(N) model in two different perturbative regimes, the d = 4 − ε expansion and the large N expansion. In both cases, crossing symmetry of a correlator of fundamental fields is combined with the Lorentzian inversion formula to find anomalous dimensions and OPE coefficients for weakly broken currents to a higher order than previously computed in the literature. In particular these are used to predict central charges in the 3d Ising model, comparing favourably with numerical results and previous predictions.

Advisor: Alday, L
Voicing the supernatural in Anglo-Saxon England

‘Voicing the Supernatural in Anglo-Saxon England’ is a study of the representation of supernatural voices in Anglo-Saxon literature, with a special emphasis on Old English poetry. Focusing primarily on representations of the direct discourse of supernatural characters, especially when, how, and why these characters’ voices are represented with unique stylistic features, the aim of this dissertation is twofold: a) to understand what representations of supernatural discourse can teach us about how Anglo-Saxon verbal artists perceived and interacted with the supernatural; and b) how these representations might inform our understanding of Anglo-Saxon poetic style and of the cultural roles of poetry in Anglo-Saxon society. In five chapters, ‘Voicing the Supernatural’ incorporates stylistic analysis of direct speech in six Old English poems: Solomon and Saturn I, The Phoenix, Soul and Body I, The Dream of the Rood, Guthlac A, and Genesis A, grounding these analyses in extensive research into their artistic, religious, and social contexts and incorporating Old English and Anglo-Latin poetry and prose as well as ecclesiastical, Germanic, Celtic, and classical sources and analogues. ‘Voicing the Supernatural’ argues that as poets translated their subject matter into the Old English poetic medium, they left traces of important historical conceptions about spirituality and poetry: for example, the consistent association between hypermetric lines and divine discourse observed in this dissertation throws into relief the genealogical relationship thought to exist between Old English hypermetric lines and Old Norse ljóðaháttr verse, which is primarily used for mythological and gnomic poems.

Advisor: Orchard, A
James Fintan Lalor’s plan ‘to rebuild Ireland from her ruins’ as outlined in his public and private writings of 1847 and 1848

This thesis examines the public and private writings of James Fintan Lalor, with particular emphasis on his treatment of the national and land questions. The three-fold objective is to elucidate Lalor’s key messages under these headings, explore possible influences on his thinking, and assess the impact of his writings on his contemporaries. The thesis attempts to address two deficiencies in the historiography. The first is the tendency of scholars to assign only a minor, supporting role to Lalor during the brief heyday of Young Ireland. He is usually portrayed merely as a catalyst in the radicalisation of figures like John Mitchel, rather than as a profound and original thinker in his own right. Although a few scholars disagree, Lalor’s proposals on land tenure are mostly interpreted as foreshadowing the creation of a ‘peasant proprietary’ later in the century. The thesis argues that Lalor advocated a much more radical plan that would link his two primary objectives: the creation of a sovereign Irish republic, and transfer of control over landholding from a small number of landlords to the entire Irish people. In framing the latter objective, Lalor anticipated the Single Tax promoted by Henry George, whereby all citizens would benefit from the income generated by land use. Elements of his doctrines on nationalism and land tenure can be found in earlier sources, such as the principles espoused by the United Irishmen or the radical ideas on landholding proposed by Chartists such as ‘Bronterre’ O’Brien. However, no clear thread of influence can be detected in the development of Lalor’s thinking. Amidst the turmoil caused by the Famine and the spread of revolutionary fervour from Europe, Lalor’s carefully-crafted ideas on landholding received little support or understanding, and his vision of a sovereign Ireland, in which the land itself would be subject to the will of the people, was largely ignored.

Advisor: Mulholland, M
Prioritisation of active compounds that are novel scaffolds using a data-driven approach

A primary aim of drug discovery is to find novel molecules that are active against a target of therapeutic relevance. With high attrition rates and the increasing costs of each stage of drug development, there is an emphasis on making the right decisions in the early stages of drug discovery. Methods are needed that will aid selection of compounds as part of the hit-to-lead process that will avoid subjective decisionmaking and make use of the recent increase in experimental data available at the start of the drug discovery process.
I have developed the CRANkS algorithm to prioritise candidate compounds based on how novel the compounds are compared to known inhibitors of the target of interest. A prospective compound is compared to known binders of the target in terms of its predicted interactions with the protein, placement in the binding site, and chemical structure. Molecules are then scored based on the overlap of conformations with grids generated from protein-ligand X-ray crystal structures. The grids capture the spatial distribution of the chemistry of the ligands and proteinligand interactions.
By using the calculated novelty scores, I hypothesised that the algorithm will prioritise both compounds that are active, but also compounds that are novel scaffolds. Scaffold-hopping is of particular importance in drug discovery for a better exploration of the activity space in order to find the most amenable lead compound. Using multi-objective optimisation, I found that the CRANkS scores could be used to select novel active scaffolds from datasets of active and inactive compounds.
Finally, I have investigated “active-guided” docking by combining the grids generated from active ligands, developed as part of CRANkS, with AutoDock – “AutoCRANkS”. I found an improvement in discriminating between active and inactive compounds when using AutoCRANkS compared to AutoDock, indicating the promise of using protein-ligand structural data to guide docking.

Advisor: Deane, C
Marsden, B
Morris, G
Paton, R
Building bridges to improve co-production in trials and its reporting | a mixed methods research analysis

Background
Participatory trials conducted over the internet are growing in scope with minimal guidance for Patient and Public Involvement (PPI). Replication and the use of trial findings in decision-making may depend on the methods used to conduct and report these trials.
Aim
To assess which research methods might be adapted to improve the conduct and degree of patient and public co-production within trials and in the work leading up to them.
Methods
A mixed-methods participatory action approach was used which included a blend of different studies, as noted under Findings.
Findings
Overall, I have shown why and how research teams struggle with building protocols for online trials and the design, conduct, and reporting of public involvement in trials generally and specifically in online trials. They express conflict about where and how to report PPI succinctly without interfering with reporting and research discussion. For instance, my systematic overview provides background from existing research on PPI in clinical trials’ design generally and my thematic analysis of social media comments about clinical trials found PPI increases the quantity and quality of patient-relevant priorities and outcomes, enrolment, funding, design, implementation and dissemination and yet roles and research boundaries were not clearly understood. An assessment of reporting quality and the methods used for self-recruited online trials of self-management health interventions, which I augmented with a survey of authors of online trials reporting quality found methods were poorly reported and seldom replicable. While a series of analyses on the use of public involvement statements in The BMJ, and surveys on supplementary materials, data sharing and dissemination found that simply requiring reporting of these areas increased the quantity and then quality. Finally, an online Delphi identified a consensus about what to include in the protocol for a participatory online trial.
Conclusions
This thesis demonstrates co-production with the public across multiple research designs with minimal funding is possible and improves research. Guidance for protocols and reporting methods in participatory online trials was identified as beneficial by stakeholders. The post-thesis development of a multi-use online trial participatory protocol template, online training and the research reporting guideline is underwritten by Stanford University.

Advisor: Clarke, M
Liew, SM
Burls, A
Howick, J
Schroter, S
Computational mechanisms of moral inference

Accurately inferring the moral character of others is crucial for avoiding social threats. Putatively “bad” agents command more attention and are identified more quickly and accurately than benign or friendly agents. Such vigilance is adaptive but can also be costly in environments where people sometimes make mistakes, because incorrectly attributing bad character to good people damages existing relationships and discourages forming new ones. Evolutionary models demonstrate that responding to wrongdoers with probabilistic forgiveness can facilitate the evolution of cooperation, but the cognitive mechanisms that enable the implementation of forgiving strategies are unknown. In this dissertation, I explore these mechanisms using novel methods derived from computational science, social cognition, and behavioral economics. Part I of the dissertation demonstrates that moral inference is described by an asymmetric Bayesian updating mechanism, where beliefs about the morality of bad agents are more uncertain (and therefore more amenable to updating) than beliefs about the morality of good agents. The model and data reveal a cognitive mechanism that rapidly discounts prior expectations to permit flexible updating of beliefs about potentially threatening others, a mechanism that could facilitate forgiveness when initial bad impressions turn out to be inaccurate. Part II of the dissertation considers the consequences that ensue when these mechanisms break down. Disruptions in learning and decision-making lie at the heart of many populations characterized by maladaptive social functioning. Consequently, I examine moral inference in two populations associated with interpersonal disturbances: individuals exposed to community violence and patients with Borderline Personality Disorder. The data reveal novel cognitive processes that may explain the emergence of maladaptive behavior related to chronic exposure to violence and Borderline Personality Disorder. Collectively, the results in this dissertation provide insights into the computational mechanisms of moral inference and their role in adaptive and maladaptive social functioning.

Keywords: moral character
person perception
Bayesian inference
computational psychiatry
impression formation
Advisor: Crockett, M
The political economy of free zones in the GCC

Free zones (FZs) in Gulf Cooperation Council (GCC) countries displayed substantial variation in the timing, scale, and scope of development between 1985 and 2017. This dissertation argues that the utilization of FZs as political instruments – both domestically and internationally – is critical for understanding FZ development outcomes in the region. The work tests this hypothesis using a comparative analysis of FZ development cases structured along three analytical dimensions: hydrocarbon dynamics, elite relationships, and global competition. Field visits to 44 of the 51 FZs observed in the work, 77 interviews with government and business officials associated with FZ development, and an extensive collection of primary source materials provide the data for this study.
As the first political economy analysis of the GCC’s FZ system, this research employs a qualified version of rentier state theory (RST) and a new conceptual categorization of rents associated with FZs – described in this work as commercialized rents. The concept builds upon existing scholarly applications of RST in the GCC by revealing previously unexplored rentier structures and the embeddedness of local and international elites in non-hydrocarbon development processes. Other aspects of FZ development trajectories, however, qualify RST’s ability to comprehensively account for economic development initiatives in the region.
The subsequent findings reveal that both resource-scarce and resource-abundant territories across the region employed FZs to generate rents, encourage rent-seeking behavior, and accomplish other political objectives. The specific trajectories of FZ development depended upon domestic, regional, and international factors, which could constrain or encourage FZ proliferation as well as shape FZ policies in a given territory. The work provides an academic foundation for future studies on FZs in the GCC and a broader methodological framework for researchers seeking to unpack the political economy of FZs in other countries and regions.

Keywords: Commercialized rents
Duqm
Trade
Dubai
Neom
Investment
Jebel Ali
economic cities
Special Economic Zones
Advisor: Robins, P
In-vacuum roll-to-roll patterning for functional devices

This thesis investigates the viability and compatibility of an industrially-mature metal thin film patterning process, that uses flexography printing in vacuum environments, for application to functional organic devices.
The integral thermal mechanism of this process, called selective metallization, is modelled, showing its compatibility with functional organics (process temperature <60°C, Al sheet resistance <1.59Ω◻-1}). The first example of sub-10μm lateral patterning, using this technique, is presented. These results demonstrate that, for this process, the flexography ink transfer defines the pattern quality.
The pattern quality of the printed metal is optimised, using custom-built in-vacuum flexography equipment. The pattern quality metrics, quantified using specially developed image analysis code, vary parabolically with printing pressure and diminish with increased printing speeds. A hierarchical phenomenological model of ink transfer is developed, which fits the data well. Optimal printing parameters reduce line edge peak-to-peak roughness to <1/2 nominal pattern gap, enough to remove electrical defects.
These optimised printed patterns are used as electrical contacts for organic thin film transistors (OTFTs), as a proof of concept. Device characterisation shows a change in transistor performance, compared to batch-processed Au contacts, resulting from a charge carrier injection layer, MoOx(x<3), which is necessary for band matching of the organic semiconductor with the high work function Al. Overall, the changes with MoOx thickness and configuration demonstrate selective metallization is compatible with OTFTs, with a contact resistivity of 1Ωcm-2.
To conclude, exploratory results, of selective metallization applied to organic light emitting diodes, and in-vacuum printing of an organic dielectric material, demonstrate the potential wide applicability of in-vacuum flexography.

Keywords: printing
flexible electronics
organic electronics
flexography
metallization
Advisor: Assender, H
Watt, A
Norm contestation in international politics

First generation norm scholars treat the meaning of a norm as if it was clear-cut and static in order to show the influence of international law on state behavior. Second generation norm scholars acknowledge that legal ambiguities and tensions give rise to debates. However, they tend to end rather than begin with the finding that norm contestation is a common occurrence in international affairs. This project begins with norm contestation as a problematic to understand norm development in international relations.
This study develops a theoretical framework on processes and possible outcomes of norm contestation that can guide empirical research. States can agree or disagree on both the norm frame (justification) and/or claim (action) when applying international law. Thus, norm contestation can have four different outcomes: norm clarification (frame and claim agreement), norm recognition (frame agreement/claim disagreement), norm neglect (frame disagreement/claim agreement) and norm impasse (frame and claim disagreement). These alternate endings have different effects on the clarity and strength of the contested norms, as well as on subsequent debate over them.
This “alternate endings” typology structures an empirical analysis using contentanalysis and elite interviews to compare the duration and effect of contestation over security norms. I further show that the malleability of norms does not make them epiphenomenal to power. States pay attention to the legal justifications they provide for their actions, so that norms both structure debates, and are constructed by them.
States act strategically when interpreting norms, but social dynamics intervene in the process, and influence the outcome: the kind of legal framing and legitimation strategy that a state or a third party to which norm interpretation was delegated to engages in matters. Next to this justificatory discourse, the reactions of in- and out-group members to norm interpretations decide over their sustainability.

Keywords: international security
norms
international law
United States - foreign relations
norm contestation
Advisor: Snidal, D
Causality, black holes, prediction, and counterfactuals in general relativity

This thesis treats foundational questions in classical general relativity. The em- phasis is towards proving new results in Lorentzian geometry which bear on these questions. For the most part, the results either improve or build upon the work of previous authors, including Geroch, Hawking, Kodama, Malament, Manchak, Newman, Penrose, Tipler, and Wald. In some cases I propose strengthened versions of known theorems, and in others I prove new results that are meant to better expose the meaning of known results. The subjects are broadly divided into three parts, II, III, and IV.
Part II focuses on black hole phenomena and is composed of three independent sections treating, respectively, Hawking’s area theorem, black hole singularities in the presence of closed timelike curves, and the causal structure of evaporating black holes in view of the Kodama-Geroch-Wald theorem.
Part III is focused on the epistemological status of observers in general relativis- tic spacetimes and the meaning of Penrose’s enigmatic conjecture of strong cosmic censorship. Here, the independent works of Malament and Manchak provide the crucial starting point.
Part IV is more discussive and less about proving new results. The essential idea is to look for a Lewisian-inspired analysis of counterfactuals that can be formu- lated about spacetimes. The outcome is a set of perspectives along with a number of naturally arising and mathematically precise questions which could bear on the discussion.

Advisor: Brown, H
Timpson, C