VictorJuiz/thesis huggingface dataset:
Optimization and imitation for pandemic policy and financial decision making

This thesis is a combination of two works using optimal control and imitation learning to address real-world problems in epidemiology and financial markets.
The COVID-19 pandemic has presented unique challenges for policymakers seeking to balance public health and economic impacts. Mathematical models can provide valuable insights to guide lockdown policies. In chapter 1, we propose an extended SIR model incorporating economic decision- making and interactions among susceptible, infected, and recovered populations. An optimal control framework balances infection spread, deaths, and economic activity under lockdown constraints. Experiments high- light trade-offs between short-term recession and long-term benefits. The model provides guidance on lockdown timing, incorporating death costs, and using status information.
In financial markets, historical data provides demonstrations for how ex- pert investors act. Imitation learning offers a data-driven approach to reproduce trading behaviours, without manual reward design needed in reinforcement learning. In chapter 2, we review main imitation learning techniques and applications in finance. Analyses provide error bounds and generalisation guarantees.
The final chapter draws conclusions and list open problems for possible future works.

Keywords: financial markets
optimization
imitation learning
Advisor: Jin, H
Wang, N
Bayesian optimization in adverse scenarios

Optimization problems with expensive-to-evaluate objective functions are ubiquitous in scientific and industrial settings. Bayesian optimization has gained widespread acclaim for optimizing expensive (and often black box) functions due to its theoretical performance guarantees and empirical sample efficiency in a variety of settings. Nevertheless, many practical scenarios remain where prevailing Bayesian optimization techniques fall short. We consider four such scenarios. First, we formalize the optimization problem where the goal is to identify robust designs with respect to multiple objective functions that are subject to input noise. Such robust design problems frequently arise, for example, in manufacturing settings where fabrication can only be performed with limited precision. We propose a method that identifies a set of optimal robust designs, where each design provides probabilistic guarantees jointly on multiple objectives. Second, we consider sample-efficient high-dimensional multi-objective optimization. This line of research is motivated by the challenging task of designing optical displays for augmented reality to optimize visual quality and efficiency, where the designs are specified by high-dimensional parameterizations governing complex geometries. Our proposed trust-region based algorithm yields order-of-magnitude improvements in sample complexity on this problem. Third, we consider multi-objective optimization of expensive functions with variable-cost, decoupled, and/or multi-fidelity evaluations and propose a Bayes-optimal, non-myopic acquisition function, which significantly improves sample efficiency in scenarios with incomplete information. We apply this to hardware-aware neural architecture search where the objective, on-device latency and model accuracy, can often be evaluated independently. Fourth, we consider the setting where the search space consists of discrete (and potentially continuous) parameters. We propose a theoretically grounded technique that uses a probabilistic reparameterization to transform the discrete or mixed inner optimization problem into a continuous one leading to more effective Bayesian optimization policies. Together, this thesis provides a playbook for Bayesian optimization in several practical adverse scenarios.

Keywords: bayesian optimization
gaussian processes
Advisor: Osborne, MA
Photoinduced chemistry of biomolecular building blocks and molecules in space

The interactions between light and matter are ubiquitous in the universe and initiate many fundamental chemical processes, such as photosynthesis and vitamin D production. Therefore, gaining a better understanding of how light interacts with molecules and how light-induced reaction mechanisms develop from reactants to products is of great interest.
This work uses a velocity-map imaging time-of-flight spectrometer to study the unimolecular photodissociation dynamics of molecules in the gas phase. The observables of the experiment are the product scattering distributions, which are a fingerprint of the chemical reaction, and the product time-of-flight, which reveals the fragment identities. The experiments aim to understand which chemical bonds break, how the system evolves on the potential energy surfaces involved in the reaction, and how the available energy is distributed over the product degrees of freedom.
The first part of this thesis studies the photodissociation of tetrahydrofuran at 193 nm, N,N-dimethylformamide at 225 nm and 245 nm, and the N,N-dimethylformamide cation at 225nm, 245nm, and 280nm. Tetrahydrofuran is a model for the DNA backbone molecule ribose, and N,N-dimethylformamide is a model for the peptide bond, which forms the backbone of proteins. Both molecules reveal complex dissociation dynamics, in which population transfer to lower electronic states is possible after the initial excitation. This population transfer probably plays an important role in the photoprotection of molecules in biological species. The great majority of the available energy is distributed into the internal product modes rather than product kinetic energy. This observation is pronounced in the N,N-dimethylformamide cation study, in which a change in photon energy of more than 0.5 eV leads to the same product kinetic energy release.
The second part of the thesis describes the design and characterization of a novel femtosecond laser beamline to the experiment which allows us to conduct Coulomb explosion imaging experiments, and a fibre-coupled laser-induced thermal desorption source capable of introducing non-volatile samples into the spectrometer. In a study combining both techniques, we investigate the fragmentation pattern of three singly and doubly charged polycyclic aromatic hydrocarbons: triphenylene, perylene, and benzo[a]pyrene. All three molecules display a common fragmentation pattern in which the summed number of carbon atoms in the fragment ions deviates from the carbon number of the parent molecule by a multiple of two, which we interpret in terms of a fragmentation mechanism involving sequential loss of neutral acetylene (C2H2) units. We also show that loss of the neutral acetylene units occurs preferably from the heavier fragment ion after an initial charge separation step.

Keywords: reaction dynamics
time-of-flight mass spectrometry
polycyclic aromatic hydrocarbons
velocity-map imaging
ion imaging
covariance
photoinduced reactions
peptide bond
LID source
lasers
Advisor: Vallance, C
Toxic justice: An ethnography of industrial pollution, environmental advocacy, and suspended damage in Italy and Taiwan

Current research in environmental justice is increasingly focusing on the international aspects of environmental inequality, advocating for new methods and tools to empower disenfranchised communities. This enables these communities to engage in global networks and influence international policy.
However, fenceline communities not actively involved in environmental initiatives are often overlooked. Grasping how politically marginalised fenceline communities perceive and respond to pollution is essential for developing a more comprehensive and inclusive concept of environmental justice.
This study delves into the collective experiences and understandings of pollution and the environment in two fenceline communities in Italy and Taiwan, both heavily affected by industrial pollution. In response to damage-centred approach to environmental justice, this research aims to produce new theoretical and methodological resources that enable these communities to engage in and contribute to a global environmental justice movement.
I begin by analysing environmental advocacy movements in the two sites, focusing on the epistemic rift between activists and marginalised residents. I identify this rift in diverging epistemic grammars that lead to different valuations and experiences of industrial chemicals. An analysis of the processes of knowledge production among marginalised residents unveils ways of understanding and relating to pollution that are temporally diluted and embodied. Specifically, I show how pollution also enables socio-cultural reproduction in fenceline communities. I conceptualise these knowledge practices in the notion of toxic justice, a framework that holds together often seemingly contradictory aspirations to justice.

Advisor: Lora-Wainwright, A
Greenhough, B
Le seuil du language: translation, multilingualism, and multimodality in the work of Julien Green and Paul Bowles

This dissertation examines the role of translation, multilingualism, and multimodality in Julien Green and Paul Bowles’ lives and work. In recent decades, there has been an upsurge of interest in how hybrid language use amongst linguistic minority communities challenges rigid conceptions of national borders, languages, and literary traditions. This study is intended to complement this important current of research: shifting the focus from authors who have adopted translation and hybrid forms as a matter of circumstance or external pressure, the analysis centres on two writers who decided to adopt these practices as a matter of artistic choice—examining their central importance and far-reaching impact in their work. In doing so, it explores how translation, multilingual writing, and multimodal expression (grouped under the term ‘hybrid creative practices’) offer a uniquely productive means for the authors to express and develop some of their oeuvres’ most significant ideas. Specifically, the chapters focus on how these practices participate in Green and Bowles’ engagement with the thresholds between: (a) the unexpressed aspects of experience and art’s perceptible articulation of meaning; (b) their work and that of other authors; and (c) their attempts to capture elements of their present environment and their work’s future trajectory as acts of preservation. In the case of both authors, considering their use of hybrid creative practices in relation to these thresholds is shown to yield a more nuanced view of their artistic agendas—especially as they relate to their spiritual or ideological commitments. More broadly, this study proposes that, beyond exploring how translation and hybrid expression can expand their practitioners’ views and creative resources—as recent research has done so effectively—it is important to consider how such practices can refine an author’s existing perspectives, particularly in light of what lies beyond their body of work.

Keywords: Julien Green
translation
comparative literature
multimodality
multilingualism
Paul Bowles
Advisor: McGuinness, P
Reynolds, M
Investigating brain-derived α-synuclein fibrils and diagnostic biomarkers of synucleinopathies

Synucleinopathies are associated with the aggregation of misfolded alpha-synuclein (αSyn) into fibrils. These αSyn fibrils are categorised into different ’strains’ according to their biological properties. In vitro-seeded fibrils generated with seeding amplification assay (SAA fibrils) have facilitated αSyn strain research, but the question remains how well they replicate the brain-derived fibrils. The SAA also functions as a highly sensitive and specific diagnostic tool for Parkinson’s disease (PD) and is usually carried out in cerebrospinal fluid (CSF), but other more accessible biofluids have also been studied, including saliva.
This thesis comprises four aims: 1) to investigate methods for characterising brain-derived αSyn fibrils, 2) to characterise biochemical and biophysical properties of brain-derived αSyn fibrils that are indicative of αSyn strains and compare these properties to the SAA fibrils, 3) to examine the diagnostic value of αSyn SAA in CSF of PD and multiple system atrophy (MSA) patients, 4) to examine saliva from PD patients for αSyn seeding activity and molecular signatures to identify biomarker candidates.
Findings revealed the biochemical and biophysical heterogeneity of αSyn fibrils from different synucleinopathies, but these properties were not replicated among the SAA fibrils. αSyn SAA with CSF samples were able to stratify between PD and MSA. The quantitative parameters correlated with MSA disease progression and PD clinical clusters. Preliminary investigation on PD saliva resulted in the detection of αSyn seeding activity and significant changes in the levels of oligomeric αSyn, alpha-1-antitrypsin (A1AT) and chitinase-3-like protein-2 (CH3L2).
Overall, this thesis demonstrates biochemical and biophysical evidence of brain-derived αSyn strains, which the SAA fibrils fail to replicate. Results raise significant implications of using SAA fibrils to model synucleinopathies. The performance of CSF αSyn SAA illustrates its diagnostic value, and the molecular signatures observed in PD saliva offer a new outlook for diagnostic tools.

Keywords: synucleinopathies
seed amplification assay
biomarker
a-synuclein fibrils
Advisor: Parkkinen, L
Civitelli, L
Chalk, R
Detection for novel pathogen pandemics

Pandemics pose a significant threat to human health and global security. Novel pathogens present substantial pandemic risks and have unique public health challenges, given the uncharacterised nature of their causative agents and the consequent uncertainty about optimal countermeasures. Early detection of novel pathogen outbreaks is crucial for timely public health responses to mitigate devastating consequences. Following outbreak discovery, further detection is essential to ascertain the prevalence and understand the features of the epidemic. This thesis explores different aspects of detection for novel pathogen pandemics, including through a systematic analysis of existing national surveillance infrastructure worldwide for novel diseases. It examines the implications of current surveillance using modelling techniques and investigates diagnostic approaches to determining community infection prevalence in the early stages of a novel pathogen pandemic. We begin by providing an overview of novel pathogens, pandemic risks, and available detection methods, reviewing the literature on “Disease X” and historical case studies of recently emerged pathogens. Our analysis of 195 countries demonstrates that only a minority have evidence publicly available of novel disease considerations in their national public health surveillance systems. For those that mandate novel disease reporting, we model time-to-detection and outbreak size using the detection thresholds specified by different countries and explore whether population-level surveillance strategies could improve upon current detection. A serial cross-sectional investigation of SARS-CoV-2 infection prevalence in a community population in the early stage of the COVID-19 pandemic is presented, with four diagnostic approaches compared. Finally, we summarise our findings in the context of current and future detection for novel pathogen outbreaks and explore research directions that could guide improvements in early warning systems, diagnostic preparedness and pandemic prevention initiatives.

Keywords: disease surveillance
global health security
early detection
biosecurity
novel pathogens
infectious disease
pandemics
mathematical modelling
outbreaks
epidemiology
public health
biology
emerging infectious diseases
medicine
Advisor: Bonsall, M
Thompson, R
π-conjugated macrocycles: synthesis, structure and electronic properties

This thesis presents an exploration of π-conjugation effects in two previously known small macrocycles, [18]annulene and [24]paracyclophanetetraene and the synthesis of new, large nanorings built of porphyrin subunits.
Chapter 1 introduces the reader to the field of aromatic macrocycles and to the concept of aromaticity. It is then followed by an overview of basic synthetic methods useful in the synthesis of macrocycles.
Chapter 2 describes the red-ox behaviour of [18]annulene, an archetypal annulene and one of the iconic molecules of organic chemistry. The highly reactive anions of [18]annulene are explored both in solution using NMR methods and in the solid state using single crystal X-ray diffraction. The results show that the [18]annulene dianion has a different geometry than described 50 years ago. The reduction can go further and the tetraanion forms a sandwich-type dimer observed both in solution and in the solid state.
Chapter 3 explores the structural manifestation of (anti)aromaticity in the solid-state structures of anions of [24]paracyclophanetetraene in various coordination environments.
Chapter 4 reports the synthesis of a phenylene-linked porphyrin nanoring built of edge-fused porphyrin dimer units. It demonstrates that fusion of porphyrins can be performed even on highly strained systems.
Chapter 5 describes the synthesis of a giant spoked 18-porphyrin nanoring, the first example of 5,15-linked porphyrin nanoring with direct bonds (and no spacer) between the porphyrin units.
Listed in the Appendix is an overview of the crystal structures obtained during the DPhil studies, resulting from X-ray measurements and refinements that I performed both for my compounds and for these obtained by other group members for their projects.

Keywords: macrocycle
porphyrin
nanoring
conjugated
annulene
aromaticity
Advisor: Anderson, H
An analysis of post conflict economic & private sector performance 

The liberal peacebuilding literature focuses on economic growth as a key factor to exiting the conflict trap. Yet, there is a lack of research, particularly in Africa, on private sector development in post conflict environments. This thesis uses the Structure- Conduct-Performance (Bain, 1959) framework, which suggests that conflict alters the conduct of economic decisions-makers, to analyse the private sector reconstruction process. This allows for the inclusion of non-mainstream critiques of peacebuilding in the analysis and view private sector development from a partially, “bottom-up” approach. Each of the three substantive chapters investigates different aspects of these relationships to determine how and why private sector performance is ultimately influenced by recent conflict. The first chapter provides analysis at a macroeconomic and country-level, determining the influence of foreign direct investment (FDI) and aid on economic growth within the post conflict period. Using a panel structural vector autoregressive model, this paper finds that on average, FDI per capita flows have a significant and positive impact on GDP, which is larger in magnitude than aid per capita. The second chapter uses firm-level data in the African continent to explore differences in what influences business growth in post conflict firms. The variations I find are i) employee training has a significant higher correlation with firm performance in post conflict regions and ii) foreign ownership and business networks only have a positive association with non-post conflict firm performance. Lastly, the final chapter of this thesis uses fifty qualitative interviews from Liberia to be used as a case study for private sector development in a post conflict African country. The evidence suggests that the conflicts experienced in Liberia had a profound and long-lasting effect on firm conduct (access to finance, human capital, innovation, and trust), which has had negative consequences on firm performance. However, different types of entrepreneurs and investors have effectively altered their conduct to navigate these post conflict barriers and survive the challenging business environment. Overall, this thesis provides novel evidence on private sector development in post conflict markets, which can ultimately contribute to reconstruction policy and programs in these regions.

Keywords: foreign aid
economic growth
private sector
post conflict
FDI
peace building
Advisor: Adam, C
Beyond the binary of the gender game: exploring experiences of genderqueer+ youth in the Czech Republic


This qualitative research project seeks to explore the experiences of Czech genderqueer+ youth. Noting the challenges and marginalisation faced by genderqueer+ youth and the paucity of Czech queer research regarding genderqueerness, this research aims to empower genderqueer+ communities by centring their identities, experiences, and voices. In embracing an emancipatory research framework, the research was conceptualised in collaboration with the LGBTQIA+ youth community group Plusko+ and consisted of two focus group discussions held in queer safe spaces.
In the focus groups, the phenomenon and framework of the gender game was collectively constructed, representing the pressures of a gender binary overcategorisation as experienced by genderqueer+ youth and the multidimensional forms of oppression, ostracisation, and invisibilisation of genderqueer+ experiences within the gender game. In spite of the self-perpetuating hegemonic nature of the gender game, possibilities of genderqueer+ resistance and empowerment are identified – the subversive ability to imagine a post-gender game world, personal ways of changing the rules of the gender game to make them work for you and lastly, the transformative potentialities of safe spaces in dis-rupting the oppressive nature of the gender game.
This research reiterates the importance of centring genderqueer+ perspectives and platforming their voices and identities. Lastly, the role of research as a part of broader collective efforts to empower genderqueer+ communities is emphasized, and the potentialities of successive research and synergetic efforts united in the aims of genderqueer+ empowerment are outlined.

Keywords: RDM2023
queer methodology
RDM
non-binary
LGBTQ+
Czech
transgender
LGBT+
youth
qualitative
genderqueer
emergent research design
emancipatory research design
queer
focus groups
Advisor: Mills, D
Tawell, A