VictorJuiz/thesis huggingface dataset:
Adversarial robustness of Bayesian neural networks

This thesis puts forward methods for computing local robustness of probabilistic neural networks, specifically those resulting from Bayesian inference. In theory, applying Bayesian inference to the learning of neural network parameters carries the promise of solving many practically vexing problems that arise under the frequentist learning paradigm. In particular, Bayesian learning allows for principled architecture comparison and selection, the encoding of prior knowledge, and calibration of predictive uncertainties. Recent studies have shown that Bayesian learning can lead to more adversarially robust predictors. Though theoretically this is the case, and empirically has been shown in particular instances, anecdotal evidence of heightened robustness does not provide sufficient assurances for those who wish to deploy Bayesian deep learning in a safety-critical context. While methods exist for arriving at guarantees of robustness for deterministic neural networks, the probabilistic nature of Bayesian neural network weights renders these methods inoperable.
In this thesis, we investigate concepts of robustness for Bayesian neural networks, which allow for robustness guarantees which consider both the stochasticity of the model as well as the model's decision. We provide methodologies which compute these quantities for a given Bayesian neural network with either a priori statistical guarantees on the precision of our estimates, or probabilistic upper and lower bounds which are provably sound. Finally, we consider robustness as a primary desideratum in the Bayesian inference of neural network parameters and demonstrate how to modify the likelihood in order to infer a posterior distribution with favorable robustness properties. The modification of the likelihood make our method transparent to the approximate inference technique for Bayesian neural networks.
We assess the practical applicability of our proposed methodology using Bayesian neural networks trained on several real-world datasets including airborne collision avoidance and traffic sign recognition. Additionally, we assess the robustness of Bayesian posterior distributions approximately inferred using five different approximate inference methods. We find that our methodology provides the first provable robustness guarantees for Bayesian neural networks, thus enabling their deployment in safety-critical scenarios. Further, our proposed methodology for robust Bayesian inference of neural network parameters enables us infer posterior distributions which have greatly heightened provable robustness even on full-color images.

Keywords: Bayesian Deep Learning
Adversarial Robustness
Deep Learning
Formal Methods
Verification
Advisor: Kwiatkowska, M
MRI biomarkers of recovery for acute stroke

Predicting stroke recovery is challenging. Imaging biomarkers might help address this unmet need. However, the majority of studies to date have been performed in the post-acute period or used simplistic biomarkers such as infarct volume and have largely ignored the dynamic processes that occur immediately after stroke such as the contribution of oedema.
This Thesis set out to address these issues in a systematic manner in a cohort of patients recruited to a clinical imaging study at the John Radcliffe Hospital. Serial imaging data were acquired starting from the first hours following symptom onset.
The first part of this Thesis focused on improving measurement accuracy. A machine learning approach was developed and validated to segment stroke lesion and separately quantify infarct volume and anatomical distortion (oedema ± haemorrhagic transformation). An independent component analysis (ICA) based approach was used for the first time to denoise arterial spin labeling (ASL) perfusion data. Minimising the potential confounding factors present in the early stroke stages enabled the robust analysis and interpretation of the results obtained.
The second part of this Thesis used Topological Data Analysis (TDA) to analyse structural (DTI tractography) and functional data (rs-fMRI). TDA allows the study of higher order complex relationships between brain regions using spatially insensitive metrics. TDA metrics showed that both structural and functional connectivity were independent predictors of recovery. The changes in functional connectivity were independent of perfusion metrics, either BOLD or ASL derived. At 1-week, oedema was associated with symptom severity and recovery. Oedema was linked to presenting vasodilation and vasoconstriction, the latter providing supporting evidence for the glymphatic theory.
The results of this Thesis open the opportunity for further work to validate TDA metrics as biomarkers of recovery and to understand whether they may play a role in clinical trial design. In addition, a greater understanding of how post-stroke oedema reflects the balance of injury and repair mechanisms is needed to guide what treatment might be appropriate and when following acute stroke. These biomarkers could allow personalised treatment.

Keywords: Recovery
Acute Stroke
Biomarkers
MRI
Advisor: Kennedy, J
Structural studies of DNA containing base and sugar modifications

Chemical modifications to DNA are ubiquitous in nature, with roles ranging from bacterial warfare to epigenetics. Unnatural modications can also be introduced to DNA and constitute important research tools. In both cases, the effect of chemical modifications on DNA structure is key to their function. This work describes structural studies of DNA containing natural and unnatural DNA modifications.
Several modified bases—5-hydroxymethylcytosine (hmC), 5-formylcytosine (fC), and 5-carboxylcytosine (caC)—were recently discovered in human DNA and appear to have crucial biological roles. The molecular basis of their function remains unclear, but structural changes to the DNA double helix have been implicated. To address this, the effect of cytosine modifications on DNA structure was probed by an array of techniques including X-ray crystallography, CD and NMR spectroscopy, DNase I and gel-mobility assays. Contrary to previous findings, no evidence was found for a unique, fC-dependent DNA conformation that is distinct from the A-, B-, or Z-forms. However, 5-methylcytosine (mC), hmC, and fC were found to induce other structural changes, which can alter DNA-protein interactions and may thus be important to their biology.
The second part of this thesis describes the structural characterisation of DNA containing nitroxide spin labels, introduced via a recently developed 2′-alkynyl labelling strategy. Using X-ray crystallography, MD simulations, EPR and NMR spectroscopy, the spin labels were localised and found to cause only modest and local perturbation to DNA conformation. These results establish 2′-alkynyl spin-labelling as an accurate and minimally perturbing method to probe DNA structure.

Keywords: Epigenetics
Structural biology
DNA
Biophysics
Advisor: Brown, T
Magnetism of the columnar ordered quadruple perovskite manganites

This thesis studies the magnetism of the A'2A''A'''Mn4O12 columnar ordered quadruple perovskite manganites. The magnetic structures of five distinct members of this family of manganite perovskites has been determined using neutron scattering and magnetometry measurements. Point charge calculations of the crystal electric field, percolation calculations and a symmetry and group theoretical based approach to data analysis has been used to motivate the microscopic origins of the determined magnetic phases, and the physical mechanisms driving the observed magnetic phase transitions. Four regions of the magnetic phase diagram have been observed; a collinear ferrimagnetic phase, a Γ-point canted ferrimagnetic phase, a Z-point canted ferrimagnetic phase, and a magnetic phase characterised by well correlated collinear ferrimagnetic order punctuated by randomly dispersed clusters of antiferromagnetic order. We show that competing superexchange interactions and disorder can tune these manganites into different magnetically ordered phases.
In these systems we observe two mechanisms for driving spin reorientation phase transitions. In Tm2MnMnMn4O12 the competition between rare-earth (Tm3+) and transition metal (Mn) anisotropies coupled via f-d exchange drives the spin reorientation, as is typical for distorted perovskites. In R2CuMnMn4O12 (R = Y or Dy) an alternative paradigm for spin reorientation was observed, which originated in frustrated Heisenberg exchange interactions, and the competition between Dzyaloshinskii- Moriya and single-ion anisotropies. Our studies on magnetic dilution in the Sm2MnMnMn4-xTixO12 systems have shown that they demonstrate an unusual variation in transition temperature, suggesting a departure from mean field physics. We observed a spin doped Griffiths phase in Y2MnMnMn4O12, and the coexistence of two magnetically distinct phases below Tc.

Keywords: perovskites
manganites
neutron diffraction
magnetism
crystallography
Advisor: Johnson, R
Radaelli, P
Towards a transformative approach to affirmative action in South Africa

The South African courts’ affirmative action jurisprudence lacks coherence and clarity on important issues that shape what is possible through affirmative action. In light of the importance of affirmative action to eradicating inequality and the courts’ powerful role, my thesis explores how the commitment to transformative constitutionalism and substantive equality should guide the courts’ affirmative action jurisprudence.
Part I explores the contested meaning(s) of transformative constitutionalism and substantive equality. I argue that these should guide the development of a transformative approach to affirmative action. The core of this approach is a focus on eradicating group-based disadvantage.
Part II draws from Part I’s foundation and suggests how the courts should grapple with several contested issues in its affirmative action jurisprudence. The first is the role that the courts should play in the judicial review of affirmative action. I argue for a value-driven proportionality assessment which is tilted in favour of preserving affirmative action measures. The second is whether there is a duty to take affirmative action. I argue that there is a duty to take positive steps to fulfil the right to equality, in some cases, through affirmative action. The third issue is whether the courts can order affirmative action as a remedy. I argue that affirmative action is available as one of the appropriate, just and equitable remedies available to courts.
Still drawing on the foundation in Part I, Part III explores and provides guidance on four important issues which arise in the design and implementation of affirmative action: the purposes that these measures should pursue (for what?); the criteria for the demarcation of the beneficiary groups (for whom?); focussing on quotas, the range of permissible forms that affirmative action could legitimately take (through what means?); and whether there is an end-date for affirmative action (for how long?).

Keywords: substantive equality
South Africa
distributive justice
affirmative action
transformative constitutionalism
equality
corrective justice
transformation
Advisor: Fredman, S
(Re)shaping ethical considerations in involuntary admission for inpatient psychiatric care: An empirical ethics inquiry drawing insights from a South African case study

Involuntary admission for inpatient psychiatric care, though common in clinical practice, remains a long-standing ethical challenge in mental healthcare. Continued disagreement over when, if ever, involuntary admission can be ethically justified (in the psychiatric ethics literature) sits against the backdrop of calls for increased access to mental healthcare in low- and middle-income countries (in the global mental health discourse). My thesis takes this normative tension as a starting point for inquiry. I first review scholarship in psychiatric ethics and global mental health to identify ethical principles relevant to involuntary admission. I argue that the principles identified diverge along normative ideologies: psychiatric ethics is rooted in a negative rights framework while global mental health is rooted in a positive entitlements framework. In light of this divergence, I adopt an empirical ethics approach to 1) explore the normative commitments that do impact decision-making for involuntary admission in practice—drawing insights from a South African case study—in order to 2) understand the normative commitments that should impact decision-making for involuntary admission in practice. Using semi-structured interviews with mental healthcare practitioners and mental health advocates, my empirical data analysis demonstrates that practitioners’ decisions are influenced by a number of extra-legal considerations. These considerations focus not only on the individual being assessed, but also on their family availability, facility-based and broader resource constraints, and the health system structure. I focus my ethical analysis on the normative value of incorporating resource- and system-focused considerations in decision-making, especially given their relevance to the provision of mental healthcare in low- and middle-income country contexts. I argue that resource-focused considerations—though essential to the proper application of a positive entitlements framework—should not be incorporated into decision-making for involuntary admission, while system-focused considerations should—in order to better meet the demands of a negative rights framework. My work offers a novel contribution to the ‘intractable’ debate over the ethics of involuntary admission by demonstrating that dominant ethical principles invoked in both psychiatric ethics and global mental health do not fully capture the range of considerations that should be taken into account in decision-making in practice.

Keywords: mental health law
mental healthcare
bioethics
involuntary admission
empirical ethics
Advisor: Dunn, M
Parker, M
The development of wealth inequality in the German territories of the Holy Roman Empire, 1300-1850

This dissertation investigates the development and causes of economic inequality in pre-industrial Germany from 1300 to 1850. To do so, it presents two novel datasets. The first is the largest pre-industrial household-level dataset of wealth taxation covering more than 35 urban and over 100 rural communities, comprising more than 100,000 observations. The second is a city-level dataset of more than 30 city budgets. These novel datasets reveal that wealth inequality in pre- industrial Germany moved in four phases: a decline in wealth inequality after the Black Death in 1347-1352, a rise in inequality from circa 1450 onwards, peaking at the eve of the Thirty Years’ War in 1618 during and after which it declined until 1700 when it started rising again. This development in wealth inequality distinguishes Germany from other European regions where inequality rose steadily throughout the early modern period. It highlights the extraordinarily destructive impact of the Thirty Years’ War. It further provides the first consistent poverty estimates for the period from 1300 to 1800. It shows that poverty and inequality largely developed in tandem except for the period of Thirty Years’ War when poverty rates peaked. Poverty rose particularly dramatically in rural communities where the destructive effect of the War was most pronounced. This dissertation also investigates fiscal extraction as one of the possible drivers of inequality and poverty. It provides the first comparative estimates of per capita fiscal pressure for a large number of German cities. It shows that throughout the late Middle Ages fiscal pressure was low and stable, but from the mid-sixteenth century onwards it started to rise and reached its maximum right before and during the Thirty Years’ War. These levels are high even compared to the level of fiscal extraction in other fiscally-advanced European regions, including England, the Netherlands and France. This finding might explain the particularly steep rise of inequality just before the onset of the Thirty Years’ War. In sum, by making use of originally compiled data, this dissertation reveals the economic consequences of the Black Death, the Thirty Years’ War and fiscal extraction to advance our understanding of inequality and poverty in pre-industrial Germany.

Keywords: pre-industrial
Germany
inequality
taxation
fiscal capacity
Holy Roman Empire
wealth
Advisor: Broadberry, S
Somatic mutation in colorectal cancer: A window to disease pathogenesis 

Cancer has long been considered to be a disease driven by mutation. In recent years, this theory has been updated to reflect increased understanding of the importance of additional factors influencing disease pathogenesis, such as the cell of origin and microenvironment. In this thesis, I explore somatic mutation acquisition and the effect of microenvironmental influence on human and animal models of colorectal tumourigenesis.
Analysis of mutations in healthy human colonic epithelium revealed a capacity to tolerate driver mutations, while inflamed epithelium exhibited increased mutation acquisition. I also investigated somatic mutation following exposure to the mutagen AOM in mice harbouring spontaneous colitis or a constitutively deranged intestinal microenvironment. Here, I show that these differences in underlying disease state influence mutation acquisition and provide novel evidence of an AOM-associated mutational signature in mice.
Although numerous studies have suggested links between morphogenetic signalling pathways and the DNA damage response (DDR), the influence of these pathways upon mutation protection mechanisms within the intestine remains unclear. To explore this, I studied the Vil1-Grem1 (VG) mouse, a model of disrupted intestinal homeostasis in which aberrant epithelial expression of the BMP signalling antagonist Grem1 results in the formation of ectopic crypts. I provide evidence of impaired activation of DDR pathways within ectopic crypts following exposure to ionising radiation and go on to propose that a novel mechanism linking BMP signalling and DNA repair results in increased genomic instability within this compartment.
I also examined the effect of therapeutic restoration of cell fate determination on mutation acquisition following AOM exposure in VG mice. I demonstrate that therapeutic restoration of morphogen gradients in VG mice can rescue disease phenotype and confer protection against mutation acquisition, but may also result in a putative skew to DNA repair-associated mutation acquisition in these mice. Finally, I provide evidence that disease progression in an immune-deficient model of inflammation-associated cancer occurs in the absence of mutation accumulation and is instead associated with dysregulated gene expression. Importantly, I demonstrate that abrogation of the inflammatory drive within this model rescues disease phenotype in colitis but not in polyps.
Overall, I have demonstrated that somatic mutation acquisition within the intestine varies and reflects the influence of the microenvironment, cell of origin and mutation protection mechanisms upon disease pathogenesis. This has translational relevance, given that the development of personalised therapies requires a holistic and accurate understanding of the mechanisms underpinning the vast heterogeneity of colorectal cancer.

Keywords: intestinal microenvironment
somatic mutation
signalling pathways
DNA damage
colorectal cancer
Advisor: Leedham , S
Tomlinson, I
Stripe melting and photoinduced enhancement of superconductivity in La2-xBaxCuO4

The interplay between superconductivity and other broken symmetry phases has emerged as a central theme in cuprate physics with increasing reports of charge order in several materials. The relationship between the superconducting state, stripe order, and the so-called low-temperature tetragonal (LTT) structural distortion is one of the great mysteries in high-TC superconductivity. It has long been believed that stripes are pinned by the LTT distortion and compete with superconductivity to result in an incoherent state with non-superconducting transport. Furthermore, there is evidence that stripes are compatible with in-plane Cooper pairing, creating phases that may involve 2D superconducting CuO2 planes decoupled as a result of the periodic charge modulation, which, it is speculated, may prevent interlayer Josephson tunnelling. In this thesis we combine photoexcitation, time-resolved resonant soft x-ray diffraction and THz time-domain spectroscopy to demonstrate that ultrafast disruption of the stripe ordered phase promptly enhances interlayer Josephson coupling in La1.885Ba0.115CuO4.
Time-resolved resonant soft x-ray diffraction demonstrates that charge order melting occurs immediately after near-infrared photoexcitation whereas the crystal structure remains intact, at least for moderate excitation fluences. THz time-domain spectroscopy reveals that, for the first 2 ps following photoexcitation, a new Josephson plasma resonance edge, at higher frequency with respect to the equilibrium edge, is induced indicating enhanced superconducting interlayer coupling. Furthermore, we show that the fluence dependence of the enhanced interlayer Josephson coupling follows closely that of the stripe order melting and not that of lattice rearrangement.
In the concluding part of the thesis, I also discuss a different excitation geometry (out-of-plane optical pumping), which compared to conventional in-plane excitation promotes a transient superconducting state characterized by both an enhanced transient superfluid density and a longer lifetime.
All in all, this work demonstrates how high-energy charge excitation constitutes, within certain conditions, an alternative method to phonon pumping to promote nonequilibrium superconducting states in high-Tc cuprates, opening new perspectives for the ultrafast optical control of complex solids.

Advisor: Cavalleri, A
Dhesi, S