VictorJuiz/thesis huggingface dataset:
Lojasiewicz inequalities for the harmonic map energy

In this thesis we study the Lojasiewicz-Simon inequality, a fundamental tool in studying the asymptotic behaviour of gradient flows and of almost-critical points. We focus on the harmonic map energy of maps from surfaces into closed Riemannian target manifolds, viewed as a functional of both map and a domain metric.
In the first part of this thesis we establish new results for the Teichmuller harmonic map flow, an L^2 gradient flow for the harmonic map energy that was introduced by Rupflin and Topping. Previous theory established that in the absence of singularities the flow converges to a branched minimal immersion, but only after passing to a subsequence of times going to infinity and pulling back by a sequence of diffeomorphisms. We show that in general both passing to a sub-sequence and pulling back by diffeomorphisms are actually necessary to obtain convergence of the flow by constructing several “winding” solutions of the flow from the torus. Next, when the target manifold is real-analytic we establish a Lojasiewicz-Simon inequality and use it to show that the flow converges as time goes to infinity, that is without the need to pass to a subsequence or pull back by diffeomorphisms, provided it does not encounter singularities. These results are joint work with Rupflin and Topping.
In the second part of this thesis we study the harmonic map energy of maps from degenerating hyperbolic cylinders into general closed Riemannian target manifolds, motivated by the singular behaviour that can occur for the metric component of the Teichmuller harmonic map flow. We prove a Lojasiewicz inequality with optimal exponent for sequences of almost-critical points which have fixed boundary values and which do not form bubbles, provided their limit satisfies a non-degeneracy condition on the second variation of the energy. Such sequences undergo a change of topology in the limit meaning that the powerful techniques introduced by Simon do not apply. We instead use an approach introduced by Malchiodi, Rupflin and Sharp and obtain a Lojasiewicz inequality in the neighbourhood of a carefully constructed family of “adapted critical points”.

Advisor: Rupflin, M
Model-based decision support with uncertain human-centric data

Both human and algorithmic decision making can be complex. To truly intertwine the two, algorithms need to understand the human decision making process and humans need to have transparent understanding of algorithmic decision analytics. In this thesis, we leverage Bayesian Gaussian processes to better understand people as well as offering a framework for people to better understand algorithms. Key to such transparency on both sides is the robust and principled reporting of uncertainty and careful consideration of preference: the latter being the foundational basis of human decision making. We consider pairwise preference modelling in which the strength of preference (e.g. strong or weak) can be seamlessly taken into account in the model, as well as confidence (uncertainty). We contribute to probabilistic functional regression by enabling the functional predictor space to be interpretable. We develop a principled, robust tool for understanding black-box algorithms, leading to a novel method for the interpretability of features in local domains. Finally, using our heteroscedastic ordinal regression model, we analyse the relationship between the features of occupations (such as their requirement for manual dexterity) and their expected share of US employment in 2030. Together, the approaches and algorithms we provide create a suite of models that increase our decision making capability with human-centric data.

Keywords: Bayesian non-parametrics
interpretability
functional regression
preference learning
future of work
human-centric data
Gaussian processes
Advisor: Roberts, S
Analysis and functional validation of candidate variants arising from human whole genome sequencing

Whole genome sequencing (WGS) is increasingly used to diagnose rare genetic diseases (RGD). WGS data contains approximately 5,000,000 variants per patient, out of which often one variant causes disease. Variant prioritisation algorithms (VPA) help identify disease-causing variants and functional studies can provide evidence to confirm a variant’s effect on a gene or gene product. In this thesis, I test and develop VPA on simulated and real patient data and conduct a functional study to contribute to the validation of HDLBP as a novel disease gene for Fine-Lubinsky syndrome (FLS).
Two established analysis frameworks, Exomiser and VAAST+Phevor, contain VPA that only use genotypic data (GA) and VPA that use genotypic and phenotypic data (GPA). The GA and GPA performance is benchmarked on eleven real WGS patient cases for which disease-causing variants were previously identified in known and novel genes. The GPA performed better than the GA, ranking more benchmark variants first (Exomiser: 4 vs. 5; VAAST+Phevor: 1 vs. 8), whilst reducing the percentage of variants requiring further analysis (Exomiser: from 32.3% to 2.2%; VAAST+Phevor: from 25.4% to 11.2%).
Identifying disease-causing variants in genes that are novel for a specific phenotype is challenging for GPA. A VPA called GPET is developed for disease-causing variant identification in novel genes based on genotypic, phenotypic, and tissue-specific expression data. GPET is benchmarked against Exomiser on a simulated dataset of disease-causing and non-disease-causing variants with imperfect phenotypic annotations, achieving an Area Under the Curve of 0.95, compared to 0.91 for Exomiser. GPET performs worse than Exomiser on the eleven RGD cases for known disease genes and better for all novel disease genes without phenotypic annotations.
Patients for one of the RGD cases are affected by FLS and carry a candidate variant in HDLBP. The variant is suspected to cause FLS by decreasing the RNA-binding activity of vigilin, the protein encoded by HDLBP. A functional study based on oligo(dT) capture is conducted, confirming reduced RNA-binding activity of vigilin due to the candidate variant.
The investigations in this thesis demonstrate that phenotypic and tissue-specific expression data can improve VPA performance for novel disease genes and provide evidence to support HDLBP as a disease gene for FLS.

Keywords: rare diseases
whole genome sequencing
diagnostic odyssey
variant ranking
Advisor: Jenny, T
John, B
David, S
A minority's agency: class, confession, and the quandaries of Muslim India, 1947-c. 1977

This thesis sets out to recover the agency of a wide range of Indian Muslim actors—elite and subaltern, secular and clerical, activist and apolitical—to illuminate the history of the world’s largest religious minority. Bringing the unity of the Muslim experience of postcolonial India from 1947 to c. 1977 under a single focus, it both generalises about the Indian Muslim condition and comments more broadly on the character of Indian democracy. The six chapters here tell of another India, as it were, one quite at variance with the exnominated account of the ‘world’s largest democracy’. Despite its best intentions, the Congress regime that ruled uninterruptedly through the period under study here appears, by turns, illiberal, intolerant, and undemocratic. Minority rights were at a discount. India’s Muslims, I document, had to contend with discrimination in the services, an electoral system that deprived them of commensurate representation, riots in which they accounted for most of the fatalities, a securitisation regime in the borderlands that dispossessed and disenfranchised them, and, a fortiori, an unresponsive leadership. Indeed, what I have called an ‘ashraf betrayal’ is the Ariadne’s thread running through the thesis. Steering between the Scylla of Islamophobia and the Charybdis of capitulation, the Muslim political elite plumped for depoliticisation and juridification. Muslim politics came to be identified with a set of elite symbols—the hajj subsidy, Urdu, Aligarh Muslim University, Muslim personal law, wasiqadari pensions, waqf income—that had little bearing on the lives of ordinary Muslims, shaped by discrimination, disadvantage, and deindustrialisation. There was no room for trade unions, mass protests, anti-discrimination legislation, and subaltern solidarity in this version of Muslim politics. The corollary was a jurisprudential habit of mind, the singular investment in two holy books, the Quran and the Constitution. ‘Muslim politics’ in postcolonial India, I conclude, has been a politics manqué.

Keywords: India
Islam
secularism
Nehru
Advisor: O'Hanlon, R
Partisanship, polarization, and political identity

This dissertation develops a normative account of partisanship sensitive to the challenges of polarization in contemporary democracies. I join recent theorists in defending the value of partisanship for democratic politics, but I do so in a different way. The first part of the project argues that many recent accounts objectionably idealize from elements of real-world partisanship, and that, consequently, their normative prescriptions are silent on the most pressing problems in real-world democracies (Chapter 1). Injecting a dose of methodological self-consciousness into the new partisanship literature, I defend an alternative idealization strategy. Chapter 2 proposes a richer account of political contestation, theorizing partisanship as a distinctive form of identity. But, drawing on work on the politics of difference, I assuage worries that such a view necessarily impinges on agency or promotes zero-sum conflict. I show how a particular kind of partisan identity could, in fact, support political agency, while lending philosophical heft to the intuition that something goes wrong when politics and social life collapse together.
The dissertation's second part further explores the normative implications of this view. I turn, in Chapter 3, to the intra-party relationship. I show how, given certain qualifications, parties can combat political alienation by inculcating the democratic virtues of solidarity and belonging while avoiding charges of exclusion that have long followed defenses of such virtues. Chapter 4 considers the relationship across party lines and asks what citizens of diverse, divided democracies must share. I show how my view of partisan identity makes available an attractive account of political cohesion for divided societies. I premise citizenship not on shared identity or shared beliefs, but on shared action among politically interdependent citizens – action of which partisanship is a principal form.

Keywords: polarization
partisanship
identity politics
identity
The role of ingroup contact in intergroup contact theory

A wealth of research examining intergroup contact theory (Allport, 1954; Brown & Hewstone, 2005) has shown that outgroup contact improves outgroup attitudes. Few studies have examined the corresponding role of ingroup contact, despite its prevalence and evidence suggesting it may detrimentally affect intergroup relations (e.g., Levin et al., 2003; Wilder & Thompson, 1980), or the corresponding effects on ingroup attitudes. This thesis addresses these lacunae by investigating the ways in which ingroup contact, in addition to outgroup contact, shapes both ingroup and outgroup attitudes. In so doing, this thesis aims to achieve a more comprehensive understanding of how contact influences intergroup relations through the incorporation of ingroup contact in intergroup contact theory. Chapter 1 details the theoretical and empirical rationale that underpins this thesis, introduces the 10 studies (total N = 34,944) comprising this thesis, and outlines the analysis techniques used to test the proposed hypotheses (i.e., latent growth modelling, meta-analysis, random-intercept cross lagged panel modelling, and longitudinal social network analysis). Chapter 2 examines the relationship between ingroup and outgroup contact and finds that, at least for friendships, more ingroup contact is associated with less outgroup contact, and vice versa. Chapter 3 investigates the effects of contact on attitudes and identifies positive between-person associations for ingroup contact and ingroup attitudes, and for outgroup contact and outgroup attitudes, yet obtains little evidence for the corresponding within-person effects. Chapter 4 explores the socialisation of ingroup and outgroup attitudes and reports that individuals’ attitudes are influenced by the attitudes held by their ingroup, but not their outgroup, friends. Finally, Chapter 5 discusses the research presented in this thesis and outlines its theoretical, methodological and practical implications. Overall, this thesis shows that ingroup contact has an important role in shaping both ingroup and outgroup attitudes, which highlights the imperative need for further research in this nascent area of study.

Keywords: socialization
outgroup attitudes
ingroup contact
intergroup contact
social network analysis
ingroup attitudes
Advisor: Hewstone, M
Wölfer, R
Reimer, N
Fell, B
Bowes, L
Random irreducible quadrangulations

In the thesis we study random irreducible quadrangulations. We aim to extend known results on local limits of random planar maps and the perceived universality to the class of irreducible quadrangulations.
The first part of the thesis establishes a multitude of enumeration results using standard generating function techniques. We introduce various classes of irreducible quadrangulations and we make a detailed study of their generating functions and asymptotics. The material of this chapter forms the backbone of the subsequent calculations.
The last chapter is conceptually divided into two parts. The first part extends known sharp concentration results for maximum vertex degree and vertex degree distribution to the class of irreducible quadrangulations. In the second part we describe the skeleton decomposition of irreducible hulls and introduce a formal operator to evaluate statistical sums over the semi-layers of the decomposition.
The concluding section of the thesis exploits the properties of the hull operator to provide a new proof of the existence of the Uniform Infinite Irreducible Planar Quadrangulation (UIIPQ). We also explore the asymptotics of the iterates of the hull operator to derive limiting probabilities for the perimeter and volume of r-hulls in the UIIPQ. Our results are (unsurprisingly) in agreement with the conjectured universal behaviour observed in other random models such as the UIPT and UIPQ.

Keywords: irreducible quadrangulations
uniform infinite irreducible planar quadrangulation (UIIPQ)
random planar maps
volume distribution
quadrangulation hulls
Advisor: Lackenby, M
Technological change and labour market institutions and their effect on employment, wages, and inequality

Technological change and labour market institutions (LMI) exert a major influence on the labour markets of developed economies. Routine-biased technological change (RBTC) has been linked to employment polarisation in numerous countries, while institutions such as unions and employment protections have been found to reduce inequalities between workers. However, much is still unknown about the labour market impact of technological change across countries and the interplay between technology and institutions. In this thesis, I integrate insights from labour economics and sociology to address some of the gaps in this literature. I investigate three closely linked research questions: how is routine intensity best measured and how does it vary between countries and over time? Under which conditions does RBTC lead to employment polarisation? And do robotisation and LMI contribute to the patterns that enable polarisation? Using data from the European Working Conditions Survey, the Luxembourg Income Study, and the International Federation of Robotics, I pursue these questions in a sample of OECD countries during the period from 1993 until 2016. First, I develop improved indices of occupational task content which show meaningful differences with established measures as well as across countries and over time. Secondly, I demonstrate that RBTC is associated with employment polarisation only in countries where routine occupations are concentrated in the middle of the wage hierarchy. Finally, my analyses suggest that robotisation has reduced the relative wages of routine manufacturing occupations and thus made employment polarisation less likely, particularly in countries with strong employment protections for temporary workers. The findings of this thesis advance the study of employment and wage changes in both economics and sociology, and illustrate the benefits of jointly analysing technological and institutional explanations for differences and changes in employment, wages, and inequality.

Keywords: technological change
labour market
inequality
occupations
power resource theory
employment
Advisor: Bukodi, E
Nolan, B
The origin of Chinese glasses and the glass trade along the Silk Road from the Warring States (475 BC – 221 BC) to the Han Dynasty (202 BC – AD 220)

The Silk Roads played significant roles in the trade of glass products. Natron glass from the Mediterranean, potash glass and mineral soda alumina glass from South and Southeast Asia have been discovered in different provinces in China. This article-based thesis mainly consists of three individual papers.
1) Lead-barium glass appeared during the late Warring States period in China and was considered a Chinese invention due to the unique presence of high barium. However, the glass replication in this research indicates that lead-barium glass could be a mixture of natron glass and lead-barium minerals, which also explains a high Na2O concentration in this type of glass.
2) To further test this theory, fifty samples, including natron glass, lead-barium glass and lead-barium faience, were analysed through laser-ablation inductively-coupled plasma mass spectrometry (LA-ICP-MS). We produced a piece of code that allows us to perform 3D kernel density estimation on four variables (i.e., four-element concentrations) in a tetrahedron plot. Then, we combined Maximum Mean Discrepancy with hypothesis testing to trace the potential silica source for producing lead-barium glass. The result confirmed that the Syro-Palestinian coast was a possible source region for the raw glass used to make lead-barium glass. Moreover, the silica source for producing lead-barium glass was not related to lead-barium faience.
3) In this DPhil project, we analysed twenty-seven mineral soda alumina (m-Na-Al) glass and eighty-seven mineral potassium glass beads unearthed in different provinces in China through LA-ICP-MS. The trace element analysis indicates that m-Na-Al glass and most of the potash glass unearthed from Guangxi were presumably produced somewhere in Southeast Asia and exported through the Maritime Silk Road. M-Na-Al glass in Henan and the rest of the potash glasses from other regions in China were probably produced in southern India or Sri Lanka through the North and Southwest Silk Roads. The connection between the spread of Indo-Pacific beads and Buddhism is discussed.
In summary, this DPhil project shows detailed research on various types of glass in China through multiple methods, and the conclusion contributed by this thesis can provide new ideas for archaeologists to rebuild the Eurasian Steppe Road. The future archaeological and archaeological science research on glasses from Central Asia will certainly provide a strong link on how glasses were traded from the Mediterranean to China.

Keywords: natron glass
lead-barium glass
potash glass
LA-ICP-MS
m-Na-Al glass
Buddhism
Silk Road
maximum mean discrepancy
kernel density estimation
Advisor: Pollard, AM
The use of biomedical big data for economic analyses of genome sequencing in rare genetic diseases: a case study from the 100,000 Genomes Project

Countries around the world are increasingly translating next-generation sequencing diagnostics from research into clinical practice, especially for rare genetic diseases, but with limited health economic evidence. In the absence of data from clinical trials, the use of linked observational real-world patient-level genomic and clinical data, defined as biomedical big data (BBD), could improve the health economic evidence base. This thesis explores the use of BBD for economic analyses of genomic diagnostics in rare genetic diseases in the context of the Genomics England 100,000 Genomes Project (100KGP) and the National Health Service (NHS) in England.
The practical and methodological challenges of using BBD for health economic analyses in the context of genomic sequencing are summarised and described by the results of a literature review. These challenges are initially explored via an analysis of the healthcare resource use of patients suspected of having a rare genetic condition, using data from the 100KGP. The health economic value of using diagnostic genome sequencing for the diagnosis is then considered by conducting economic evaluations for two disorders: hereditary ataxia and craniosynostosis. For hereditary ataxia, a cohort-based analysis is presented that uses diagnostic yield as the outcome measure. For craniosynostosis, a model-based analysis is presented that uses quality-adjusted life years (QALYs) as the outcome measure. In each case, the choice of methodological approach is supported by evidence from a literature review that summarises economic evaluations that have compared genomic and traditional diagnostic pathways.
The results of the costing analysis indicate that patients with suspected rare genetic diseases consume considerably more healthcare resources than the general population in England. The results of the economic evaluations indicate that genome sequencing is a cost-effective use of scarce healthcare resources in the English NHS. However, these results are characterised by considerable uncertainty, so should only be considered as an early assessment of the likely cost-effectiveness of genome sequencing in this context. The thesis concludes that the use of BBD for economic analyses presents many challenges that may not be easily overcome, and which may require an evolution in health technology assessment and policy-making in this context.

Keywords: health economics
genomics
rare diseases
big data
Advisor: Buchanan, J
Wordsworth, S