VictorJuiz/thesis huggingface dataset:
Time-parallelisation techniques with applications to plasma simulation

Parallel-in-time (PinT) methods have become an increasingly popular tool in the numerical solution of time-dependent Partial Differential Equations (PDEs), in light of their potential for extracting additional concurrency when spatial parallelism saturates. Particularly complex applications, such as the ones involving plasma simulations for fusion research, would benefit greatly from the implementation of such methods, given the large computational time usually necessary for the numerical solution of their governing equations.
In the first part of this thesis, we develop the concept of Space-Time Block Preconditioning (STBP), a technique for simplifying the task of time-parallelising the solution of a whole system of PDEs by reducing it to that of inverting space-time operators acting on single variables only, which are more amenable to be tackled by PinT algorithms. This technique borrows from block preconditioning strategies developed for spatial operators in the framework of time-stepping algorithms, and extends them to the whole space-time setting. After illustrating the guiding principles behind STBP, we measure its effectiveness with applications in fluid dynamics and magnetohydrodynamics. In both cases, the resulting pre-conditioners show excellent scaling properties with respect to mesh refinement, and their applications come at little-to-no overhead cost in terms of iterations to convergence with respect to their time-stepping counterpart, thus providing evidence for their potential parallel efficiency.
Ultimately, however, the parallel performance of a space-time block preconditioner depends on that of its internal components, which still rely on already-existing PinT methods. This might become an issue when dealing with advection-dominated or hyperbolic equations, as classical PinT algorithms have shown to struggle in this case. For this reason, the second part of this thesis is dedicated to investigating the causes behind this degradation in performance, as well as to study more recent PinT approaches for overcoming this limitation.

Keywords: circulant preconditioning
computational fluid dynamics
multigrid
high-performance computing
block preconditioning
parallel-in-time methods
Advisor: Wathen, A
Debasmita, S
Predicting the T2K neutrino flux and measuring oscillation parameters

T2K is an experiment designed to study the ways in which neutrinos evolve as they propagate through space. The experiment uses an artificial beam of muon neutrinos, produced at the J-PARC facility in Japan. The spontaneous mixing of these beam neutrinos with other flavours is measured after 295 kilometres, at the location of the Super-Kamiokande detector. The initial beam composition is measured after 280 metres, using a combination of two near detectors. T2K is optimised for measurements of electron neutrino appearance, and muon neutrino survival. Essential for these measurements is a detailed knowledge of the initial beam composition, before neutrino oscillations had occurred. The production of intense neutrino beams at accelerator facilities is challenging, and requires exceptional understanding of chains of hadronic interactions initiated within thick targets. Most of T2K neutrinos are produced from in-flight decays of focused pions and kaons, emitted from an extended graphite target (90 cm) bombarded with a 30 GeV proton beam. Besides internal constraints from near detector data, T2K relies on hadron production measurements collected by other experiments, most importantly NA61, for accurate modelling of the initial neutrino flux.
This thesis presents a new T2K neutrino flux prediction, using the NA61 replica-target dataset from 2009. The earlier flux prediction relied on NA61 measurements collected with protons incident on a thin graphite target (2 cm). The following analysis incorporates NA61 data collected on the full length replica of the T2K target in 2009. In light of this new data, the flux calculation technique has been modified. A dramatic reduction in the unoscillated muon neutrino fractional flux uncertainty has been achieved, from ~10% to ~5% around the T2K flux peak. The impact of the improved flux prediction on oscillation measurements has been examined, by performing separate fits to ND280 data, and joint ND280 and Super-K data, in the well-established Bayesian Markov Chain Monte Carlo analysis framework.

Advisor: Hartz, M
Weber, A
Modelling seafaring in Iron Age Atlantic Europe

The extent to which a European ‘Atlantic Zone’ was connected by maritime links in the Iron Age is debatable, as direct evidence is fragmentary and no accounts from contemporary inhabitants of Atlantic Europe survive. This thesis contributes to this debate by developing a new navigation model and deploying the model in the western English Channel. This thesis seeks to understand (1) whether proposed routes across the Channel would have been viable and whether other alternatives may have existed, (2) whether or not promontory forts could have been used as landmarks for navigator, and (3) how aspects of navigation – such as speed potential, landmarks, and ability to read conditions – may have affected Channel crossings. The model developed for this analysis is a fully agent-based model, in which simulated navigators follow a set of instructions without input from a human operator. A model that allows simulated ships to go off-course and potentially not reach their destinations can be used to evaluate routes in terms of risk and reliability.
The main analysis here consists of a comprehensive survey of simulated Channel crossings from March-September 2018. The results of this analysis suggest that crossings were most successful in brief windows, critique pre-existing schemes of Channel crossing, and evaluate whether certain coastal ‘nodes’ may have been more or less useful as points of departure across the Channel. Case studies focus on (1) the identification of a Continental node ‘corresponding’ to Hengistbury Head, and the potential of Guernsey as a ‘staging port’ for northbound voyages; (2) the connection between Iron Age settlements at Le Yaudet and Mount Batten, and the relative effects of parameter inputs to the model; and (3) the visibility of landmarks at the end of the Cornish and Breton peninsulas. These results demonstrate the value of the model for future analysis and its potential for further development.

Keywords: Maritime Archaeology
Agent-Based Modelling
Landscape Archaeology
Iron Age
Visibility Analysis
Navigation
Movement Analysis
Advisor: Schulting, R
Pouncett, J
Essays on financial markets

This thesis is a collection of three stand-alone essays.
The first essay, Modelling the Maker-Taker Pricing in Financial Markets, investigates the trading fees charged by stock exchanges to brokers. In particular, it studies the maker-taker pricing structure which is a form of second degree price discrimination. This is a theoretical work which develops a model of a limit order book with a closed-form solution that proxies a modern electronic trading platform. The model builds on the current literature by introducing competition among exchanges and allowing depth to build, thus providing predictions for market quality (spread, depth, and volume) and trading activity (limit and market orders) following a change in the trading fees. Maker-taker fees are the most prominent pricing scheme amongst stock exchanges.
The second essay, Assessing the Attributes and Implications of Mini Flash Crashes, investigates all mini flash crashes (MFCs) by U.S. equities between January 3, 2006 and February 3, 2011. A mini flash crash is defined as a change in the stock price that is larger than 0.8%, takes place in less than 1.5 seconds for at least 10 consecutive trades, and recovers to within 0.1% of the starting price. This is an empirical work that explores both the causes (or attributes) and implications of MFCs, and it is concluded that MFCs negatively affect market quality (measured as inside spread and BBO depth) over a 10-minute window around the MFC. Besides, the phenomenon of MFCs has deep repercussions on market agents, e.g. brokers trading at the volume-weighted average price.
The third essay, Leadership of the Price Discovery Process at Outer Levels of the Book, investigates price discovery, defined as the impounding of newly formed fundamental information into the observed price of the asset, and measured by the contribution different trading venues make to the common efficient price. This work contributes to the literature by showing that the market which leads the price discovery process at the BBO needs not enjoy leadership at other levels of the book, particularly at outer levels, i.e. levels that are distant from the BBO. This is of relevance since less than 50% of liquidity is posted to the BBO so focusing exclusively on the first level of the book does not provide a full understanding of which market truly leads the price discovery process.

Advisor: Tsai, J
Investigating the role of SET1A and SET1B in the regulation of gene expression

The development of complex multicellular organisms relies on the precise spatiotemporal control of gene expression. The post-translational modification of histone proteins within chromatin has emerged as an important mechanism by which the regulation of gene expression can be achieved. One such histone modification, H3K4me3, is intrinsically linked to transcriptional activity; levels of H3K4me3 at gene promoters are positively correlated with gene expression and numerous H3K4me3 ‘reader’ proteins have been identified that could elicit a positive transcriptional outcome. Despite this, H3K4me3 appears to be dispensable for gene transcription in simple eukaryotes. Studying H3K4me3 in mammalian cells is complicated by the diversification in the H3K4 methylation machinery during evolution. Mammalian cells produce six complexes proposed to methylate H3K4: MLL1-4 and SET1A/B. SET1A/B broadly associate with gene promoters and have been proposed to place the majority of H3K4me3 in mammalian genomes. However, the effects of SET1A/B removal on gene expression have typically been subtle and lacked directionality. Therefore, the contribution of SET1A/B to the regulation of gene expression, either through the deposition of H3K4me3 or otherwise, has remained largely unclear.
To address the role of SET1A/B in mammalian gene expression I have developed cell lines in which SET1A and SET1B can be rapidly depleted from cells either individually or in combination. By using these rapid depletion systems coupled with quantitative gene expression analysis I find that SET1A/B function to support active gene expression in embryonic stem cells. In contrast to the prevailing views in the field, I reveal that SET1A/B make a rather subtle contribution to H3K4me3. Furthermore, I find that SET1A/B are transcriptional activators that are able to activate gene transcription independently of their catalytic activity. I then begin to dissect the catalysis-independent mechanisms by which SET1A/B regulate gene expression and find that their interaction with WDR82 is essential for transcriptional activation. Furthermore, I discover that SET1A/B influence the occupancy and phosphorylation of RNA polymerase II. Together, these observations reveal an unexpected role for SET1A/B in supporting active transcription independently of their catalytic activity.

Advisor: Klose, R
Benchmarking memory and logic gates for trapped-ion quantum computing

Trapped ions are a promising platform for experimental quantum computing, possessing the longest decoherence times and the highest fidelity logic gates of any candidate technology. The challenge remains to scale up ion-trap systems to larger numbers of qubits. This thesis benchmarks two fundamental operations for scalable trapped-ion quantum computing: the memory performance of a 43Ca+ hyperfine qubit, and mixed-element entangling gates between 43Ca+ and 88Sr+.
Decoherence is usually measured over long timescales, where the memory errors ε are large compared to state-preparation and measurement errors. Information about the small-error regime relevant for quantum computing is inferred by extrapolation. In this work we use randomised benchmarking to directly measure errors as small as 1.2(7) × 10−6 after a storage time of 1 ms, which is around an order of magnitude smaller than would be expected based on the usual model of exponential decay. We find εm < 10−4 for up to 50 ms with no additional dynamical decoupling, and εm < 10−3 for up to 2 seconds using a simple CPMG sequence. These timescales exceed previously-demonstrated gate or measurement times in trapped-ion systems by several orders of magnitude — a requirement for quantum error correction, and a highly desirable feature for near-term processors. The qubit is robust to offsets of the external magnetic-field strength, with εm < 10-4 for 1 ms even at a 50 mG offset, and we identify phase noise on the reference oscillator as the limiting factor on the memory performance.
We provide a comparison of different implementations of mixed-element geometric phase gates in the same experimental system. This includes a light-shift gate which can be implemented on both ion species using a single laser, with a fidelity of 99.8(1)% or 99.7(1)%, measured using partial state tomography or interleaved randomised benchmarking respectively. We also demonstrate several Mølmer–Sørensen gates with measured fidelities of up to 99.6(2)% (by partial state tomography); this mechanism is more susceptible to errors arising from instability of the external magnetic field. For the first time, this pushes mixed-element entangling gate fidelities over the fault-tolerant threshold level (above which error correction is possible), and puts them on par with state-of-the-art single-species gates.

Advisor: Lucas, D
Some problems in topology

This thesis explores generalizations of category in the sense of Lusternik-Schnirelmann. The material falls naturally into two parts.
Chapter 1 is concerned with numerical invariants. Following Berstein, for a closed n-manifold M let N(M) (resp. n(M)) denote the minimum cardinality of a covering of M by open subsets, each of which embeds (resp. immerses) inIRn. In Chapter 1 the values of N(M) and n(M) are determined when M =112Pn -- with the exception of N(1RPn ) when n = 31 or 47. For a vector bundle C over a space X, James has defined Vecat(ξ) to be the minimum number of open subsets required to cover X with the restriction of C to each subset stably trivial. In Chapter 1 the categories of all vector bundles over all real projective spaces are also determined.
In Chapter 2 it is undertaken to define LusternikSchnirelmann category solely in terms of the category of spaces modulo weak equivalences. This is done by equipping the homotopy category with a notion of covering. The reason for doing this is to obtain a more conceptual definition of cocategory. It turns out that there are many possible definitions of cocategory. The relationship between two of them is discussed in Chapter 2.
The category of a connected space X is closely related to the Milnor filtration of X regarded as the classifying space of its loop space. This in turn is intimately related to the H-space structure on 2X. The framework of homotopy coverings is exploited in Chapter 3 to yield a filtration of a (k-1)-connected space analogously related to its k-fold loop space. There results a theory of higher associativity for k-fold loop spaces and a dual theory for k-fold suspensions.
Homemaker or breadwinner? A cross-sectional analysis of parental leave policies and their impact on gender role attitudes across European countries.

Despite the widespread increase in female labour force participation, gender role attitudes towards the gendered division of labour remain diversified with stark variations across Europe. Given the significance of parental leave policies in shaping the division of labour between parents, this study examines how parental leave policies influence the formation of gender role attitudes across Europe. Drawing on time series, cross-sectional data from the European Value Study (EVS), and the Organisation for Economic Co-operation and Development (OECD) family database, I study the effects of three parental leave design dimensions, (1) duration, (2) compensation, and (3) flexibility across countries and across time (1990-2017). The results suggest that an increase in the duration of parental leave for fathers as well as a flexible parental leave design that allows parents to split the parental leave have both a strong and positive effect on the formation of egalitarian gender role attitudes. However, an increase in the duration of parental leave for mothers carries a negative effect on the formation of egalitarian gender role attitudes. Further, this study points towards a new emerging cleavage across European countries with some moving further towards a dual-earner model and others reversing the egalitarian advancements and resorting to a more traditional gendered division of labour. The broad perspective on cross-country differences as well as the usage of new evidence on gender role attitudes gives new insights on the debate over the relationship between macro-level policies and their impact through policy feedback on micro-level gender role attitudes.

Keywords: gender role attitudes
parental leave
female labour force participation
policy feedback
gendered division of labour
Advisor: Bukodi, E
Advancing ultrasound image analysis by capturing operator gaze patterns

Obstetric ultrasound scanning is a safe and effective tool for the early detection of fetal abnormalities and therefore crucial for determining the necessity of clinical intervention. However, ultrasound relies on operator expertise, which is a scarce resource globally. Moreover, there are large geographical and inter-observer variations of clinical outcomes. To address this, the PULSE project aims to develop a new generation of ultrasound scanning capabilities based on big data and machine learning models which capture the knowledge of experienced sonographers. To this end, the project team acquired a first-of-its-kind large-scale dataset of routine clinical ultrasound scanning with gaze-tracking data.
In this thesis, we first examine shortcomings of the operator-machine interaction. We find that sonographers adjust the biometric measurements of fetuses with potential growth abnormalities towards the healthy expected value, providing a possible explanation for the known deficiencies of these measurements. Moreover, we study the adherence to safety recommendations regarding thermal energy emission and find that, while sonographers keep within the appropriate limits, they rarely check the safety indices. We provide suggestions for the modification of the ultrasound machine interface to address these two issues.
Second, we develop the first model that predicts sonographer gaze-tracking data on ultrasound video through the method of visual saliency prediction. In addition, we propose the first unified visual saliency model for the prediction of gaze on both images and videos. Besides unifying the two modalities, the model obtains state-of-the-art performance on both tasks for all relevant computer vision benchmarks.
Third, we show that sonographer gaze-tracking data is a powerful supervision signal for ultrasound image feature representation learning. We develop a general framework for representation learning and transfer of the trained neural network to the downstream tasks of standard plane detection and automatic biometry plane annotation. We also show that the learned representations, in combination with the sonographer gaze prediction, can be used to discover and localize visually salient anatomical landmarks, i.e., landmarks that sonographers use for visual navigation.
Finally, we provide an overarching discussion and an extended outlook chapter which describes a system for guiding sonographers during standard plane acquisition.

Keywords: ultrasound
ultrasound image analysis
obstetric ultrasound
saliency prediction
machine learning
ultrasound video analysis
visual saliency
saliency modeling
eye tracking
ultrasound probe movement guidance
gaze tracking
ultrasound safety
expected value bias
Advisor: Noble, A
Temporal prediction as principle underlying sensory representations

Neurons in sensory pathways respond selectively to specific features of dynamic natural inputs. For example, in primary auditory cortex (A1), neurons respond selectively to sounds with specific spectral and temporal content. Retinal neurons prefer localized spots of light, primary visual cortical (V1) neurons moving bars, and those in higher cortical areas, such as middle temporal (MT) cortex, favour complex features like moving textures. Understanding the principles behind these specific forms of selectivity is a central aim of systems neuroscience. In this thesis I explore the idea that a key goal of sensory systems is to represent features of natural inputs that are efficiently predictive of future inputs. First, I show that a single hidden-layer artificial neural network that is optimized to predict the future of natural sound inputs from their past produces receptive fields (RFs) with spectrotemporal tuning properties that both qualitatively and quantitatively resemble those of A1 neurons. Furthermore, I show that the better a network predicts the future, the more the receptive fields of its units resemble those recorded in A1. Next, I show that when the identical model is trained to predict the future of natural video inputs rather than sounds its RFs resemble those of V1 simple cells in both their spatial and temporal tuning properties. Finally, I extend the temporal prediction model to a hierarchical form and show that it recovers the tuning properties of neurons as they change from the retina to higher visual cortex. The fact that these simple neural network models, when optimized to efficiently predict the immediate future of natural inputs, display the tuning properties of sensory neurons at so many levels of the visual and auditory hierarchies suggests that this principle may be a fundamental goal of sensory systems.