VictorJuiz/thesis huggingface dataset:
Improving representation learning through variational autoencoding
Keywords: Unsupervised learning
Representation learning
Variational autoencoders
Uncertainty estimation
Anomaly detection

Representation learning aims to distill useful knowledge from raw data and apply this knowledge to a wide range of applications. This ability to extract information that is useful not only for selected tasks but also generalizes to new settings is a key step towards artificial intelligence.
In this thesis, we focus on representations derived through a specific type of generative model, i.e. variational autoencoders (VAEs). VAEs have several desirable properties. Thanks to the use of variational inference and the convenient model assumptions of Gaussian posteriors and a simple prior, VAEs are often easy to train and exhibit fast convergence. The probabilistic modelling formulation allows VAEs to derive a smooth latent representation of the raw data (i.e. semantically similar data samples are likely to be projected to nearby regions in the latent space). VAEs compress the raw data to a much lower dimension latent space. Working with the low-dimensional representations rather than the raw data can significantly reduces costs in memory and computation. With these advantages, VAEs have been widely applied to many applications, including robotics, drug discovery and digital content creation.
Despite the widespread application of VAEs, improving the generative modelling of VAEs further remains an active research topic. In this thesis, we focus on two challenges in the VAE training: 1) over-regularized posterior distributions are often encountered in VAEs with Gaussian decoders and simple prior models; 2) the auto-encoding function may cause severe information drift and alter the information in the raw data in successive encodings. We propose solutions to both phenomena. Specifically, we optimize a variance parameter in the Gaussian decoder to balance competing loss terms in the ELBO objective. We adopt a flexible prior model that is implemented as a VAE in the latent space to mitigate the over-regularization effects. To reduce the information drift, we propose to modify the ELBO objective with a consistency loss that penalizes such drift. We show that these proposals can effectively address the challenges identified previously and improve the likelihood score of the VAEs.
In addition to the contributions related to improving VAEs, we also demonstrate the power of VAEs' representation learning in two important machine learning applications. Firstly, we show that a VAE's ability to compress complicated, high-dimensional data is key to achieving good performance in anomaly detection. We design a VAE-LSTM anomaly detection system that can accurately identify anomalous effects in a time serious. Secondly, we show that a classifier which incorporates a VAE module can give better calibrated predictions. This is the result of a VAEs' capability of expressing the uncertainty between similar data samples in the spread of the posterior distribution and of identifying out-of-distribution samples.
Structural studies of low X-ray-scattering-contrast sites in light-element-doped inorganic energy materials
Keywords: xray diffraction
energy materials
resonance diffraction
electrochemistry
ammonia
zeolites
lithium ion batteries
catalysis
hydrogen
phototcatalysis
synchrotron science

The agile ammonia synthesis is a collection of energy generation and storage infrastructure, which allows sustainable, local, and independent energy provision by converting renewable energy to hydrogen and ammonia, as well as in battery energy storage systems such as lithium-ion batteries. Many of these systems utilise archetypal inorganic materials, in particular due to enhanced performance from the incorporation of light-element dopants. Here, three components of the agile ammonia synthesis pathway are investigated in order to better understand the complex structure-activity relationship, in particular by using complex in-situ, in-operando, and inelastic synchrotron X-ray powder diffraction.
The nitrogen doping of titania is shown to impart increased structural and electronic defects that can be exploited by photo-absorption of visible light to split water using nothing else but solar irradiance. The generation of oxygen vacancies was observed by anisotropic thermal expansion, and supported by DFT calculations and photocatalytic performance. The use of palladium nanoparticles as an electrochemical energy store by lithium intercalation has been evaluated, and in-depth phase transitions characterised. Though the intercalation process reduces the order of the host framework, the cycling capacity remains constant, indicating amorphisation does not equate to performance degradation. The location of preferential substitutional aluminium sites in zeolite ZSM-5 has been yielded by observing probe molecule adsorption, but also directly by exploiting high-contrast anomalous scattering. The results of various techniques are in broad agreement of the siting, which will have impact the understanding of zeolite synthesis and performance mechanisms.
Multi-omics analysis and modelling of T cell immunity and interferon signalling pathways for engineered T cell therapy
Keywords: Breast Cancer
Spatial Transcriptomics
Immunotherapy
Multi-Omics
CAR T Cells
T Cells
Clinical Samples
scRNA-Seq
Interferons
Tumour Immunology
cGAS–STING

This thesis examines the nature of T cells through the lens of genomics. It delves into type I interferon (IFN)-mediated signalling in the tumour microenvironment (TME), focusing on the GMP-AMP synthase (cGAS)-stimulator of IFN genes (STING) pathway, and explores novel strategies to optimise T cell-based immunotherapy for triple-negative breast cancer (TNBC). In the first chapter, gene expression patterns of distinct T cell subtypes are studied to gain insight into the diverse T cell landscape. Cell type annotation methods are evaluated for their ability to identify closely-related T cell populations in single-cell RNA sequencing (scRNA-seq) data. In the following chapter, single-cell and spatial transcriptomics methods, mainly scRNA-seq, single-cell immune profiling, Slide-seq, in situ sequencing and Molecular Cartography enable the comprehensive analysis of immune infiltrates in tissue biopsies from patients with TNBC. The advantages and limitations of emerging spatial transcriptomics technologies are put into context. Tumour-infiltrating T cells were characterised at varying levels of resolution and cGAS was found to be most highly expressed in proliferating T cells. Tissue-wide spatial patterns revealed a strong relationship between programmed cell death-1/programmed cell death ligand-1 and cGAS but not STING. In addition, gene transcripts encoding the downstream protein kinase TANK-binding kinase 1 were found to spatially associate with hypoxia markers. Finally, T cells genetically engineered to express chimeric antigen receptors (CARs) are investigated using a systems biology approach. An agent-based model is developed to explore the effect of CAR tuning on on-target off-tumour toxicity and therapy efficacy. Gene regulatory networks are used to present readily testable hypotheses for combination strategies using immune checkpoint inhibitors, oncolytic viruses, and cGAS-STING-targeting treatments to potentiate anti-tumour responses. The work presented therein will feed into a novel computational framework to enable the modelling of patient-specific responses to T cell-based immunotherapy and synergistic combinations.
'Literary studies must be a science' (Yury Lotman): representing and interpreting character relationships in Russian drama by means of quantitative methods
Keywords: computational linguistics
digital literary studies
social network analysis
Russian drama
digital humanities

This thesis explores and demonstrates the possibility of using quantitative and digital methods to analyse Russian drama texts. The methodology under discussion lies within the fields of Digital Humanities and Digital Literary Studies, and includes Social Network Analysis (SNA) and Natural Language Processing (NLP) techniques. The project is structured as several independent case-studies that are united by a discussion of the advantages and limitations of the methodology.
The first chapter of this thesis introduces the reader to the encoding standards of the texts (TEI XML) necessary for carrying out the quantitative analysis of the plays, as well as the basics of the methodology, including definitions and formulas for calculations. These methods are then illustrated in detail by presenting a first case-study, showing how automatic methods can be used to establish the hierarchy of the protagonists in three 19th-century Russian plays.
This thesis aims to reflect the exploratory and innovative nature of the application of digital methods to literary data. Hence, each chapter introduces new methods in addition to the ones discussed in the Introduction. The next case-study is devoted to the comparison of two plays with similar plots but different network structures, and includes a more detailed analysis of the speech of the characters in the two plays.
The third case-study focuses on the representation of women in 19th-century Russian drama and attempts to combine ‘distant’ and ‘close’ reading methods, to explore the full capacity of the digital approach. It is followed by a final section discussing the applicability of the methods to contemporary plays from the Soviet period and the beginning of the 21st century, with a greater focus on the limitations of the methodology.
The work is rounded off with a concluding section, in which an overview is provided of the general structural evolution of Russian-language drama, alongside a discussion of the potential for further research in this area.
Damping and fretting of frictional contacts in the steady-state
Keywords: asymptotic analyses
shakedown
fretting wear
partial slip
stress intensity factor
coupled contact
distributed dislocations
fretting fatigue
half-plane contact

Contacts in mechanical assemblies are often subject to a constant load together with an oscillatory component. The latter might originate from vibration such that the component experiences a high number of load cycles. Different dissipative processes affect the steady-state behaviour of the assembly. In terms of contacts the most apparent is friction along the interface, which might lead to surface damage. Locally, the contact might act as a stress raiser, such that the material in the neighbourhood experiences plastic deformation. Cracks nucleating from the damaged surface and propagated in each load cycle are another limiting factor for the component's life. All these effects can be studied individually, but in reality they will affect each other to a certain degree. After a review of analytical and asymptotic contact descriptions, this thesis aims to describe the interaction between interfacial slip and other dissipative or life-limiting effects. A graphical method is presented to determine if a given loading causes the material in the contact region to reach the onset of plasticity. The limits of the elastic regime are explored and evaluated with this method.
Strong analogies exist between plasticity and slip. Shakedown, a process in which the generation of residual stresses in the first load cycles counteracts further dissipation, is one example. In the context of plasticity the residual stresses are generated due to plastic deformation, while it is due to relative slip displacements in the context of friction. However, it is shown that principles, established in the context of plasticity, are not generally transferable to friction. Repeated frictional slip may lead to surface degradation with a reduction of the contact extent. Simple calibrations are derived between the external contact loading and multipliers characterising the stress field around the edge of the resulting contact. Following the same basic idea makes it possible to identify crack tip stress intensity factors of cracks nucleating from the contact region. These intensity factors characterise the stress field around the crack tip, but also are used to assess the crack propagation per load cycle.
Translation and circulation of Romanian and Slavonic biblical books in the Romanian lands: a textual analysis of the sixteenth century Apostolos and Psalter texts
Keywords: church Slavonic
comparative philology
Old Romanian
bible translation
Psalter
Apostolos

This thesis is concerned with the early rise of old Romanian as a written language, as represented by the textual traditions of biblical books translated from Church Slavonic. My primary sources are limited to sixteenth-century manuscript and printed books of the Apostolos and Psalter texts in Romanian and the relevant primary sources of the Slavonic tradition. In answering the questions of why and how the earliest Romanian writings appear, I argue that the philological study of the source tradition of the texts, that is, the Slavonic tradition, as well as of the textual varieties identified in the Romanian primary sources, can help us understand better the way in which Romanian came to be used as a literary language.
After a brief Introduction to the sources and method of philological analysis, Chapter one investigates the history of book production and circulation in the Romanian lands between the fifteenth and sixteenth centuries and gives some essential historical context to the cultural dynamics defining the voivodeships of Moldavia, Wallachia, and the principality of Transylvania at the time.
Chapters two and three analyse in depth the textual traditions of the Psalter text first, and then that of the Apostolos: each chapter identifies the source tradition of the respective text and provides an affiliation diagram of the Romanian sources.
Chapter four explores the translation and revision techniques employed in rendering and subsequently altering the text of the Apostolos and the Psalter.
The Conclusions draw together the information from the previous chapters and survey the prospects for further avenues of investigation.
Spaces of paradox: The poetics of disruption in twenty-first century speculative fiction
Keywords: speculative fiction
speculation
literature
narrative traction
urban sociology
poetics of disruption

How do speculative novels post-2008 signal paradigm shifting ambiguities and uncertainties about literary genres in the first two decades of the twenty-first century? How might the poetics of disruption in contemporary speculative fiction signal a complex mediated interaction between formal literary devices and the transitional period from neo-liberalism into an unknown future global system defined by the uneven distribution of urban modernity? The six novels treated in this dissertation, published between 2009 and 2020, present a poetics of disruption that complicates distinctions between genres and modes, and demands a negotiation of ongoing paradigm shifts. Disruption of the status quo is a crucial tactic in social organising: just as speculation has literary and real-world referents, so too does disruption defy the borders of the text. I focus on three key spaces of paradox that are produced by the speculative mode in Anglophone literature in this century: urban interstices as depicted in China Miéville’s The City & The City (2009) and Lauren Beukes’ Zoo City (2010); hyperbole as a critical tool in Kim Stanley Robinson’s New York 2140 (2017) and Mohsin Hamid’s Exit West (2017); and writing as a resistant act of reproduction in apocalyptic narratives that renegotiate the binaries of urban and wilderness as portrayed in Louise Erdrich’s Future Home of the Living God (2017) and Lauren Beukes’ Afterland (2020). Produced in the urgent socio-political contexts of the last two decades, these texts engage in discourse about the future, gesturing to an emerging paradigm in the literary market in which disruption is generative of literary activism through the imbrication of utopian ideals in the speculative mode. While presenting sometimes pessimistic outlooks, the speculative mode in this century interpolates a utopian impulse in its very form.
Category theory for quantum natural language processing
Keywords: category theory
natural language processing
quantum computing

This thesis introduces quantum natural language processing (QNLP) models based on a simple yet powerful analogy between computational linguistics and quantum mechanics: grammar as entanglement. The grammatical structure of text and sentences connects the meaning of words in the same way that entanglement structure connects the states of quantum systems. Category theory allows to make this language-to-qubit analogy formal: it is a monoidal functor from grammar to vector spaces. We turn this abstract analogy into a concrete algorithm that translates the grammatical structure onto the architecture of parameterised quantum circuits. We then use a hybrid classical-quantum algorithm to train the model so that evaluating the circuits computes the meaning of sentences in data-driven tasks.
The implementation of QNLP models motivated the development of DisCoPy (Distributional Compositional Python), the toolkit for applied category theory of which the first chapter gives a comprehensive overview. String diagrams are the core data structure of DisCoPy, they allow to reason about computation at a high level of abstraction. We show how they can encode both grammatical structures and quantum circuits, but also logical formulae, neural networks or arbitrary Python code. Monoidal functors allow to translate these abstract diagrams into concrete computation, interfacing with optimised task-specific libraries.
The second chapter uses DisCopy to implement QNLP models as parameterised functors from grammar to quantum circuits. It gives a first proof-of-concept for the more general concept of functorial learning: generalising machine learning from functions to functors by learning from diagram-like data. In order to learn optimal functor parameters via gradient descent, we introduce the notion of diagrammatic differentiation: a graphical calculus for computing the gradients of parameterised diagrams.
Electromagnetic instabilities and plasma turbulence driven by the electron-temperature gradient
Keywords: TAI
ETG
plasma
turbulence
instabilities

Electromagnetic instabilities and turbulence driven by the electron-temperature gradient are considered in a local slab model of a tokamak-like plasma. Derived in a low-beta asymptotic limit of gyrokinetics, the model describes perturbations at scales both larger and smaller than the electron inertial length de, but below the ion Larmor scale rho i, capturing both electrostatic and electromagnetic regimes of turbulence. The well-known electrostatic instabilities --- slab and curvature-mediated ETG --- are recovered, and a new instability is found in the electromagnetic regime, called the Thermo-Alfv\'enic instability (TAI). It exists in both a slab version (sTAI, destabilising kinetic Alfv\'en waves) and a curvature-mediated version (cTAI), which is a cousin of the (electron-scale) kinetic ballooning mode (KBM). The cTAI turns out to be dominant at the largest scales covered by the model (greater than de but smaller than rho i), its physical mechanism hinging on the fast equalisation of the total temperature along perturbed magnetic field lines (in contrast to KBM, which is pressure balanced). A turbulent cascade theory is then constructed, with two energy-injection scales: de, where the drivers are slab ETG and sTAI, and a larger (parallel-system-size-dependent) scale, where the driver is cTAI. The latter dominates the turbulent transport if the temperature gradient is greater than a certain critical value, which scales inversely with the electron beta. The resulting heat flux scales more steeply with the temperature gradient than that due to electrostatic ETG turbulence, giving rise to stiffer transport. This can be viewed as a physical argument in favour of near-marginal steady-state in electron-transport-controlled plasmas (e.g., the pedestal) at sufficiently high values of the electron beta. Numerical simulations are then used to demonstrate that electrostatic turbulence driven by the slab ETG does indeed saturate via a critically-balanced, constant-flux cascade of free-energy, which is shown to be the dynamical manifestation of the scale-invariance of electrostatic drift kinetics. Data from simulations shows excellent agreement with the theoretically predicated one- and two-dimensional spectra of the perturbations. Failure of saturation in electromagnetic turbulence driven by the sTAI is then identified, characterised and discussed. While the model in which these results are derived is simplistic, the new physics that is revealed by it should be of interest to those attempting to model the effect of gradient-driven turbulence in tokamak-relevant configurations, particularly those with high beta and large electron-temperature gradients, in which electromagnetic effects play a significant role.
Whose triumph? The reception history of Bertel Thorvaldsen’s frieze ‘Alexander the Great’s entry into Babylon’ (1812)
Keywords: Rome
Quirinal Palace
Romanticism
Alexander the Great
Political art
reception history of
Bertel Thorvaldsen
Napoleon
Neoclassicism

The Neoclassical sculptor Bertel Thorvaldsen’s (1770-1844) art has rarely been examined in a political context although his lifetime was characterised by major political upheaval and societal change in which art played an important role. Several reasons can help explain this negligence such as the modernist dismissal of the Neoclassical style as well as the conflicted view of Romanticism and politics, especially in Germany. In this dissertation, I’ll examine one of Thorvaldsen’s most famous works, the Alexander Frieze, and its reception history until c. 1850. The plaster frieze was commissioned in 1812 by Napoleon and installed the same year in the Quirinal Palace, the former papal residence, now the new imperial palace. I aim to show how the frieze reflects the relationship between art and power in the period and how this relationship evolved during the dramatic decades of Thorvaldsen’s lifetime.
Thorvaldsen had a conflicted relationship with Napoleon and was generally critical of monarchical power, an attitude which was probably cultivated both by his education and by his social circle which consisted of liberal intellectuals such as Wilhelm and Caroline von Humboldt and Friederike Brun, a close friend and confidante of Madame de Staël. Apart from the frieze itself my source material is comprised of a variety of text genres such as letters, diary entries, poems and newspaper articles concerning Thorvaldsen and the frieze.
This material will in the first chapter enable an inquiry into whether Thorvaldsen may have expressed criticism of Napoleon in the frieze as claimed by some contemporaries. In the second and third chapters I will delve into the reception history of the frieze. This will uncover how various factions perceived and used the frieze as part of their political communication and what this reveals of the political conflicts and mentalities of the era.