VictorJuiz/thesis huggingface dataset:
Automated and verified deep learning

In the last decade, deep learning has enabled remarkable progress in various fields such as image recognition, machine translation, and speech recognition. We are also witnessing an explosion in the range of applications. However, there are many challenges that stand in the way of the widespread deployment of deep learning. In this thesis, we focus on two of the key challenges, namely, neural network verification and automated machine learning.
Firstly, deep neural networks are infamous for being `black boxes' and making unexpected mistakes. For reliable AI, we want systems that are consistent with specifications like fairness, unbiasedness and robustness. We focus on verifying the adversarial robustness of neural networks, which aims at proving the existence or non-existence of an adversarial example. This non-convex problem is commonly approximated with a convex relaxation. We make two important contributions in this direction. First, we propose a specialised dual solver for a new convex relaxation. This was essential because although the relaxation is tighter than previous relaxations, it has an exponential number of constraints that make the existing dual solvers inapplicable. Second, we design a tighter relaxation for the problem of verifying robustness to input perturbations within the probability simplex. The size of our relaxation is linear in the number of neurons, which enables us to design simpler and efficient algorithms. Empirically, we demonstrate the performance by verifying the respective specifications on common verification benchmarks.
Secondly, deep neural networks require extensive human effort and expertise. We consider automated machine learning or meta learning which aims at automating the process of applying machine learning. We make three contributions in this context. First, we propose efficient approximations for the bi-level formulation of meta learning. We show its efficiency in the context of learning to generate synthetic data for training neural networks by optimizing state-of-the-art photorealistic renderers. Second, we propose a technique to automatically optimize the learning rate of gradient-based meta learning algorithms. We demonstrate a substantial reduction in the need to tune training hyperparameters. Third, we show an application by tackling video segmentation as a meta learning problem and demonstrating state-of-the-art results on common benchmarks.

Keywords: Neural network verificaiton
Meta learning
Optimization
Neural networks
Advisor: Torr, PHS
Mudigonda, PK
Halogen bonding and chalcogen bonding host systems for charged guest recognition

This thesis describes the preparation of halogen bonding and chalcogen bonding macrocyclic and mechanically interlocked systems for the recognition of anions and ion-pairs.
Chapter 1 introduces the field of supramolecular host-guest chemistry, with particular focus on the recognition of anions and ion-pair species. The synthesis and applications of mechanically interlocked molecules are also reviewed.
Chapter 2 details the fundamental charged guest recognition properties of a novel family of σ-hole [2]rotaxanes incorporated with multiple halogen bonding and chalcogen bonding triazole-based donor motifs.
Chapter 3 investigates the anion sensing capability of halogen bonding receptors functionalised with photo- and redox-active reporter groups. This entails the construction of zinc(II) metalloporphyrin-BODIPY [2]rotaxanes for the dual optical- and electrochemical sensing of anions.
Chapter 4 describes the exploitation of halogen bonding and chalcogen bonding interactions to mediate ion-pair recognition in heteroditopic/multitopic macrocyclic and catenane host systems.
Chapter 5 summarises the conclusion of this thesis.
Chapter 6 provides the experimental procedures employed in this work, including synthetic protocols and characterisation of novel compounds.

Keywords: ion-pair recognition
rotaxanes
anion recognition
catenanes
Advisor: Beer, PD
The afterlife of site-specific sculpture: a self-referential study through practice

As practice-led research, this thesis takes the form of a portfolio documenting a series of works and exhibitions through which that research was conducted. It explores issues related to site-specific sculpture and begins by examining my existing methods of site-specific sculptural intervention within the exhibition environment. This raises some problematic issues regarding the temporality of site-specific sculpture, which are brought into clearer focus in my subsequent experiments in exhibition making. In the next transitional phase, the inflexibility of my previous approach is dissolved to a degree, which opens up possibilities for new sculptural and installation practices in several alternative directions.
The possibilities and limits inherent in site-specific sculptures are specifically explored through the notion of afterlife. This focuses on questions of temporal availability; the forms of dependency involved in site-specificity, and the sentiments that accompany them. Here, the notion of afterlife seeks not only to overcome the time constraints inherent in most exhibition practices, but also to expand the contextual understanding of sculpture in relation to the frame of art. The spatial and contextual frame has been as significant as each work in my practice, and since the work and the frame have an effect on each other, this generates a strong sense of inevitability. This over-determination raises several further issues, including the question of the artist’s authorship, which are then explored through both the textual and the sculptural forms of the research by opening up the space to the viewer.
The most noticeable characteristic of this research is its self-referentiality and reflexivity in developing both practice and textual elements. The work explores what has been done in the past and pursues the next phase by reflecting previous attempts in stages, therefore, occasionally bringing in the concept of a meta-structure. This methodology re-influences the development of the practice and renews its formal structure. The research not only resonates with its own development, but reveals the invisible boundaries of site-specific practice that constitute what might be termed the trap of art.

Keywords: Self-referentiality
Meta-structure
Inter-subjectivity
Site-specific
White cube
Architectural/Sculptural/Spatial Intervention
Institutional Critique
Exhibition
Exhibition Space
Sculpture
Viewer
Afterlife
Trap
Third Person
Advisor: Bull, M
Palmer, K
Exploring the carbon isotopic ratio and chemistry of coccoliths and coccolith associated polysaccharides as a proxy for CO2

Our planet is habitable, in part, due to the carbon dioxide (CO2) that resides in our at- mosphere. Whilst the presence of CO2 ensures that ambient surface temperatures remain above freezing, additional inputs of CO2 drive global temperatures higher. The long-term increase in temperature associated with an increase in the mixing ratio of CO22 in the at- mosphere (pCO2) is, however, not certain. In order to understand how much our planet’s temperature rises given an increase pCO2, we look to the sedimentary record to reconstruct coupled changes in past temperature and pCO2. Yet, reconstructing pCO2 is marred by inaccurate proxies, which often require numerous assumptions and only provide snapshots of past change. Recent work has linked chemical signals recorded in coccolithophores, unicellular phytoplankton, to changes in the CO2 concentration of seawater ([CO2(aq)), which reflects pCO2 in certain ocean settings. Such signals manifest in calcium carbonate plates, know as coccoliths, that coccolithophores produce and their associated polysac- charides, which assist with coccolith calcification. This thesis set out to investigate the use of coccoliths and coccolith associated polysaccharides (CAPs) as a proxy for pCO2. I first invert an existing coccolithophore cellular carbon isotopic flux model to reconstruct pCO2 given novel carbon isotopic data from size separated coccoliths dating to the Eocene period (56-34 million years ago). This work takes advantage of the understanding that the external concentration of CO2 in seawater, in part, controls the carbon isotopic composition of coccolith calcite. I find that pCO2 declined over the Eocene period with a corresponding shift to less calcified coccolithophore species. Second, I recalibrate an existing cellular carbon isotopic flux model with novel isotopic data measured from culture experiments to derive insight into modern day species carbon acquisition strategies. I find that two modern coccolithophore species, Gephyrocapsa Oceanica and Coccolithus pelagicus, have differing responses to CO2(aq) limitation. Whilst G. Oceanica likely upregulates HCO−3 transporters under carbon limitation, Coccolithus pelagicus utilises HCO−3 over all carbonate parameter space. Finally, I investigate the chemical and isotopic response of CAPs trapped within coccoliths from both culture and the sedimentary record to changes in CO2(aq). I find that both the monosaccharide composition and carbon isotopic ratio of CAPs vary over CO2(aq) space. Whilst species specific behaviour is apparent, collective changes observed across species point towards the potential development of a CAP based pCO2 proxy. Taken together the work presented in this thesis lays the foundation for a suite of novel pCO2 proxies that may, with supplementary work, reconstruct pCO2 back to the Triassic period when coccoliths first appeared in the fossil record.

Keywords: Geochemistry
Biogeochemistry
Coccolithophores
Paleoclimate
Advisor: Rickaby, R
Lee, R
McClelland, H
Investigating the transcriptional response of rDNA to hypoxia

Hypoxic conditions initiate a multitude of transcriptional adaptations including increased expression of a family of well-characterised stress-inducible genes by hypoxia-dependent transcription factors. In contrast, the mechanisms of transcriptional repression in hypoxia have not been well characterised. Here, I show that hypoxia leads to global transcriptional repression, including at the site of ribosomal DNA (rDNA) transcription in the membraneless subcellular organelle, the nucleolus. Transcriptional repression occurs in both cancer and noncancer cell lines in an oxygen-dependent manner. Both transcription of the rDNA and processing of the pre-ribosomal RNA (pre-rRNA) is repressed in hypoxic conditions. I describe the rapid accumulation of DNA/RNA hybrids, also known as R-loops, in hypoxia and demonstrate that these R-loops are most prominent in the nucleolus. Mechanistically, neither hypoxia-mediated activation of the DNA damage response kinases ATM or ATR, nor the nucleoprotein TCOF1 contribute to rDNA transcriptional repression in hypoxia. Instead, it was determined that R-loops rapidly accumulate on the rDNA in hypoxia and that this limits RNA polymerase I mediated transcription. Finally, I show that R-loop formation increases heterochromatin formation, specifically H3K9me3 on the rDNA and that R-loop accumulation is mediated by the RNA/DNA helicase senataxin (SETX) at rDNA loci, suggesting a chromatin-based mechanism that contributes to hypoxia-mediated repression of rDNA transcription. Together, these findings shed light on the control of RNPI transcription in response to hypoxic conditions and presents a unique mechanism of RNPI shutdown in response to stress.

Keywords: Hypoxia
Transcription
Ribosomal DNA
R-loops
Replication stress
Advisor: Hammond, E
Diagnostic tools for rapid eye movement sleep behaviour disorder

There is clear evidence to support Rapid-Eye-Movement (REM) sleep behaviour disorder (RBD) as an early predictor of Parkinson’s disease, dementia with Lewy bodies, and multiple system atrophy. Those diagnosed with RBD enact their dreams and therefore present an abnormal characteristic of movement during REM sleep. This unusual sleep disorder presents an opportunity to better understand neurological degeneration and in-turn develop preventative medicine. However, manual polysomnograph (PSG) analysis is mandatory when diagnosing RBD, which demands complex monitoring equipment, specially trained staff, bed availability, and clinicians to interpret abundant amounts of data. Inevitably this process is time consuming and expensive, creating a demand for automated diagnostic support tools to better utilise the time of clinicians.
The first aim of this thesis was to achieve automated sleep stage classification using signal processing and machine learning techniques. A total of 159 features were calculated using Electroencephalography (EEG), Electrooculography (EOG), and Electromyography (EMG) signals. After extracting the features a Random Forest (RF) algorithm was used to classify five sleep stages. With respect to REM stage classification, this technique achieved an accuracy of 93%, sensitivity of 63%, and specificity of 97% (five stage Cohen kappa of 0.63).
After sleep staging, clinicians must manually identify abnormal REM sleep behaviour. Several methods have been proposed for RBD detection that use EMG recordings to objectively quantify abnormal REM movement. In this work we further develop these proven techniques with additional features that incorporate the relationship of muscle movement between sleep stages and general sleep architecture. Using an RF classifier with established and additional features, the performance of RBD detection was shown to improve upon established metrics (achieving 94% accuracy, 94% sensitivity, and 94% specificity). This technique used in combination with automated sleep staging sustained a high performance in RBD detection, with an accuracy, sensitivity, and specificity of 90%, 86%, and 94%, respectively.
Lastly, this thesis investigated a minimal set of sensors to fully-automate the detection of RBD, integrating automated sleep staging followed by RBD detection without the need for cumbersome EEG sensors. This thesis demonstrated a costeffective, practical, and simple RBD identification support tool using an EOG and EMG sensor to achieve an accuracy, sensitivity, and specificity of 86%, 82%, and 90%, respectively.

Keywords: automated sleep staging
sleep
RBD detection
Advisor: De Vos, M
The case against the (strong) rights-based judicial review of citizen-initiated referenda

Direct democratic institutions – such as citizen-initiated statutes and citizen-initiated constitutional amendments – are a fact of political life in Switzerland and several US states. However, the question then arises whether the outputs of such institutions (warts and all) should at any point be subject to strong rights-based judicial review. This thesis argues that they should not. Instead, judicial review of direct democracy should be replaced by a Constitutional Council of Revision, a partly-appointed, partly randomly-selected body which at any point in time can propose amendments or revisions to any pending or past ballot measures.
Drawing on a diverse array of historical case studies, I suggest that my hypothesised Constitutional Council of Revision might well be an institutionally superior institutional mechanism to address any alleged drawbacks associated with citizen lawmaking. This is especially so, given that: (1) voters typically lead, rather than trail, the judiciary when it comes to progressive social change; (2) the glaringly counter-majoritarian character of judicial review, which thwarts the votes cast by millions of voters, and thereby threatens to breed greater cynicism about the democratic ideal; (3) the backlash that comes with judicial intervention can sometimes do more harm than good and may even unwittingly cause public policy to shift to an even more extreme anti-minority position; (4) most constitutional objections to direct democratic outputs can be remedied by minor amendments or "tweaks" to the original proposal without needing to invalidate the proposals in their entirety; (5) direct democratic measures involve reasonable almost invariably involve attempts to defend fundamental rights and heated but good faith attempts to secure what justice or good policy requires; (6) direct democratic outputs already face multiple potential roadblocks in order to be successfully implemented, even without an additional vetopoint like strong rights-based judicial review.

Keywords: referendums
referenda
direct democracy
judicial review
judicial review of direct democracy
citizen-initiated referendums
bills of rights
populism
Advisor: Endicott, TAO
Williams, RA
Investigating functions of human group 2 innate lymphoid cells in health and disease

Group 2 innate lymphoid cells (ILC2) have emerged as important effectors of type 2 immune responses that contribute to protection against extracellular parasites and tissue repair. Dysregulated ILC2 responses have been implicated in allergic inflammatory disorders such as atopic dermatitis (AD), a chronic inflammatory skin disease associated with epidermal barrier defects and dysregulated type 2 inflammation. However, much remains to be understood regarding ILC2 effector functions, especially in the context of cutaneous inflammation.
Using an in vivo human skin blister model, extensive multianalyte profiling revealed significant differences in the protein expression profile of healthy and AD skin; and skin ILC2 were found to express a range of cytokine- and chemokine-encoding genes following intradermal allergen challenge. In vitro experiments confirmed secretion of a broad range of cytokines and chemokines, including granulocyte macrophage colony-stimulating factor (GM-CSF) and the chemokines CCL22 and CCL17, by human ILC2 in response to activation by alarmin cytokines. Elevated levels of CCL22 and CCL17 were detected in both sera and skin blister fluids from individuals with AD compared to healthy controls, and increased surface expression of CCR4, the shared receptor for CCL22 and CCL17, was detected on blood ILC2 and T cells from individuals with AD. In vitro, ILC2 were found to promote recruitment of both ILC2 and T cells, directly and indirectly through induction of monocyte-derived dendritic cell (moDC) chemokine production, involving CCL22 and CCL17. Thus, ILC2 may contribute to AD pathogenesis by promoting the accumulation of CCR4+ ILC2 and Th2 cells. Moreover, through GM-CSF secretion, human ILC2 were identified as inducers of monocyte differentiation into CD1a+ moDC, resembling in vivo inflammatory moDC. ILC2-induced moDC were capable of activating CD1a-reactive T cells, resident in healthy skin and increased in abundance in AD skin.
Taken together, this study identified previously unrecognised roles of human ILC2 in the chemotactic recruitment of ILC2 and T cells and as inducers of moDC differentiation with implications for cutaneous inflammation.

Keywords: skin
group 2 lymphoid cells
atopic dermatitis
Advisor: Ogg, G
Hardman, C
Towards a mechanistic understanding of the ocean's biological carbon pump

Marine particles lock atmospheric CO2 into organic structures that sink and export carbon into the ocean interior, a process known as the biological carbon pump (BCP). Part of this flux of particulate organic carbon (POC) is attenuated in the mesopelagic ocean as respiration, disaggregation and solubilisation wear out the sinking particles and return the organic carbon into its inorganic form. Sediment traps and imaging systems have revealed the importance that particle material composition and microstructure have in the degradation of mesopelagic POC flux. However, the data collected are scarce and have too many spatiotemporal biases to provide a mechanistic picture of which particle attributes, particle dynamics and biogeochemical factors control it. Here, I present a stochastic model of Lagrangian marine particles that mechanistically interact with each other and their biogeochemical environment as they sink through the water column. A Lagrangian framework tracks particles throughout their life history and allows recording their fractal radius, porosity, density, stickiness and sinking velocity, providing information of particle attributes alongside POC fluxes. The model is applied globally to quantify spatial variations in the vertical attenuation rate of POC flux (Martin’s b) and its dependence on proposed controlling factors such as NPP, phytoplankton community composition and seawater temperature. I find that Martin’s b is lowest in productive, diatom-rich ecosystems and highest in oligotrophic, picophytoplankton-rich ecosystems. Particle density and ballast provided by the opal sourced by diatoms are the particle attributes that contribute the most to the transfer of POC flux to the mesopelagic, and particle dynamics of coagulation and zooplankton egestion assist in spreading the opal amongst the broader pool of particles. These results emphasise the role of both surface water conditions (NPP and phytoplankton community composition) and mesopelagic conditions (particle transformation dynamics) in controlling the BCP-mediated transfer of carbon to the ocean interior.

Keywords: marine snow
particulate organic carbon
ocean carbon cycle
numerical modelling
biological carbon pump
Monte Carlo method
ocean biogeochemistry
Lagrangian particles
Advisor: Khatiwala, S
Martin, A
Information learning bias in depression

Major depressive disorder is a mood and emotional disorder characterized by persistent low mood and lack of interest. Both reward and punishment learning deficits have been associated with depression. In this thesis, we aim to examine whether biases in reward and punishment learning adaptations to the volatility level of the environments could also be associated with depression disorders. We developed a task in which we independently manipulated the volatility of win and loss outcomes and systematically examined the underlying mechanisms of adaptive learning in depression using computational modelling, fMRI, pharmacological manipulation and pupillometry recordings. We first showed that currently depressed patients had lower loss learning rate volatility adaptations, estimated using a volatility adaptation model, compared to remitted depressed patients and healthy controls. This might be associated with reduced norepinephrine responsibility to loss outcomes, evidenced by reduced loss volatility modulation of pupil responses to loss outcomes in the currently depressed group compared to the other two groups. Using a similar volatility adaptation model, we then showed that loss learning rate adaptation estimates negatively correlated with individual differences in overall negativity levels (depression and anxiety), with might be associated with decreased segregation of win and loss volatility signals in a distributed brain network of outcome sensitive regions, especially in the ACC. Finally, we showed that manipulating norepinephrine level using an antidepressant, reboxetine, a norepinephrine reuptake inhibitor (NRIs), could increase loss learning rate adaptations to volatility. This was also associated with a reduced volatility effect on the pupil responses to loss outcomes, particularly when wins were volatile. Together, the results have provided some consistent evidence that link depression with inadequate learning adaptation to the volatility of loss outcomes which might be caused by maladaptive norepinephrine responsibility to loss outcomes.

Keywords: depression
norepinephrine
volatility
punishment
ACC
reward
learning
Advisor: Browning, M
Hunt, L
Pulcu, E