VictorJuiz/thesis huggingface dataset:
Investigating graph neural networks and classical feature-extraction techniques in activity-cliff and molecular property prediction
Keywords: GNNs
PDVs
MIM
hash-based folding
molecular machine learning
AI drug discovery
molecular descriptors
twin neural network
attention
ECFPs
sort &amp; slice
feature extraction
Morgan fingerprints
graph neural networks
neural fingerprint
activity-cliff prediction
hashing
weisfeiler-lehman
self-attention
vectorisation of structural fingerprints
drug discovery
computational drug discovery
message-passing neural networks
MMPs
self-supervised learning
extended-connectivity fingerprints
molecular property prediction
message passing
QSAR
dual architecture
molecular featurisation
feature vectors
gins
mutual-information maximisation
machine learning
filtering
matched molecular pairs
substructure pooling
qsar prediction
deep learning
graph-based machine learning
graph isomorphism networks
smiles
activity cliffs
physicochemical descriptors

Molecular featurisation refers to the process of transforming molecular data into numerical feature vectors. It is one of the key research areas in molecular machine learning and computational drug discovery. Recently, message-passing graph neural networks (GNNs) have emerged as a novel method to learn differentiable features directly from molecular graphs. While such graph-based techniques hold great theoretical promise, further investigations are needed to clarify if and when they indeed manage to definitively outcompete classical molecular featurisations such as extended-connectivity fingerprints (ECFPs) and physicochemical-descriptor vectors (PDVs).
In this thesis, we systematically explore and further develop classical as well as graph-based molecular featurisation methods for two important tasks: the well-studied problem of molecular property prediction, in particular quantitative structure-activity relationship (QSAR) prediction, and the largely unexplored challenge of activity-cliff (AC) prediction. We first give a mathematical description and critical analysis of PDVs, ECFPs and message-passing GNNs, with a focus on graph isomorphism networks (GINs). We then conduct a rigorous computational study to compare the performance of PDVs, ECFPs and GINs for QSAR and AC-prediction. Following this, we mathematically describe a novel twin neural network model for AC-prediction and experimentally evaluate ECFP-based and GIN-based versions of this dual architecture. In an additional project, we introduce substructure pooling as a general mathematical operation for the vectorisation of structural fingerprints that represents a natural counterpart to graph-pooling in GNN-architectures. We propose Sort & Slice as a simple substructure-pooling technique for ECFPs that robustly outperforms hashing at molecular property prediction. Finally, we outline two ideas for future research: (i) a graph-based self-supervised learning strategy to make classical molecular featurisations trainable, and (ii) trainable substructure-pooling via differentiable self-attention.
Solving the carried interest puzzle
Keywords: venture capital
carried interest
private equity
taxation
capital gains

Carried interest is a proportion of the investment return that private equity fund partnerships allocate to the fund’s manager. In the United States and the United Kingdom, carried interest is treated as a capital gain for tax purposes. Many view treating carried interest as a capital gain as unfair, arguing that carried interest (or at least some portion thereof) should instead be treated as earnings from employment. Others vigorously defend the status quo. Both sides of the debate have put forward flawed arguments that obscure a satisfying solution to the carried interest puzzle.
The tax treatment of capital gains is advantageous in two key respects: reduced tax rates and deferred timing of taxation. A number of justifications have been put forward for offering these two tax preferences to capital gains. This paper examines the extent to which these justifications also apply to carried interest. The applicability of these reasons to carried interest would strengthen the argument to maintain the status quo of taxing carried interest as a capital gain. Conversely, the status quo is not defensible if these reasons fail to apply.
The analysis of this paper suggests that taxing carried interest at preferential rates is not supported by the reasons for taxing capital gains at preferential rates. However, taxing carried interest under the realisation principle is defensible, supported by the same valuation concerns that justify taxing capital gains upon realisation. As a result, two proposals to change the tax treatment of carried interest stand out as sensible solutions to the carried interest puzzle. The first is to tax carried interest as ordinary income upon realisation. The second, the cost-of-capital approach, puts the fund manager in the position of financial capital supplier and, therefore, a legitimate recipient of preferential capital gains treatment.
Motivating the professional learning community; assembling a framework for generative professional development
Keywords: time
professional learning community
teachmeet
configuration
generative learning
engagement
process theory
sustainability
narrative coding
continuous growth
experience
collaboration
narrative blocking
low stakes
autonomy
professional identity
momentum
deficit model
motivation
professional development
professional knowledge
situation

This project examined teachers’ motivation to engage with the construction of a framework for professional development (PD), underpinned by generative learning principles in a school requiring a shift in practice for its teacher. The project also explored how generative PD practices within such a framework might support the development of an emergent Professional Learning Community (PLC). It was proposed that a shift in ownership of PD, through the application of generative practices, might enhance teachers’ intrinsic motivation to engage with PD and provide momentum for PLC genesis.
Participants contributed to the school’s PD cycle for one year. TeachMeet principles were employed, where anything of interest within teachers’ professional spheres was shared in a low-stakes setting. Data emanated from semi-structured interviews (SSIs) after the implementation of the generative framework, followed by inductive coding and narrative analysis. This permitted an exploration of beliefs and authentic experiences of each teacher, with a holistic recount of teachers’ experiences of PD throughout their careers emerging, in tandem with their current engagement and motivation regarding the generative framework.
Teachers clearly articulated that some models of PD, such as the deficit model, had been detrimental to motivation. Teachers expressed eagerness to share knowledge and skills with colleagues in the findings, with the generative PD framework facilitating the co-creation of knowledge within spheres of professional interest. Teachers were clear that the new framework supported their motivation to engage with PD and was supportive of their growth as autonomous professionals. These findings indicated that generative learning principles, when applied to PD, supported the early formation of a PLC in the project school and suggested that a significant contributory factor was engaging with the process of seeking to understand teachers’ motivation to engage with the PD framework itself.
Localisation of ground range sensors using overhead imagery
Keywords: robotics
state estimation
mobile robotics
machine learning

This thesis is about outdoor localisation using range sensors as an active sensor and cheap, publicly available satellite or `overhead' imagery as a prior map. Range sensors such as lidars and spinning FMCW radars are ideal for large-scale, outdoor autonomous navigation due to their long sensing range, invariance to lighting conditions, and robustness against weather changes. Nevertheless, existing methods for range sensor localisation typically rely on prior maps collected from a previous mapping phase. On the other hand, off-the-shelf overhead imagery, such as public satellite images, is readily available almost anywhere in the world and can be acquired easily from the internet with little cost or effort.
Public overhead imagery can capture geometric cues of the scene also observable by ground lidars and radars, therefore having the capability to act as a map for range sensor localisation. In particular, in corner case scenarios where the prior sensory map is unusable or unavailable, for example if the robot travels to a place it has not visited before, public overhead imagery can act as an alternative map source for range sensor localisation as a fall-back choice. Under normal operation conditions, the localisation result by comparing range sensor data against overhead imagery can act as an additional information source for redundancy.
In this thesis, we present various methods to solve the localisation of a ground range sensor using overhead imagery by learning from data, enabling them to adapt to different environments. This surpasses the methods in literature which employ hand-crafted features designed for only specific types of scenery. Specifically, we address both topological localisation, also known as place recognition, and metric localisation in overhead imagery maps. Furthermore, we investigate self-supervised strategies that allow the tasks to be learned without accurate ground truth data.
Missing "the little things that make you human": medical students' experiences of digital teaching and learning

Keywords: repertory grid method
medical student
affective response to learning

Recent decades have seen a significant global scale-up in the training of doctors with an increased pressure on training resources. This thesis began with a question about how scalable digital materials could be designed to support medical students’ learning of clinical reasoning - the process of making informed judgements about the likely causes and best action to be taken when faced with a clinical problem. My initial research was underpinned by an assumption that it would be possible to design digital tools that students would find as motivating as face-to-face encounters. However, my early empirical work using design research raised doubts about that and caused me to take a step back and examine medical students’ digital learning engagement more generally.
In this thesis, I ask the question: why, and in what ways, is digital learning engagement different from face-to-face learning engagement? I test a hypothesis about digital learning engagement that is derived from Silvan Tomkins’ Script Theory, using a series of repertory grid interviews with clinical medical students. I have taken an ontological position on the human mind, arguing that it is an embodied entity that actively scans the environment looking for meaning, and in which learning is driven by curiosity but motivated by the affective response of interest-excitement. Although Tomkins provides my main theoretical framework, I have triangulated his ideas with George Kelly’s Personal Construct Psychology, partly to add extra metaphorical depth, but also because Kelly’s theory offers a logic of enquiry and a method that I did not find in Tomkins. I also draw on Alexander Bain’s ontological description of the embodied mind, but update this with more contemporary ideas about perception and curiosity.
My script theoretical hypothesis was not supported by the empirical data, because it was based on a false assumption that students’ engagement with digital learning was superficial. However, several important findings emerged. Medical students, on the whole, appreciate the convenience and safety of digital learning but do not actually enjoy it. Students experience digital learning as lonely and perceptually poor, and they explicitly link this to difficulty in sustaining attention. I contextualise these findings within the idea of the embodied, curious, affect-susceptible mind, and argue that a sense of place is important for learning, as is the real presence of others. Learning in three-dimensional “real” worlds allows students to derive meanings from place and person that support the affective response of interest-excitement. This, in turn, supports sustained attention.
I argue that when considering learning media, we should distinguish between the efficient and the human, identifying the contexts in which the efficiency gains of digital media outweigh the de-humanising nature of digital learning, and continuing to value the human attributes of face-to-face teaching and learning.
Investigating the role of the eosinophil in COPD
Keywords: Oxidative stress
COPD
Eosinophils
ROS

Now the third leading cause of death worldwide, chronic obstructive pulmonary disease (COPD) is characterised by unpredictable acute worsening of symptoms. A third of these crisis events are associated with an eosinophilic phenotype that has an unknown mechanism of injury. In this thesis, I have shown that RNA-sequencing of eosinophils isolated during exacerbations revealed upregulation of genes related to redox systems. Furthermore, eosinophils isolated during crisis events had increased capacity to produce reactive oxygen species (ROS), had a higher resting state of ROS generation, and released more mitochondrial specific ROS compared to neutrophils. Eosinophils also had comparatively low levels of the antioxidant enzyme glutathione, which appeared to be less oxidised, indicating that eosinophils have a weak ability to scavenge excess ROS. Finally, in a co-culture system, eosinophils were shown to disrupt epithelial barriers and induce hyperpermeability, which was further increased upon eosinophil stimulation. These findings would suggest that when COPD patients experience an eosinophilic exacerbation and consequently, an influx of activated eosinophils into the airways, there is damage caused to the local tissue milieu due to the release of ROS. This mechanism proposes a new therapeutic avenue at the point of an eosinophilic exacerbation. Additionally, analysis of serum and sputum samples highlighted IL-5 as a key eosinophil mediator released during eosinophilic exacerbations. Flow cytometry analysis identified the IL-3 receptor as a potential marker of eosinophil activation status.
Foundations: an integrated landscape analysis of Romano-Celtic temple locations in South-West Roman Britain
Keywords: Roman
Romano-Celtic temples
archaeology
Roman religion
landscape archaeology
Romano-British

Research into rural Romano-Celtic temples in Britain has been predominantly site- based, with consideration of their landscape context generally confined to descriptive observations. This dissertation pilots a landscape archaeology methodology to explore the selection of temple locations by their ‘builders’, with a particular focus on case studies of Cold Kitchen Hill and Lamyatt Beacon. The methodology draws on the academic and grey literature, modern and historic mapping, aerial photography and LiDAR data, supplemented by field visits. The use of GIS, including visibility analysis, is also central to the project, which is underpinned by relevant theory.
The results provide new evidence for roads, villas and field systems, whilst viewshed analysis offers insights into the visual relationships between the temple locations and the surrounding landscape. An interpretation of the synthesised evidence suggests that the Cold Kitchen Hill location is likely to have been selected by the native elite based at Brixton Deverill villa for its pre-existing and potentially sacred significance dating to the Iron Age, together with its strategic importance at the convergence of three roads and on the boundary of three civitates. Whilst Lamyatt Beacon is likely to have been connected to the villa at Ditcheat, its accessibility and visual prominence are likely to have been key factors in the selection of its location. These attributes coupled with the adoption of same cult as Cold Kitchen Hill are likely to have combined to attract pilgrims, including people from the civitas capital at Ilchester and its prosperous environs. The success of this ‘new’ temple at Lamyatt Beacon is illustrated by its connections with the later temple at Brean Down.
The wider implications include further evidence for close connections between temples and villas, and that notions of elite social display might be usefully extended to Romano-Celtic temples. Furthermore, that binary interpretations in the literature, particularly those relating to concepts such as ‘estate temples’ or ‘cult centres’, and ‘sacred’ or ‘secular’, risk masking the complexity of decision making regarding the selection of temple locations. Additionally, rural temples may not have been as isolated as previously suggested, and notions of local pilgrimage offer much potential for future research. Finally, the dissertation is significant in demonstrating that a landscape archaeology methodology can make an important contribution to the interpretation of Romano-Celtic temples.
Clayful Phenomenology and material engagement: explorations in contemporary cognitive archaeology
Keywords: extended consciousness
Material Engagement Theory
extended mind
clay
sculpture
Clayful Phenomenology

The thesis explores the phenomenology of creative cognition from the viewpoint of a contemporary ceramic workshop. Over five chapters, six clay sculptural projects track the development of a method I call ‘clayful phenomenology’. Informed by Material Engagement Theory (MET), the method takes sculptural development (normally understood to be the realization of an artist’s vision) and reformulates it so that a body of clay becomes a transient, diffuse, knowledge-producing assembly. The reformulation replaces subjective experience with a systemic, phenomenological proposal for extended sentience. Clayful Phenomenology turns material culture from an object of study into a method for investigating its own creative becoming. Videos, photos and written notes record the materialization and evolution of ideation as it is enacted in the gestural relationship between clay and hand, what Malafouris calls “creative thinging”. This account of sculpting by sculpting gives unique access to the three principles of MET and focuses on how: 1. thoughts, feelings and sensations establish themselves through gestural activity in the workshop rather than neural activity in the brain, thus extending the mind; 2. intention develops through the making and breaking of habitual practices imbuing material with agency; 3. signification, enacted and ideated through material change, enables each project to learn itself into existence. Clayful phenomenology gives reason to question the meaning of ‘cognitive’ in ‘cognitive archaeology’ by suggesting the discipline might move away from retrofitting cognitive science models to past human thinking and towards using the archaeological study of material culture to challenge neuro-centric conceptions of the mind. The first three chapters develop the method by elaborating five contemporary examples of creative thinging. The final two chapters introduce a form of experimental cognitive archaeology during which clayful phenomenology explores the enactive signification of a prehistoric artefact: a Jōmon flame pot. This diffractive analogical approach does not attempt to uncover past meanings but to make sense of the archaeological record by creating new experiences of its traces in the present. The thesis concludes with a review of extended sentience in relation to the ownership of feelings and letting go of affective intentions.
The violinist in London's concert life, 1750-1784 : Felice Giardini and his contemporaries
Keywords: music
violin music
England
London
18th century
Felice Giardini
concert life
eighteenth century
violinists
concerts

According to Burney, Giardini began 'a memorable æra in the instrumental Music of this kingdom' with his first performance in London in 1750 [1751]. The period up to his departure in 1784 saw a proliferation of musical activities - winter subscription and benefit concerts (featuring the most modern music), oratorio performances, societies (some favouring ‘ancient’ music) and summer gardens concerts, besides productions at the Italian Opera and English playhouses. Private concerts abounded and music at court was far from negligible.
Many foreign violinists were attracted by British wealth. Still prominent were Italians, notably Giardini, but later in the period Germans rivalled them, especially Cramer and Salomon; and occasionally a Frenchman such as Barthelemon came to London. These four, together with the natives Pinto, Hay and Fisher, were London's principal resident violinists, , opposition occasionally being provided by visitors such as Pugnani and Lamotte. Though several were significant composers, London's violinists were primarily in demand as leader and soloist. The violin solo (with continuo) remained a virtuoso showpiece until 1773, after which it rapidly declined in face of the textural variety of concert chamber music. The violin concerto was able to survive stylistic changes and its popularity was not threatened by the sinfonia concertante, a genre often heard from 1775.
Accounts of some 80 violinists are included, and also a biography of Giardini, an outstanding violinist of the century, noted for his tone and graceful. style rather than for technical wizardry. He was involved in concert and opera management; he organised charitable performances (especially for the Lock Hospital); he was a noted leader and teacher, as well as a prolific composer; and he was acquainted with many members of aristocratic and artistic circles.
Appendices list London's concert and oratorio series during the period, Giardini's works, contemporary violinists and their violin music.
Generalized spatio-temporal model for the optimal sizing, operation, and location of energy system assets
Keywords: optimization
systems engineering
system of systems
renewable energy
energy systems optimization

Future energy systems will contain large amounts of distributed energy resources (DER). In DER-based energy systems asset related to energy demand, supply, transport, storage, conversion, and demand response will be deeply coupled. This thesis develops the Space-Time Energy Vector Flow Networks (STEVFNs; pronounced like the name “Steven”) unified asset model, framework, and tool for the optimal design of DER-based energy systems. This thesis is the first to develop a generalized spatiotemporal asset model that unifies energy demand, energy supply, energy transport, energy storage, energy conversion, and demand response assets. STEVFNs enables energy system design by co-optimizing the sizing, operation, and location of energy system assets. It utilizes modern advancements in convex programming and is the first to enable the optimization of energy system design with rapid scenario assessment. It is demonstrated using a case study of designing an energy system to satisfy Singapore’s hourly electricity and high temperature heating demand using intercontinental solar and wind farms, distributed batteries, HVDC lines, distributed ammonia storage, ammonia transport, and various conversion technologies. STEVFNs is available as an open-source tool on GitHub for the co-optimization, with rapid scenario assessment, of the sizing, operation, and location of energy system assets that can provide energy demand, supply, transport, storage, conversion, and demand response.