VictorJuiz/thesis huggingface dataset:
Modular network comparison with application to labour flow networks

Evolutionary economic geography emphasises the role of locally embedded skills and knowledge in regional economic development processes. A region grows into new economic activities by combining locally available skills. This is typically modelled as a branching process on an inter-industry labour flow network, where a region’s probability of entering an industry is a function of the related industries available. In this thesis, we develop new methodologies that support the analysis of these labour flow network models.
In the first part of this thesis, we develop new metrics to compare the modular structure of different networks. The motivating application is the comparison of different countries’ inter-industry labour flow networks. More specifically, we present a novel approach for the global modular comparison of two node-aligned networks. The measure quantifies the difference in the quality of the partition of two graphs by projecting the community structure of each graph onto the other. The technique is advantageous as it captures the influence of the underlying network structure and applies to a broad range of networks as it is agnostic to the quality function adopted.
Building on this framework, we also present a fine-grained modular comparison technique, which compares the modular structure of a single community across two networks. The measure compares the expected escape probability of a random walker, initially starting in the community, across the two networks. The measure is advantageous as it captures the impact of edge density and connectivity on the modular structure of the community.
In the second part of the thesis, we investigate two economic questions. First, we investigate whether the presence of related multinational enterprises (MNE) results in knowledge spillovers that foster new related domestic industries in Irish regions. We propose a new dynamic-based cohesion measure for an inter-industry labour flow network that captures the impact of higher-order linkages between an industry and the industrial portfolio of a region. We find that industries containing both domestic and MNE firms enhance the entry and survival of related domestic industries within a region, while industries dominated by MNEs have the opposite effect.
Finally, we consider the indirect impact of an affirmative action policy on inter-industry gendered labour mobility patterns in South Africa. By harnessing a regression discontinuity design with an entropy-based centrality measure, we investigate how the policy has impacted the sectoral diversity of new employees in firms. We find that the policy widened the sectoral diversity of female workers, particularly the related variety of skilled female workers. However, unlike results in the literature, this did not translate into any significant impact on firms’ performance.

Keywords: labour flow networks
economic geography
knowledge flows
network comparison
Advisor: O'Clery, N
Grindrod, P
Radio wave activated chemotherapy

As one of the most common cancer treatments used in treating patients, chemotherapy has saved countless lives. However, due to the lack of specificity provided by conventional chemotherapy, healthy tissue as well as tumour tissue is destroyed as a result of collateral damage. The side-affects reduce the quality of life of patients so much so, that in some cases, they refuse the potentially lifesaving treatment altogether. The underlying problem with conventional chemotherapy lies in the fact it is not discriminant enough in targeting cancerous cells.
This thesis presents a nanoparticle copolymer complex that is capable of actively targeting cancer cells and limiting drug release until an external stimulus “activates” the complex. The targeting manifests itself through the enhanced permeation and retention effect between nanoparticles and cancer cells, and magnetic localisation at the target location in vivo. Activation is triggered by radio wave induced inductive heating of an iron oxide nanoparticle core that causes a structure change in the grafted copolymer, releasing drug bearing proteins. The novel grafted copolymer has been meticulously designed to reversibly immobilise drug bearing proteins and undergo a structure change at a temperature of 42.5 ˚C, above that of human body temperature, but below that of hyperthermic temperatures.
Ultimately, this nanoparticle copolymer complex would be administered to patients via injection or consumption, magnetically localised in tumour locations within the body using external magnets, and selectively taken up by cancer cells due to the EPR effect. When particles have accumulated in the desired site, a harmless alternating magnetic field would be induced in target areas around the body and the drugs released. If successful, this complex treatment could provide an effective delivery system for many types of chemotherapy molecules while eliminating side effects of treatment completely.

Keywords: nanotechnology
smart materials
nanomedicine
remote activation
targeted drug delivery
Advisor: Townley, H
Understanding mechanisms of pathogenesis and resistance in Neisseria gonorrhoeae

Neisseria gonorrhoeae is a leading cause of sexually transmitted disease worldwide. Recently, N. gonorrhoeae has become a significant public health concern due to increasing antimicrobial resistance (AMR). Therefore, novel ways to tackle N. gonorrhoeae infection are required. My work aimed to address this by further understanding gonococcal interactions with complement and by providing insights into plasmid-mediated AMR.
Previous research demonstrated that N. gonorrhoeae binds Complement Factor H (CFH), a negative regulator of the human complement system, to avoid complement killing. Here, I showed that N. gonorrhoeae also binds to Complement Factor H Related protein 5 (CFHR5) which does not negatively regulate the complement system. I demonstrated that CFHR5 binds to PorB, a gonococcal surface porin, and that CFHR5 and CFH bind to several of the same external loops of PorB.
The spread of plasmid-mediated AMR in N. gonorrhoeae is due to the conjugative plasmid, pConj. Therefore, I investigated the spread and maintenance of pConj. I showed that pConj is largely restricted to N. gonorrhoeae, is extremely stable once acquired, and is highly conserved. I investigated the basis of why pConj is mostly found in particular gonococcal lineages, and showed a correlation between prevalence of the plasmid in a lineage, and the ability of strains from that lineage to acquire pConj. A subsequent unbiased genetic screen failed to identify chromosomal genes involved in pConj acquisition.
Finally, I defined the mechanisms of pConj maintenance and showed that both partitioning and toxin-antitoxin (TA) systems are involved in plasmid maintenance; TA systems on the gonococcal cryptic plasmid could contribute to pConj maintenance through a split TA system. Lastly, I showed that pConj can be cured by interfering with plasmid partitioning.
Overall, my findings provide insights into novel ways of that could be exploited for tackling gonococcal disease through immunotherapy or plasmid destabilisation.

Keywords: Neisseria gonorrhoeae
conjugation
serum resistance
plasmid
CFHR
Advisor: Tang, C
Cehovin, A
Raff, J
Musical warriors: British military music and musicians during the French Revolutionary and Napoleonic Wars

Military music was pervasive in Britain and Ireland during the French Wars but has received limited attention from historians. This thesis interprets martial music-making as a core military activity and an integral part of wider musical culture. A critical tool of communication and discipline, music sounded the alarm, aided recruitment, and governed soldiers’ routines and bodily movements. Officers invested heavily in military bands, regarding them as social amenities, sources of prestige, and essential for maintaining soldiers’ morale. Regiments competed and cooperated in a seller’s market for musical labour, engaging knowledgeable civilian performers and training a mass of novice instrumentalists through a cogent instructional programme.
Attention to music reveals the depth and reciprocity of interactions between the military and society. Regimental bands provided sought-after entertainment at myriad public events, staged free open-air concerts for socially diverse audiences, and amplified wartime expressions of patriotism. Military performers also promoted cultural dissemination and exchange, rehearsing eclectic repertoires and adopting melodies from other regiments, armies, and peoples.
Military mobilisation palpably shaped nineteenth-century musical culture. Volunteer and militia bands established in wartime continued playing together for decades after Waterloo while discharged regimental instrumentalists actively contributed to provincial and colonial musical life as teachers, performers, and retailers. The expansion of military music-making also encouraged the post-war spread of amateur wind and brass bands, which were often led by old soldiers and modelled on regimental lines. Ingrained in popular culture after two decades of conflict, martial music was widely emulated by political reformers with the involvement of musically trained ex-servicemen.
Military music, in sum, was an everyday and intrusive part of wartime life, a source of entertainment and opportunity, and a politically charged exponent of both patriotism and protest. The legacies of martial music-making, as this thesis argues, echoed far beyond the barrack gates.

Keywords: music
popular politics
army
war and society
military
musicians
Advisor: Harris, B
Charters, E
Variational autoencoders for supervision, calibration and multimodal learning

Learning representations of data has long been a desirable goal in machine learning. Constructing such representations enables downstream tasks such as classification or object detection to be preformed efficiently. Furthermore, it is desirable to have these representations be constructed in such a way so they are interpretable, which allows for fine grained intervention and reasoning on characteristics of the input. Other tasks may include, cross-generation between modalities, or calibrating predictions such that their confidence matches their accuracy. An effective way to learn representations is through a Variational Autoencoder (VAE), which performs variational inference on the latent variables of the observable input. In this thesiswe show how the VAE, can be utilised to: incorporate label information into the learning process; learn shared-representations of multimodal data; and calibrate predictions of existing neural classifiers.
Data sources are often accompanied by additional label information, which may indicate the presence of a characteristic in the input. A question naturally arises as to whether the additional label information can be used to structure the representation such that it provides a notion of interoperability about the characteristic; such as “to what extent is the person smiling?”. The first contribution of this thesis is to address the aforementioned problem and propose a method which successfully uses label information to structure the latent space. Furthermore, this allows us to perform additional tasks such as fine grained interventions; classification; and conditional generations. Moreover, we are also successfully able to handle the case when label information is missing, drastically reducing the data burden when training these models.
Rather than being presented with labels, we sometimes instead observe another unstructured observation of the same object, e.g. a caption of an image. In this scenario, the objective changes slightly to one where the model is able to learn shared-representations of data, allowing it to perform cross-generations between modalities. The second contribution of this theses addresses this problem. Here, learning is performed by employing mutual supervision between the modalities and introducing a bi-directional objective, which faithfully ensures symmetry in the model. Furthermore, by virtue of this approach, we are able to learn these representations in situations where some of the modalities may be missing during training.
Uncertainty quantification is an important task in machine learning, with it now being well known that current deep learning models severely overestimate their confidence. The final contribution of this thesis is to address how the representations of VAEs can be used to extract reliable confidence estimates for neural-classifiers. This investigation leads to a novel approach to calibrate neural-classifiers, which is applied post-hoc to off the shelf classifiers and is very fast to train and test.

Keywords: VAEs
semi-supervised learning
calibration
multi-model Learning
Signatures of quantum gravity

This thesis discusses the hurdles that are frequently encountered in attempts to quantize gravity or rather, while gravitizing quantum mechanics. Among the issues we consider here are the lack of observable signatures of the quantum nature of gravity despite the considerable amount of effort directed towards theoretical approaches such as string theory and loop quantum gravity, to name a few. Here, we examine observable consequences of quantum gravity through superpositions of primordial massive particles and quantum witnesses in table top experiments involving Bose Einstein Condensates. We compute the decoherence timescales of a primordial superposition and outline its effects in the form of an interference pattern, characteristic absorption spectra or entanglement effects. While it is difficult to conceive of a way to control measurements that occur in the early universe, such as the measurement of curvature perturbations during inflation, we have a significant degree of control over quantum systems in the laboratory such as Bose Einstein Condensates for which we propose a non-Gaussianity based witness of the quantum nature of gravity. Non-Gaussianities are also discussed in the context of cosmological observations where it becomes important to distinguish primoridal non-Gaussianities from secondary effects. While observing any of these signatures can give credence to the requirement that gravity should be quantum, insight can also be drawn between conflicts that exist between general relativity and quantum mechanics. One such anomaly we discuss is the cosmic censorship conjecture and its reconciliation with quantum information theory. In particular by employing the complexity-volume conjecture from the AdS/CFT correspondence, we show that for Kerr black holes, spacetime must continue across the Cauchy Horizon where solutions to the Einstein field equations break down. Finally, we introduce a formalism that attempts to bridge the gap between quantum theory and relativity by putting spacelike and timelike events on the same footing. The notion of an event, redefined as a correspondence between a system and an apparatus, gives rise to interesting predictive phenomena and allows us to apply the tools of quantum information theory in their characterisation.

Keywords: quantum gravity
quantum information
events
spacetime
Advisor: Vedral, V
Engagement, surprise and exploration in the macaque frontal lobe

In this thesis I investigate how macaque monkeys make reward-guided decisions. Specifically, I investigate behavioural, computational, and neural mechanisms for detecting and learning from surprising events, choosing whether to explore or exploit, and staying engaged. Using fMRI data of macaques performing different tasks, I identify neural activity patterns underlying these types of behaviours. I demonstrate that macaques notice reward-based surprises beyond scalar reward prediction errors: I link neural activity on the orbital surface both to obtaining a surprisingly rare amount of reward (Chapter 2), and to counterfactual prediction errors associated with an unchosen option (Chapter 3). I show that the signals related to rare reward surprise only occur when the reward-environment is sufficiently complex and incentivises learning: such surprise signals could only be detected when the underlying reward probabilities changed over the course of a session, while I find no surprise signal for static reward environments. I also demonstrate that macaques strategically modulate their tendency to explore or exploit depending on the reward-environment, and link such behaviours to different signs of reward-value signals in anterior- and mid-cingulate gyrus (Chapter 3). Finally, I identify general neural signals associated with engaging with a task rather than pausing to respond (Chapter 4). To this end, I show that a network of regions spanning perigenual anterior cingulate cortex, orbitofrontal cortex and striatum is more active when animals are engaged with a task, and causally link activity in perigenual anterior cingulate to task engagement using transcranial ultrasound stimulation. By contrast, mid- and posterior cingulate are more active when animal spontaneously disengage from a task. Using data from four distinct decision-making tasks, and controlling for all factors that were manipulated in these tasks, allows me to show that these engagement-patterns are task-independent and capture an intrinsic component of motivation not previously studied.

Keywords: learning
motivation
fMRI
decision-making
macaque
Advisor: Rushworth, M
Kolling, N
'You can write whatever you want': exploring the relationship between student self-concept and creative writing practices

This project sought to investigate whether guided creative writing processes can have an impact on students’ self-concept in domains related to the topics about which they are writing. To investigate this, a creative writing project focused on prose science fiction was designed and delivered to a class group of secondary school students in Dublin, Ireland. A second class group from the same school took part in a poetry writing project and served as the control group for this study. A questionnaire to measure self-concept in two domains (creative and scientific) was delivered to both groups before and after the intervention. Results were to be triangulated using semi-structured interviews with participants in the intervention group and the adult collaborators who worked with them but, as a result of the COVID-19 pandemic, these could not be completed. Due to the disrupted research, conclusions could not be drawn from the data collected. An evaluation of the intervention design, however, indicates that it satisfied most of the criteria suggested by the literature review and that a repeat investigation, when circumstances allow, is warranted.

Keywords: MLT 2020
MLT
A study on Chinese ethnic minority university students' attitudes toward minority education policies and their sense of national identity


In China, research into ethnic minorities' national identity has increased significantly since the development of ethnic group theory. However, most existing research on minorities’ national identity has relied primarily on theoretical studies, with relatively few empirical studies conducted. Aiming to better understand minority students’ perceptions toward relevant educational policies, and the potential association between policy attitudes and their sense of national identity, this study takes an online survey as the data collection method which is philosophically grounded in pragmatist position. Specifically, the questionnaire includes a policy attitude scale, a scale of sense of national identity, and an open-ended question, in which the two scales were adapted from previous research. Findings suggest that the sampled students (n = 119) generally hold positive attitudes towards ethnic minority education policies and have relatively strong sense of national identity. The responses generated from the open-ended questions indicate three major themes: perceived benefits of multilingualism, the diversity of opinions on preferential admission policies, and the perceived importance of preserving minority cultures both within minority groups and in the Chinese mainstream society. This study revealed that gender did not significantly influence policy attitudes or senses of national identity among sampled students, but that students' grade level may have a significant influence on both. Most importantly, findings indicate that students' policy attitude can explain 46.8% of the variance in students' sense of national identity when controlling for their gender. The results triggered multiple policy and practical implications, leading to further considerations of how sense of national identity could be taken into account in the formulation, adjustment, and improvement of minority education policies, and how relevant education policies could help build and enhance ethnic minority university students’ sense of national identity.

Keywords: RDM
attitudinal research
questionnaires
ethnic minority students
sense of national identity
minority education policy attitudes
RDM2022
Advisor: Lindorff, A
Attitudes towards academic dishonesty: Russian and British students 

Literature on academic dishonesty has been widespread, but it has been approaching the issue from either the standpoint of morality or convention and plagued by methodological shortcomings. Going beyond previous studies based on Social Domain Theory, a vignette experiment was created to include both students’ perceptions of moral (fairness) and conventional (acceptability) judgements using a one between (Culture) × two within (Stakes and Exposure) factors design, controlling for academic integrity involving students from British (N = 113) and Russian (N = 453) universities. The vignettes were carefully calibrated using cognitive interviews and back-translations to fit both contexts. New findings emerged. First, this study found that perceptions of academic dishonesty involve both moral (fairness) and conventional (acceptability) judgements. Second, these judgements were affected by cultural and, in some instances, contextual factors. Specifically, British students perceived cheating as unfair and unacceptable, while Russian students regarded cheating as unfair but somewhat acceptable. Third, contextual drivers, such as harm perceptions, affected Russian students’ judgements on the fairness and acceptability of academic misconduct, while British students’ judgements were immune to contextual differences. Thus, Russian students had less negative attitudes toward cheating if it did not harm other students, and they condemned whistle-blowing in such cases, referring to a whistle-blower as a “snitch”. Finally, higher academic integrity was associated with lower perceptions of fairness and acceptability. These findings underscore that students’ judgements of academic dishonesty are multifaceted and malleable, urging more nuanced and cross-cultural investigations. On the policy side, they also suggest universities should introduce honour codes and develop courses on academic ethics, which have the potential to decrease the level of academic dishonesty.

Keywords: cross-cultural research
Moral judgements
vignette experiment
RDM
cheating
survey
RDM2022
cognitive interviews
back-translation
academic dishonesty
Advisor: Malmberg, L