VictorJuiz/thesis huggingface dataset:
Extending probabilistic programming systems and applying them to real-world simulators
Keywords: machine learning
simulators
probabilistic programming
statistics
Bayesian inference
AI

Probabilistic programming is a paradigm that enables us to efficiently write probabilistic models as program code that we can sample, infer underlying parameters and predict outcomes based on complete or incomplete observations. Naturally, stochastic simulators, a special sub-class of simulators containing random variables, internal inference procedures, and the simulation of observations, are structurally rich probabilistic models. However, most simulators are not written in the probabilistic programming paradigm, as they are written in arbitrary programming code. This means that it is challenging to automatically update the variables in these simulators to account for observations from conducted experiments, which limits the simulators' use.
Furthermore, there are two components to a probabilistic programming system i) the language and compilation procedure, ii) the inference procedures. These components can limit our ability to compile particular classes of probabilistic models, such as models that contain mixtures of parameter types, due to restrictions in the expressiveness of the language. Restrictions in the expressivity of the language can also inhibit our ability to generate efficient inferences, as this naturally influences the design of the probabilistic programming system and the set of available inference backends. Creating probabilistic programming systems that are expressive enough for different probabilistic models leads to the creation of many different probabilistic programming systems, which is inefficient - it would be more efficient if we could repurpose existing probabilistic programming systems.
In this thesis, we develop three pieces of original work through four papers. The first piece of work describes how to extend differentiable first-order probabilistic programming systems to perform statistically correct and computationally efficient inference on models with mixtures of continuous and non-continuous parameters, without having to modify the underlying language, or develop an entirely new probabilistic programming system. The second describes how to translate real-world stochastic simulators written in arbitrary program languages to probabilistic programming systems. And finally, in the third piece of work, we develop two new Bayesian inference schemes to make inference more computationally and statistically efficient in nested models, models that contain probabilistic programs, within probabilistic programs, which arise in many real-world stochastic simulators.
Electrification & renewable energy integration: a case study of methanol production
Keywords: methanol
model-based optimisation
renewables
electrification

The electrification of the chemical industry is of paramount importance in meeting reduction targets in greenhouse gas emissions. However, it is tenable only if the electricity is generated from renewable sources. This project aims to investigate electrification schemes using methanol production processes as a case study, and to explore strategies for how to power such an electrified process with renewable energy. Taking a methanol production basis of 400,000 tonnes per annum, the energy and material flows are obtained from process simulations while renewable energy systems dedicated to the production are optimised through a modelling approach. In this work, direct (via heat pumps) and indirect electrification strategies (via sourcing alternative feedstocks) are compared, with results showing that the indirect electrification scheme has a more significant impact on the process energy structure. Based on the fully electrified methanol process, renewable power systems with an optional dispatchable power backup are modelled to fulfil the energy requirement aiming at the economic optimality. A two-regime behaviour of renewable penetration against dispatchable energy price has been found, which increases dramatically at the onset and slowly approaches 100% when the dispatchable energy price is above a critical point. The optimal operation of the renewable energy systems results in voluntary curtailment of renewable power, of which the cost analysis shows modest economic potential for its further utilisation. The benefits of a flexible process are shown to be significant, which can reduce the levelised methanol cost by up to 35%. Two geographical locations with distinct meteorological data are selected to investigate the impact of renewable source characteristics on the performance of methanol production and its renewable energy system. In particular, the diurnal and seasonal fluctuations of renewable sources and their impact on energy storage need are compared. The lessons of this project not only provide numerical results in terms of energy needs and production costs but also implications to policymaking, both of which will facilitate the energy transition from the current fossil fuels-based chemical industry to greener production.
Theories of cosmic time in the Mahābhārata
Keywords: cosmic time
Mahābhārata
Hinduism
Religious aspects

This thesis presents an examination of the Indian theories of cosmic time as they are found in the Mahabharata. It looks at the theories in detail and analyses their essential characteristics and structures of its three main elements: the divisions of time; the cycle of creation and destruction; and the characteristics of the four yugas. Special attention is paid to aspects of the theory that have been little explored, such as the nature of the cyclical repetition; the relationship between the yugas and the avataras of Visnu; the characteristics of the junctures between the yugas, etc. In the few areas where the theories of cosmic time found in the Mahabharata differ from those of the Purad nas, the differences are indicated. Ideas of cosmic time in literature preceding the Mahabharata are examined, and it is argued that the fundamental structures and concerns of the later theories can be seen to have clear antecedents in the cosmogony of the Vedas and the cosmogonic implications of certain sacrifices found in the Brahmad nas: Vedic cosmogonies show that the primary creative act is the imposition of order on chaos, in the spatial, temporal and ethical spheres, and the sacrifices show the existence of a cycle of creation and destruction, where creation must be periodically re-established by the sacrifice and the sacrificer. These principles are seen to still inform the later theories, and often help to throw light on obscure areas within them.
Modelling the collective migration of neural crest cells
Keywords: neural crest
collective cell migration
domain growth
hybrid model

Collective neural crest cell migration contributes to the formation of several spatially and biologically diverse tissues during vertebrate development. If neural crest cells fail to reach a target or populate an incorrect location, then those cells may undergo improper cell differentiation or uncontrolled cell proliferation, leading to developmental defects. A wide range of mechanisms that drive collective cell migration are displayed by distinct types of neural crest cells that emerge at different axial levels of the neural tube and are affected by different local signals. For example, chick cranial neural crest cells are understood to be guided by a cell-induced chemotactic gradient and their migration occurs within a growing tissue, whilst in Xenopus, cranial neural crest cells are understood to be guided by co-attractive and co-repulsive intercellular interactions in the absence of growth. However, there are still many open questions as to how neural crest cells interact with each other and their microenvironment to undergo successful migration. Answers to these questions would not only help us understand embryonic development, but also provide insights into other less experimentally tractable collective migration phenomena, such as wound healing and tumour formation.
In this thesis we investigate the migration of chick cranial neural crest cells using a hybrid computational model, which consists of a discrete, off-lattice model for the motile behaviour of neural crest cells coupled with a continuum, reaction-diffusion model for the chemoattractant concentration. We work in parallel with our experimental colleagues who perform imaging of chick embryos under certain perturbations. In particular, we use our model to explore the role of the water-specific aquaporin 1 channel and spatial confinement on the migration of neural crest cells. We also investigate how domain growth affects collective cell migration. In the final part of the thesis, we develop a unified individual-based stochastic model to include the different cell-cell interaction mechanisms observed in Xenopus and chick. The model is used to compare and contrast the behaviour of neural crest cells in different organisms and to further investigate the cell-cell interaction mechanisms in chick.
Procedural fairness at the police station
Keywords: fairness
police station
police questioning
England
arrest

This thesis questions whether it is right to allow the police to detain and interrogate suspects at the police station. It asks whether there are procedures in place to ensure that suspects are not coerced or intimidated into confessing falsely; whether it is consistent with adversarial ideals of adjudication for the courts to endorse confessions of guilt which have been made in an inherently coercive atmosphere; and whether it is justifiable to use powers of arrest to facilitate interrogation. The thesis provides some historical background to current police powers, and then goes on to demonstrate that controls on police questioning were gradually relaxed in the period of the Judges' Rules (1912-84). It is shown that the arguments put forward to justify the increase in police powers, namely that the police were neutral investigators from whom suspects had nothing to fear and that powers of questioning were vital for crime control, could not be sustained in the light of then known facts. The legal framework which currently regulates police powers is described, and it is argued that it pays insufficient regard to due process values. The thesis draws upon interviews with defendants in order to address the issue of whether those who go through the process perceive police station procedures as fair or unfair. Through a combination of interview and observational data, the thesis seeks to establish that granting legal 'rights' to those detained at the police station does not always empower them to resist police pressure and coercion.\The thesis concludes that police powers of detention and questioning contribute little to the task of identifying and convicting offenders, sometimes lead to miscarriages of justice, and may be used to inflict arbitrary and summary punishment. It is therefore recommended that the police right to interrogate suspects be abolished.
Measuring the effect of heterogeneity and trust on cooperation in common-pool resources
Keywords: Sociocultural Heterogeneity
Trust
Cooperation
Economic Heterogeneity
Common-Pool Resources

In this doctoral thesis I measure the effect of economic and sociocultural heterogeneity on cooperation through trust in the context of common-pool resources, using different techniques. The thesis is made up of three separate papers that are all trying to answer the same overarching question: how and to what extent does heterogeneity affect cooperation between appropriators of common-pool resources, and what is the role of trust in this process? The first paper applies innovative imputation techniques to use the famous CPR Database, compiled by the Nobel- prize winner Elinor Ostrom, to its full potential. The second paper uses data from a CPR laboratory experiment conducted in the United Kingdom and the Netherlands, in which a cooperation dilemma is simulated that is experienced in fishing grounds. The third paper uses data from the earlier experiment and an additional CPR experiment conducted in India, and analyses and interprets the difference in behaviour between the two experiments by using player type classification and agent-based models. Findings of this thesis suggest that heterogeneity does not necessarily impact cooperation negatively: sociocultural heterogeneity is not found to be negatively related to cooperation, economic heterogeneity is found to be positively related to cooperation under certain conditions and the combination of economic and sociocultural heterogeneity is found to be positively or negatively related to cooperation in CPRs depending on the operationalisation of sociocultural heterogeneity. In addition, it is found that trust has a positive effect on cooperation and that heterogeneity may impact trust negatively under some conditions.
The Press and English local authorities
Keywords: English local authorities
Press
Newspapers
Journalism
Great Britain

For over a century the press hag been engaged on a battle for certain rights and facilities which it considers necessary to the reporting of local government, some of these rights, like that of attending council meetings, secure for the journalist opportunities to obtain news and information:others, like the defence of qualified privilege in libel actions, secure a right to print and publish it. In both aspects of the problem the press still feels that it has a grievance, and the controversy persists.
Continued in thesis
The Protestant cause : religious alliance with the West European Calvinist communities as a political issue in England, 1585-1630
Keywords: Europe
Calvinism
England
Protestant cause
religion and politics
West European
Calvinist
religious alliance

It has long been accepted that protestant ideological aspirations played an important role in the foreign policy of England in the period from the Henrican Reformation to the Civil War; but little attempt has been made systematically to analyse the effects of this role. Most discussions of the question have been characterised by a lack of sympathy for protestant aspirations, and have concentrated upon anti-catholicism,relegating the Protestant Cause to the rank of provincial bigotry.
This study has been undertaken with the contrary assumption ~ that the Protestant Cause should be seen not merely as a response to catholic threats, but as a positive force which posed the central problem to English foreign policy in this period. Not only did England have the central role to play in the creation of working religious alliances with continental protestant states; but the defence of religion was the leading motive for English intervention on the continent beyond the coastal periphery. The years between Leicester's expedition to the Netherlands in 1585 and England's withdrawal from the Thirty Years War in 1630 mark the period in which the issue had the greatest political effect, for with Leicester's expedition the English monarchy came the closest to undertaking the leadership of the Cause, which it rejected finally upon withdrawal from the Thirty Year’s War.
Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly
Keywords: Self-assembly
DNA nanotechnology
Chemical kinetics
Complex systems
Statistical mechanics
Molecular simulations

In this thesis, we develop a novel approach for modelling self-assembling systems that use the single-stranded-tile (SST) assembly method, an increasingly popular nanoconstruction approach in the field of DNA nanotechnology, developed primarily in the Molecular Systems Lab (Harvard University). In the SST method, a desired target structure is produced by mixing together a set of short DNA molecules (called SSTs) where each SST is provided with a judiciously chosen base sequence such that it will bind to a predetermined set of local neighbours in the target structure. Our approach for modelling these systems involves the use of simulations with a relatively fine-grained model of DNA (here we opt for oxDNA [1]) to parametrise coarser stochastic models that represent these systems at the level of the SST (the basic subunit of the method), and can probe effectively the timescales required for self assembly. As a test system for our approach we choose a rectangular-shaped SST-based object made out of 334 42-base-long SSTs, first reported in Ref. [2].
We first introduce a stochastic model that describes the growth of one target structure under a fixed background concentration of SSTs. We use the model to study nucleation pathways, finding that structures with a high number of bonds between SSTs and compact shapes are typically the most likely to form. However, we also find that for certain (recurrent) sizes, maximally-bonded structures are actually disfavoured due to statistical factors. We then devise a simple model that describes the bonding of incorrect SSTs to a (otherwise correctly formed) structure, finding that these bonds are typically very weak, and have a relatively minor impact on the overall kinetics and thermodynamics of self assembly.
We then introduce a stochastic model that describes the simultaneous growth of multiple target structures in a system where subunits are present in finite numbers (rather than present at constant supply). Under isothermal conditions the model predicts that there is only a small temperature window (∼2ºC) where self assembly is not hindered by excessively high nucleation barriers nor depletion traps. Finally, we simulate a cooling ramp similar to the original experiments of Refs. [2, 3]. The model predicts a peak in base-pairing formation in close agreement with Ref. [3]. However, the models predicts assembly yields that are significantly above those achieved in experiments. This differences are attributed to non-specific contacts between structures, a type of assembly that is not yet well understood, and thus not described by the model.
Democratising public reason
Keywords: Political liberalism
Justificatory liberalism
Public reason
Democracy
Legitimacy

This thesis is about the relationship between liberalism and democracy. It argues that so-called public reason liberalism, a view of legitimacy that says that citizens must have sufficient reason to accept the laws that bind them, does not pay enough attention to democratic values. It then shows what public reason must look like to uphold the values of both liberalism and democracy.
The first part of the thesis is devoted to the critical argument. It argues that the value of civic equality, the idea that citizens are and should be fundamentally equal before the state, can explain why we should care about both liberalism and democracy. The idea is formalised as a principle of liberal collective self-legislation that says that citizens must be able to democratically choose to enact laws and policies that do not violate civic equality. Prominent versions of public reason liberalism fail to satisfy the principle – either because they do not leave enough room for democratic decision-making, or because they have not provided answers to known problems from social choice theory.
The second part of the thesis develops and defends a democratic form of public reason, built on the ideal of civic equality. To respect the civic equality of all, laws must be justified with reasons that are accessible to each citizen in light of evaluative standards that they themselves hold. This view leaves sufficient room for democratic decision-making and it can provide a previously unexplored escape route to the social choice problems. For this argument to work, individual citizens must offer one another public reasons in their political advocacy. The thesis ends by showing that such public-reason-giving requirements should be assigned asymmetrically in debates over invasive laws.
Using the penguin watch network to examine phenology and breeding success in pygoscelis penguins
Keywords: pygoscelis
chinstrap
marine conservation
penguin
machine learning
breeding success
citizen science
fisheries
adelie
climate change
South Georgia
krill
gentoo
Antarctic tourism
Southern Ocean
Falkland Islands
phenology
Antarctica

Remote time-lapse cameras can facilitate high-frequency monitoring of wild animal populations over large spatial and temporal scales, yet the volume of imagery they produce can be overwhelming for small research teams. As ecological studies transition towards a ‘big data’ approach, we must develop ways to deal with the ‘data deluge’, in the form of integrated processing frameworks. In this thesis, I present and examine data-processing pipelines for the Penguin Watch project – a network of approximately 80 time-lapse cameras positioned in penguin colonies across the Scotia Arc region of the Southern Ocean. I show that both the Penguin Watch online citizen science project and the Pengbot computer vision algorithm are efficient and reliable image annotation tools, which can be used in combination to maximise output and minimise error. I present new methodologies to extract biologically meaningful metrics from citizen science annotations, and show that spatial data – for example ‘nearest neighbour distances’ – can be used to examine behaviour, such as chick huddling.
Seabirds, including penguin species, are often considered indicators of marine health. As such, effective monitoring of their populations offers an invaluable opportunity to assess the health of the wider marine ecosystem. An essential part of this process is obtaining baseline data, and here I use the Penguin Watch project to extract phenological dates for a number of new Chinstrap penguin (Pygoscelis antarcticus) colonies and seasons – a species which has historically been understudied. Through a ‘virtual’ mark-recapture study I examine breeding success in Gentoo penguin (P. papua) colonies across a substantial part of their range in the Atlantic sector of the Southern Ocean. Investigation of the impact of three key anthropogenic stressors (precipitation, the krill fishery, and tourism) on breeding success revealed no significant effects over the study period. However, there is evidence that the relationship between chick survival and precipitation could be highly non-linear, with severe precipitation events associated with high chick mortality. This has implications for a number of Southern Ocean bird species, and with precipitation levels expected to increase under climate-change scenarios, continued monitoring is essential. Repetition of this study on Adélie (P. adeliae) and Chinstrap penguins – species which have a higher dependency on krill than Gentoos – is a key future research priority.
Equivariant Seidel maps and a flat connection on equivariant symplectic cohomology
Keywords: Seidel map
floer cohomology
equivariant symplectic cohomology

We construct shift operators on equivariant symplectic cohomology which generalise the shift operators on equivariant quantum cohomology in algebraic geometry. That is, given a Hamiltonian action of the torus
T
, we assign to a cocharacter of
T
an endomorphism of
(
S
1
×
T
)
-equivariant Floer cohomology based on the equivariant Floer Seidel map. We prove the shift operator commutes with a connection. This connection is a multivariate version of Seidel's
q
-connection on
S
1
-equivariant Floer cohomology and generalises the Dubrovin connection on equivariant quantum cohomology. We prove that the connection is flat, which was conjectured by Seidel. As an application, we compute these algebraic structures for a few specific examples and provide a method to compute them for toric manifolds using the moment polytope.