VictorJuiz/thesis huggingface dataset:
Rational verification in multi-agent systems
Keywords: Model checking
Automata
Temporal logic
Games
Synthesis
Computational complexity
Nash equilibrium

Rational verification problem is concerned with checking which temporal logic properties will hold in a system composed of multiple agents which are assumed to behave rationally and strategically in pursuit of individual objectives. Unfortunately, the problem is generally hard from computational point of view, and for the purpose of practical implementations, usually requires specialised techniques.
This thesis aims to develop algorithms and study computational complexity results for rational verification in multi-agent systems. Firstly, a practically amenable technique which relies on a reduction to the solution of a collection of parity games is proposed. The technique in this thesis uses a model of strategies that is bisimulation invariant—that is, in which individual strategies for system components are valid across all bisimilar systems, and which satisfy the same temporal logic properties in equilibrium. This approach has been implemented in the Equilibrium Verification Environment (EVE) system. Secondly, some cases in which the problem of rational verification is computationally tractable are investigated. In particular, it is shown that the complexity of rational verification can be reduced from 2EXPTIME-complete to fixed-parameter tractable. Furthermore, improved complexity results when considering quantitative goals, namely mean-payoff utility functions, are also studied. In doing so, a concept called equilibrium design is proposed. This concept is concerned with the design of incentives so that a desirable equilibrium is obtained.
Charge selective contacts and interfaces for perovskite solar cells with improved stability and efficiency
Keywords: Photovoltaic
Thin film

This thesis improves charge selective contacts for perovskite solar cells. First, mesoporous modification of n-type metal oxides is discovered to shift the work function of the perovskite, which enables n-type doping at the interface. A chapter on ZnO contacts elucidates chemical degradation mechanisms at the perovskite-ZnO interface, and a methylammonium-free perovskite is employed to suppress these reactions. Next, a Cs salt-treatment is developed to improve both the thermal stability and the Voc of cells on SnO2. In the following chapter, a novel organic p-type is one of the first alternatives to Spiro-OMeTAD that enables 20% power conversion efficiency. Finally, a dopant-free photo-cross-linkable polymer is presented that offers exceptional thermal stability for p-i-n cells, with device lifetimes exceeding 3,000 hours at 85°C.
Species conservation in the era of digital big data
Keywords: Wikipedia
conservation culturomics
conservation
big data
biodiversity
flagship species
digital conservation

The Earth is in the midst of a global biodiversity crisis. Populations of plants and animals are declining dramatically, and thousands of species are predicted to go extinct in the coming century. This thesis explores how a new technological resource, digital ‘big data,’ can help conservationists combat this challenge. Big data has led to revolutionary advances in multiple fields but until recently has received limited attention in conservation. I focus on one aspect of big data, the data generated by people’s activity online, and on one type of conservation, the conservation of species. I develop methods to access and interpret data related to people’s interest in species using a prominent online platform, Wikipedia, and identify methodological challenges associated with this. I highlight the ability of Wikipedia pageviews to address questions of public interest in species across broad social and geographic scales and over vast numbers of online interactions. After developing methods to access and interpret relevant Wikipedia data, I explore patterns that these data reveal. I identify the biological traits of species that influence public attention and highlight the importance of seasonal and geographic patterns in determining public interest in species. I find that the presence and abundance of a species in a region is a significant predictor of its public interest across temporal and geographic scales. I conclude by identifying ways in which the insights revealed through these methods can be applied to conservation. Specifically, I argue that online data can provide awareness as to why people prefer, and thus are more inclined to conserve, some species rather than others; be used to systematically identify species of high interest at global and regional scales; monitor temporal and spatial variations in public attention; and, in some cases, track the distribution and abundance of species. I conclude that online big data are a valuable compliment to existing conservation methods. Knowing how to access and interpret these data should be part of every conservationist’s tool kit in the twenty-first century.
The prevalence, mechanism and evolution of agrochemical resistance in natural populations
Keywords: Fungicide
Caenorhabditis elegans
Natural variation
Insecticide
Resistance
Food security
Wild isolates
Evolution
Agriculture
Pesticide
Benzimidazole
Carbendazim
Nematicide

Agrochemical resistance is a growing problem endangering global food security. The cumulative increase in the number of resistant species since the introduction of the first synthetic pesticides in the 1940s and the projected increase of the global population place more stringent requirements on the yields of agricultural food production. An increased amount of damage is predicted to result from resistance to currently used agrochemicals due to the dearth of new chemicals being developed. Despite this, resistance biology lacks methods to study the phenomenon as a whole, beyond the identification of resistance conferring mutations in particular pest or lab populations.
This thesis tests the utility of using the model organism C. elegans to study the prevalence of naturally occurring resistance alleles, the dynamics of resistance emergence in controlled conditions, and the genetic basis of resistance from multiple sources. Assessing the presence of natural variation in chemical susceptibility utilising a genetically diverse panel of C. elegans indicated that resistance-conferring variation is widespread, as suggested by the identification of wild isolates naturally resistant to carbendazim and aldicarb. The observation of rapid adaptation to carbendazim exposure suggested a link between a high prevalence of natural resistance with fast emergence of resistance for benzimidazoles, while compounds of other modes of action, with high and low variation, saw no adaptation in experimental populations under the conditions tested. Identification of the genetic basis of carbendazim-resistance in strains of three different biological origins linked a C. elegans β-tubulin to the trait in all cases, indicating a high level of convergence and lack of stochasticity in the evolution of benzimidazole resistance. Furthermore, no fitness cost of benzimidazole resistance in the compound-free environment was identified under laboratory conditions, which is troubling as the presence of a fitness cost underlies many resistance management strategies.
Overall, the findings presented in this thesis provide evidence that C. elegans is a useful model system to study resistance biology in a holistic manner, particularly in an evolutionary context. An increased understanding of the natural prevalence, evolutionary biology and molecular basis of the phenomenon would better inform field strategies of resistance mitigation as well as computational models that study the interplay of complex parameters in emergence of resistance. Ultimately, this improved understanding could assist in minimising the danger of rapidly emerging resistant pest populations on global food security.
Reconciling philosophy and scripture in renaissance Italy: Obadiah Sforno's Hebrew and Latin versions of the Light of the Nations
Keywords: Obadiah Sforno
Averroes
Aristotle
Maimonides

This dissertation is a study of Obadiah Sforno's (c. 1475–c. 1550) philosophical-theological treatise, Light of the Nations, entitled in Hebrew Or ammim (1537), and in Latin, Lumen gentium (1548). The purpose is to provide an in-depth examination of the author's response to a particular variety of Aristotelian-Averroan philosophy—such a study has not yet been undertaken. The dissertation maintains that the key to understanding the author's approach to this work is to examine which sources he used and how he read them. Three aspects of the treatise are discussed. The first is the author's heavy reliance on Averroes' interpretation of Aristotle's conceptual framework even as he sought to undermine its central theses from within. This study argues that Sforno's seemingly negative attitude toward philosophy should be viewed in terms of his reading strategies by which he made every effort to ensure that his examination of philosophy agreed with his religious beliefs. For this, the twelfth inquiry—proving the intellective soul's immortality—is taken as a case study to look at how Sforno interpreted and modified Averroes' mature noetic doctrine. The second aspect is the author's relationship to the medieval Judeo-Arabic philosophical tradition. Using his discussions on epistemology and moral philosophy, his system is evaluated in terms of certain positions advocated by Maimonides and Samuel Ibn Tibbon—the only Jewish philosophical authorities cited in the Hebrew text of the treatise. The third aspect is scriptural exegesis. The dissertation explores how Sforno attempted to achieve a reason-based assent to the tenets of religion through an allegorical reading of Scripture. It argues that the author's approach to the interpretation of biblical passages is determined by his desire to resolve the contradictions between philosophy and religion so that his reader could draw from both systems of thought. It analyses how Sforno followed in the footsteps of his medieval forebears in imposing the concepts and terminology of Greco-Arabic philosophy onto the biblical text in order to achieve a reconciliation of the Peripatetic and scriptural traditions. Throughout the study, the author's appreciation of his disparate readerships is evaluated by examining the differences between the Hebrew and Latin texts.
Measurement of localized oxygen extraction fraction in brain using magnetic resonance imaging
Keywords: TRUST
Oxygen extraction fraction
Regional Oxygenation

Magnetic resonance imaging (MRI) is a non-invasive medical imaging technique which, thanks to the variety of both structural and functional information it provides, is increasingly used throughout the world for clinical diagnosis. Due to the different magnetic properties of haemoglobin when it is bound to oxygen, MRI is sensitive to the oxygen saturation levels of the blood, however, accurate measurement of this property remains challenging in the brain. Specifically, there does not yet exist a robust MR method for quantifying regional differences in brain tissue oxygenation, which can provide important diagnostic information in cases where oxygen delivery to a specific region of the brain may be impaired, e.g. in stroke. In this thesis a new method for measuring the oxygen extraction fraction of tissue in the brain on a regional level is presented. The technique is called Selective Localized T2-Relaxation-Under-Spin- Tagging, or SL-TRUST and measures the oxygen saturation of outflowing venous blood in the superior sagittal sinus.
Using SL-TRUST venous oxygen saturation measurements are achieved in individual brain hemispheres and in a smaller tissue region, approximately 70x70x80 mm3, above the middle cerebral artery. Comparison of two contralateral regions can be achieved in a scan time of less than 5 minutes. The robustness of SL-TRUST is assessed in healthy volunteers in a reproducibility study and the coefficients of variation for regional measurements found to be comparable to those of global measurements.
SL-TRUST is developed further as a method of mapping the oxygenation of venous blood from across the whole brain using phase encoding methods. Low resolution T2 maps in healthy volunteers are obtained as proof-of-concept of this method.
Colour constancy for glossy objects under complex lighting environments
Keywords: Illuminant Metamerism
Colour Constancy
Environmental Illumination
Specular Reflection

Colour constancy refers to our visual ability to identify the colour of objects under different illuminations. As a result of research over decades, our understanding of the mechanisms underlying this ability has advanced considerably.
However, a significant limitation of past studies has been that they have mostly employed oversimplified experimental stimuli that only partially reflect the properties of surfaces and illuminations in the natural environment. Stimuli were mostly matte, two-dimensional, and uniformly illuminated by single illumination. In the real world, in contrast, we know that objects sometimes include gloss (perceptual attribute of specular reflection), and their shape is usually three-dimensional rather than flat. Moreover, an object placed in the natural environment receives illumination from every direction as light is reflected from other objects in the scene, and the spectra of those lights might vary from one direction to another.
In this thesis, I report five research projects. The first three are all experiment based, and they were designed to find mechanisms that underpin human colour constancy for three-dimensional glossy objects that are placed under complex lighting environments. We conducted first an experiment where observers were asked to judge surface and illuminant colour changes for glossy objects under point light sources. The second and third experiments explored our ability to identify surface colours of glossy objects under environmental illumination that introduces a complex spatial pattern of specular highlights on the surfaces. All experiments used computer-rendered objects that take account of the complex interaction between material and illumination in the real world. Collectively these experiments suggest that observers are able to extract surface colour, even with complex stimuli in which simple heuristics are unlikely to be reliable. Instead, the results suggest that observers may build up complex internal models from which they can segregate colours of surface and illumination.
The fourth chapter is based on field work that was conducted in collaboration with Prof. Sergio Nascimento at University of Minho, Portugal. We report newly collected hyperspectral environmental illuminations recorded in eight outdoor scenes and four indoor scenes. The aim was to characterise the directional spectral variation that occurs in natural environments and its application to more precise simulation of objects using computer graphics. Subsequent fifth chapter was motivated by the striking variation of illuminant spectra in natural environments. We revisited a classical problem in human colour vision, called illuminant metamerism where two distinct surfaces appear the same under a specific illumination. We showed theoretically that this metamerism is less of an issue than previously thought thanks to the presence of directional variation of illumination.
Synthesis without syntactic templates
Keywords: CEGIS
Syntax-guided synthesis
Formal Verification
Formal synthesis
Programming languages

Program synthesis is the mechanised construction of software. One of the main difficulties is the efficient exploration of the very large solution space, and tools often require a user-provided syntactic restriction of the search space. Writing such templates is often challenging, particularly since any constants required in the solution must be given in the template. In this dissertation we explore the research hypothesis that synthesis of programs without provision of such syntactic templates is computationally feasible using methods based on CounterExample Guided Inductive Synthesis (CEGIS).
The key contribution of this dissertation is a new approach to program synthesis that combines the strengths of a counterexample-guided inductive synthesizer with those of a theory solver, exploring the solution space more efficiently without relying on user guidance. We call this approach CEGIS(T ), where T is a first-order theory. Notably, since the publication of CEGIS(T ), a variant of the algorithm has been implemented inside leading synthesis solver CVC4. CEGIS(T) is as complete (or incomplete) as CEGIS, and it does not affect worst-case run-time complexity considerations.
In combination with the development of CEGIS(T ), we introduced several algorith- mic improvements that enhance both the performance of CEGIS(T ) and the baseline CEGIS algorithm. The first of these improvements is a significant change to the way we encode the synthesis problem for the SAT-based synthesis component of CEGIS in order to produce smaller formulae that can be more efficiently solved by SAT and SMT solvers. The second of these improvements is the use of incremental satisfiability solving in the synthesis component of CEGIS. Incremental satisfiability solving allows the SAT solver to re-use clauses learnt in previous CEGIS iterations, thus reducing the time per synthesis iteration.
We evaluate our contributions on a set of benchmarks taken from the Syntax Guided Synthesis Competition, and note that CEGIS(T ) is able to solve benchmarks which elude a standard implementation of CEGIS, specifically benchmarks that contain non-trivial constants. We find that the novel proposed encoding provides a substantial speed-up on all the benchmarks that require synthesising a program of length greater than one instruction. The use of incremental first-order solving in CEGIS decreases the solving time in some cases but not all, and we hypothesise that these are the benchmarks on which SAT-solver pre-processing is less important.
Homeric hymn to Apollo: introduction and commentary on lines 1-178
Keywords: Homer
Homeric Hymns
Apollo

Chapter 1: Unity. This chapter surveys the various arguments (formal, religious, geographical, etc.) that have been adduced to prove that DAp and PAp did not always form a single unified hymn. It is argued that these are all insufficient and that the hymn should be considered an original unity.
Chapter 2: Structure. This chapter analyses the hymn’s double structure, noting the numerous close correspondences between its two parts and some of the major devices (priamel, apostrophe, journeys) that are used to signal divisions.
Chapter 3: Date and Context. This chapter discusses the evidence for the dating of the hymn and for its context. Most of the supposed historical allusions are discounted as highly dubious. The hymn’s description of the Delian festival (147-76) suggests it had some original link to Delos, but this would not exclude later performances elsewhere. It is tentatively suggested that the hymn’s particular blend of Delian and Pythian themes would suit a Delian performance in the second half of the sixth century, perhaps in connection with the activities of the tyrants Peisistratus or Polycrates.
Chapter 4: Authorship. This chapter discusses the poet’s description of himself as the ‘blind Chian’ (172-3). It is argued that this reflects, and seeks to promote, an already existing legend about Homer, that this legend was at least partly fostered by the guild of Chian rhapsodes called Homeridae, and that therefore the ancient attribution of the hymn to the Homerid Cynaethus, which would not be incompatible with its likely date, may be tentatively accepted.
Chapter 5: Language. This chapter discusses the hymn’s language relative to the rest of early Greek hexameter poetry. Some signs of post-Homeric diction are noted. The difficulties of using language to construct a relative chronology of early epos are discussed. Doubt is cast upon the linguistic evidence for the hymn’s division. Non-Homeric and non-Hesiodic forms are assembled and briefly examined. The large number of parallels with the Homeric poems are assessed and it is suggested that, while much of this material is probably traditional, a close relationship between HAp and these poems is possible at certain points.
Chapter 6: Metre and Prosody. This chapter analyses the hymn’s inner and outer metric, and certain prosodic features. In most cases its practice does not diverge significantly from that of Homer and the other Hymns.
Chapter 7: Text and Transmission. This chapter summarises the hymn’s textual transmission. Places where the commentary diverges from Càssola’s text are noted.
Chapter 8. Commentary on lines 1-178.
Theory of killing and regeneration in continuous-time Monte Carlo sampling
Keywords: Monte Carlo inference
Markov chain Markov chain
Quasi-stationary distribution
Diffusion

We consider the theory of killing and regeneration for continuous-time Monte Carlo samplers. After a brief introduction in Chapter 1, we begin in Chapter 2 by reviewing some background material relevant to this thesis, including quasi-stationary Monte Carlo methods. These methods are designed to sample from the quasi-stationary distribution of a killed Markov process, and were recently developed to perform scalable Bayesian inference.
In Chapter 3 we prove natural sufficient conditions for the quasi-limiting distribution of a killed diffusion to coincide with a target density of interest. We also quantify the rate of convergence to quasi-stationarity by relating the killed diffusion to an appropriate Langevin diffusion. As an example, we consider a killed Ornstein-Uhlenbeck process with Gaussian quasi-stationary distribution.
In Chapter 4 we prove convergence of a specific quasi-stationary Monte Carlo method known as `ReScaLE'. We consider the asymptotic behavior of the normalized weighted empirical occupation measures of a diffusion process on a compact manifold which is also killed at a given rate and regenerated at a random location, distributed according to the weighted empirical occupation measure. We show that the weighted occupation measures almost surely comprise an asymptotic pseudo-trajectory for a certain deterministic measure-valued semiflow, after suitably rescaling the time, and that with probability one they converge to the quasi-stationary distribution of the killed diffusion.
In Chapter 5 we introduce the Restore sampler. This is a continuous-time sampler, which combines general local dynamics with rebirths from a fixed global rebirth distribution, which occur at a state-dependent rate. In certain settings this rate can be chosen to enforce stationarity of a given target density. The resulting sampler has several desirable properties: simplicity, lack of rejections, regenerations and a potential coupling from the past implementation. The Restore sampler can also be used as a recipe for introducing rejection-free moves into existing MCMC samplers in continuous time. Some simple examples are given to illustrate the potential of Restore.
We conclude the thesis in Chapter 6 with some concluding comments and open questions for future work.