VictorJuiz/thesis huggingface dataset:
Applications of probabilistic programming
Keywords: model induction
program induction
probabilistic inference
automatic programming
Markov chain Monte Carlo
generative models
data-driven proposals
automatic modelling
probabilistic programming

This thesis describes work on two applications of probabilistic programming: the learning of probabilistic program code given specifications, in particular program code of one-dimensional samplers; and the facilitation of sequential Monte Carlo inference with help of data-driven proposals. The latter is presented with experimental results on a linear Gaussian model and a non-parametric dependent Dirichlet process mixture of objects model for object recognition and tracking.
We begin this work by providing a brief introduction to probabilistic programming.
In the second Chapter we present an approach to automatic discovery of samplers in the form of probabilistic programs. Specifically, we learn the procedure code of samplers for one-dimensional distributions. We formulate a Bayesian approach to this problem by specifying a grammar-based prior over probabilistic program code. We use an approximate Bayesian computation method to learn the programs, whose executions generate samples that statistically match observed data or analytical characteristics of distributions of interest. In our experiments we leverage different probabilistic programming systems, including Anglican and Probabilistic C, to perform Markov chain Monte Carlo sampling over the space of programs. Experimental results have demonstrated that, using the proposed methodology, we can learn approximate and even some exact samplers. Finally, we show that our results are competive with regard to genetic programming methods.
In Chapter 3, we describe a way to facilitate sequential Monte Carlo inference in probabilistic programming using data-driven proposals. In particular, we develop a distance-based proposal for the non-parametric dependant Dirichlet process mixture of objects model. We implement this approach in the probabilitic programming system Anglican, and show that for that model data-driven proposals provide significant perfomance improvements. We also explore the possibility of using neural networks to improve data-driven proposals.
The reception and transformation of homeopathy in Japan
Keywords: homeopathy
illness narratives
Japan
complementary medicine
medical pluralism

This thesis examines from a medical anthropological viewpoint how the practice of the newly imported complementary and alternative medicine (CAM) has been transplanted, received and transformed in Japan. More specifically, I focus on homeopathy, which was introduced into Japan in the late 1990s.
To address the research question, I focus on the practice of homeopathy from the anthropological viewpoint. The adoption of any new form of medicine is influenced by the prevailing medical, social and cultural context. So, how and why was homeopathy introduced into Japan the late 1990s? I explore this question by focusing on three aspects of the reception of homeopathy in Japan: (1) the institutionalisation of the homeopathy, including the formation of associations of practitioners and homeopathic colleges; (2) the translation of the theory and practice of homeopathy by the practitioners into a culturally acceptable form; (3) the utilisation and consumption of homeopathy by the patients, their families and self-prescribers. Over eighteen months of fieldwork in Japan led me to focus on these three elements of homeopathic practice.
Regarding the theoretical framework, this mainly explores medical pluralism and the health care system in Japan from an anthropological perspective, and the globalisation and transmission of medicine.
I argue that the success of homeopathy in Japan was largely thanks to the transmission strategies set by the founders of the colleges for lay homeopaths. Mothers in particular, concerned by worries over family health care, were drawn by this approach. Furthermore I also argue that this group not only became consistent users of homeopathy but also propagated the therapy through mothers’ self-help groups, creating thereby a strong tie with the lay homeopaths. I argue that mothers gained a sense of the empowerment through homeopathy. Within the Japanese health care system it was the popular sector that received and developed homeopathy.
Effect of multiple-antibiotic treatments on the evolution of antibiotic resistance in Pseudomonas aeruginosa
Keywords: drug resistance
evolution
multiple antibiotic resistance
multi-drug resistance
antibiotic resistance
Pseudomonas aeruginosa
environmental heterogeneity
drug interactions

To combat the ever-growing clinical burden imposed by antibiotic-resistant pathogens, multiple-antibiotic treatments are increasingly being considered as promising treatment options. The impact of multiple-antibiotic treatments on the evolution of resistance is not well understood however, and debate is ongoing about the effectiveness of various multiple-antibiotic treatments. In this thesis, I investigate how aspects of multiple-antibiotic treatments impact the rate of evolution of antibiotic resistance in the opportunistic human pathogen Pseudomonas aeruginosa. In particular, I look at the impact of interactions between antibiotics in combination on the evolution of resistance, and how creating heterogeneity in the antibiotic environment by rotating the antibiotics used may change the rate of evolution of resistance.
I characterise the interactions present in 120 combinations of antibiotics and find that the type of interaction can be predicted by the mechanism of action of the antibiotics involved. I investigate the effect of a subset of these combinations on the evolution of antibiotic resistance. My results refute the influential but poorly-evidenced hypothesis that synergistic combinations accelerate the evolution of resistance, even when synergistic combinations have the same inhibitory effect on sensitive bacteria as additive or antagonistic antibiotic combinations. I focus on a combination of the antibiotics ceftriaxone and sulfamethoxazole and test whether it is more effective in preventing the evolution of resistance than predicted by the inhibitory effect of the combination on sensitive bacteria. I do not find the combination to be more effective than predicted.
Finally, I create heterogeneous antibiotic environments by rotating the antibiotic present at different rates. For the first time in a laboratory setting, I test how varying the rate of fluctuation in the antibiotics present in a heterogeneous antibiotic environment impacts the rate of evolution of resistance. Unexpectedly, I find the rate of evolution of resistance increases with increasing levels of antibiotic heterogeneity.
The Dirac-Higgs bundle
Keywords: Dirac operators
instantons
Fourier-Mukai transform
self-duality equations
Nahm transform
Higgs bundles

The Dirac–Higgs bundle is a vector bundle with a natural connection on the moduli space of stable Higgs bundles on a compact Riemann surface. It is a vector bundle of null-spaces of a Dirac-operator coupled to stable Higgs bundles. In this thesis, we study various aspects of this bundle and its natural connection.
The Dirac–Higgs bundle is hyperholomorphic on the smooth hyperkähler moduli space of stable Higgs bundles. This property is a generalisation of the four-dimensional anti- self-duality equations to hyperkähler manifolds. One use of the Dirac–Higgs bundle is the construction of a Nahm transform for Higgs bundles. This transform produces hyperholo- morphic bundles on the moduli space of rank one Higgs bundles.
The Higgs bundle moduli space is non-compact and we study the asymptotics of the connection in the Nahm transform of a Higgs bundle. We show that elements of the null- spaces concentrate at a finite number of points on the Riemann surface. This asymptotical behaviour naturally defines a frame for the Nahm transform, which is conjectured to be asymptotically unitary.
By considering only the holomorphic structure, the Nahm transform of a Higgs bundle extends to a holomorphic bundle on the natural compactification of the rank one Higgs bundle moduli space. We discuss various aspects of this extended holomorphic bundle. Most importantly, it is a sheaf extension in which the constituent sheaves and the extension class have natural interpretations in terms of the original Higgs bundle. Furthermore, the extended bundle is not fixed at the divisor at infinity; explicit examples show that it depends on the type of Riemann surface, for example.
The Dirac–Higgs bundle has a parabolic cousin. In the parabolic case the rank depends on the number of marked points and the total multiplicity of the zero weights in the parabolic structure. The moduli space of stable rank two parabolic Higgs bundles on the Riemann sphere with four marked points has complex dimension two. Furthermore, there is a combination of parabolic weights such that the Dirac–Higgs bundle is a line bundle with an instanton connection. We study the topology of this line bundle and find that the instanton does not have finite energy. As in the non-parabolic case we define a Nahm transform for parabolic Higgs bundles, and in the case of genus one Riemann surfaces use it to produce doubly-periodic instantons of finite energy.
Galois groups and anabelian reconstruction
Keywords: Galois Theory
p-adic arithmetic
Anabelian Geometry
Valued Fields

In this thesis we investigate the problem of recovering arithmetic structure on a field F from small quotients of its absolute Galois group. In particular, we are interested in recovering the p-adic valuation on a p-adic field from such quotients. After establishing several such results, we apply this to obtain strong versions of the Birational Section Conjecture for curves over p-adic fields. We also discuss the model-theoretic interpretation of these results, as well as begin investigating the foundations of a model-theory of schemes.
Non-reductive geometric invariant theory and compactifications of enveloped quotients
Keywords: Geometric Invariant Theory
non-reductive groups

In this thesis we develop a framework for constructing quotients of varieties by actions of linear algebraic groups which is similar in spirit to that of Mumford's geometric invariant theory. This is done by extending the work of Doran and Kirwan in the unipotent setting to deal with more general non-reductive groups.
Given a linear algebraic group acting on an irreducible variety with a linearisation, an open subset of stable points is identified that admits a geometric quotient in the category of varieties. This lies within the enveloped quotient, which is a dense constructible subset of a scheme that is locally of finite type, called the enveloping quotient. Ways to compactify the enveloped quotient---and the quotient of the stable locus therein---are considered. In particular, the theory of reductive envelopes from Doran and Kirwan's work is extended to the more general non-reductive setting to give ways of constructing compactifications of the enveloped quotient by using the techniques of Mumford's geometric invariant theory for reductive groups.
We then look at two ways in which this non-reductive geometric invariant theory can be used in practice. Firstly, we consider a procedure for constructing quotients inductively, using the extra data of a choice of appropriate subnormal series of a group. Related to this is a method for constructing an approximation of the stable set. Secondly, we study the actions of certain extensions of unipotent groups by multiplicative groups on projective varieties with very ample linearisation. Here we identify an open subset of points that admits a geometric quotient by the action of the extended group and which is explicitly computable via Hilbert-Mumford-like criteria.
Modelling and verification for DNA nanotechnology
Keywords: verification
nanotechnology
DNA walkers
DNA Nanotechnology
self-assembly
probabilistic model checking
uniformization
DNA folding
Markov chain
molecular motors
uniformisation
DNA
parameter synthesis
DNA Origami
model checking
DNA self-assembly

DNA nanotechnology is a rapidly developing field that creates nanoscale devices from DNA, which enables novel interfaces with biological material. Their therapeutic use is envisioned and applications in other areas of basic science have already been found. These devices function at physiological conditions and, owing to their molecular scale, are subject to thermal fluctuations during both preparation and operation of the device. Troubleshooting a failed device is often difficult and we develop models to characterise two separate devices: DNA walkers and DNA origami. Our framework is that of continuous-time Markov chains, abstracting away much of the underlying physics. The resulting models are coarse but enable analysis of system-level performance, such as ‘the molecular computation eventually returns the correct answer with high probability’. We examine the applicability of probabilistic model checking to provide guarantees on the behaviour of nanoscale devices, and to this end we develop novel model checking methodology.
We model a DNA walker that autonomously navigates a series of junctions, and we derive design principles that increase the probability of correct computational output. We also develop a novel parameter synthesis method for continuous-time Markov chains, for which the synthesised models guarantee a predetermined level of performance. Finally, we develop a novel discrete stochastic assembly model of DNA origami from first principles. DNA origami is a widespread method for creating nanoscale structures from DNA. Our model qualitatively reproduces experimentally observed behaviour and using the model we are able to rationally steer the folding pathway of a novel polymorphic DNA origami tile, controlling the eventual shape.
Influences of visuospatial mental processes and cortical excitability on numerical cognition and learning
Keywords: number-space
number cognition
non-invasive brain stimulation
numerical representation
numerical cognition
synesthesia
synaesthesia
transcranial alternating current stimulation
transcranial random noise stimulation
spatial cognition
transcranial direct current stimulation
cognitive neuroscience

Numerical cognition has been shown to share many aspects of spatial cognition, both behavioural and neurological. However, it is unclear whether a particular type of spatial cognition, visuospatial mental imagery (VSMI), may play a role in symbolic numerical representation. In this thesis, I first show that mental rotation, a form of VSMI, is related to two measures of basic numerical representation. I then show that number-space synaesthesia (NSS), a rare type of VSMI involving visualised spatial layouts for numbers, does not show an advantage in mental rotation, but shows interference in number line mapping. I next present a study investigating links between NSS and the ability to learn novel numerical symbols. I demonstrate that NSS shows an advantage at learning novel numerals, and that transcranial random noise stimulation, which increases cortical excitability, confers broadly similar advantages that nonetheless differ in subtle ways. I present a study of transcranial alternating current stimulation on the same symbol learning paradigm, which fails to demonstrate effects. Lastly, I present data showing that strength of numerical representation in these newly-learnt symbols is correlated with a measure of mental rotation, and also with visual recognition ability for the symbols after, but not before, training. All together, these findings suggest that VSMI does indeed play a role in numerical cognition, and that it may do so from an early stage of learning symbolic numbers.
The role of anisotropy and fiber dispersion in the mechanics and remodeling of biological tissues
Keywords: finite elasticity
fiber reinforced materials
Nonlinear elasticity
soft biological tissue
growth and remodeling
fiber dispersion
anisotropy

In many soft biological tissues mechanical strength and anisotropy are determined primarily by the presence of fibers, in particular collagen.
When an isotropic material is subject to a uniaxial tension, the principal strain transverse to the direction of applied load is always negative. However, in fiber reinforced materials the transverse principal strain can change its sign as the load increases, passing through the zero-points, known as perversions. We investigate how the number of perversions in a material reinforced by two symmetrically aligned families of distributed fibers depends both on the degree of fiber dispersion and the model used for fiber dispersion. Angular integration and three variants of the generalized structure tensor approach are considered and discussed. The study of perversions clearly demonstrates the qualitative difference between these approaches in the case of high dispersion of fibers. The results suggest that this difference is primarily due to the way compressive fibers are modeled.
Fiber alignment in biological tissues is created and maintained by the cells, which respond to mechanical stimuli arising from properties of the surrounding material. This coupling between mechanical anisotropy and tissue remodeling can be modeled in nonlinear elasticity by a fiber-reinforced hyperelastic material where remodeling is represented as the change in fiber orientation. We study analytically a simple model of fiber reorientation in a rectangular elastic tissue reinforced by two symmetrically arranged families of fibers subject to constant external loads. In this model, the fiber direction tends to align with the maximum principal stretch or strain. We characterize the global behaviour of the system for all material parameters and applied loads, and show that provided the fibers are tensile initially, the system converges to a stable equilibrium, which corresponds to either complete or intermediate fiber alignment.
Finally, we consider a model for the coupled growth and fiber reorientation in an elastic incompressible disk. The dynamics of our model is extremely sensitive to the initial condition and characterized by an infinite number of equilibrium states of fiber arrangement. We observed that the stress-induced fiber reorientation and growth laws used in our model produce specific fiber orientation pattern, which suggest a possible mechanism for self-organisation.
The role of dispersal in life history and population dynamics: an experimental and theoretical approach
Keywords: dispersal
complex life cycle
environmental variation
population dynamics
Integral Projection Model
life-history

Understanding the evolution and maintenance of phenotypic and genetic variation within populations is a key challenge in population biology. Discrete phenotypic variation such as alternative reproductive strategies and dispersal strategies are extreme forms of this. To understand phenotypic variations, such as male dimorphisms and dispersal expression, requires investigating the costs and benefits of these different phenotypes. In this thesis I do so. First, at the individual level, I determine trade-offs between life-history traits and phenotypic expression. The influence of male morph expression is assessed by determining whether male morph survival is frequency dependent. Costs of dispersal expression were assessed by comparing individuals that expressed the dispersal phenotype during their ontogeny with individuals that did not. Second, at the population level, I specifically investigate costs of phenotype expression to the natal population when dispersers fail to disperse. To determine any demographic costs to natal populations, I used structured integral population models to calculate population biology quantities, which I compared between populations that produced dispersers that fail to disperse and populations that produced no dispersers. I show that expressing a dispersal morph is costly to life-history traits and skews the male morph ratio, indicating that these two conditional strategies interact during ontogeny. This questions whether current models explaining single conditional strategies, such as the environmental threshold model, should consider interactions between different conditional strategies. In natal populations where dispersal is expressed, but dispersers fail to disperse, populations suffer reduced fitness and this demographic cost is enhanced in stochastic environments. These results do not include benefits of successful dispersal or other costs such as inbreeding. However, they do provide a cost of dispersal expression which indicates what the benefits of dispersal would need to be for dispersal to evolve. One aspect that the results do not inform on is possible eco-evolutionary dynamics in populations. Future work should look to incorporate eco-evolutionary feedback, within a metapopulation structure, to identify the maintenance and evolution of male dimorphism and dispersal.
Probing molecular gas and its physical conditions in disc galaxies
Keywords: star formation
molecular gas
galaxies

New observations of multiple molecular gas tracers in nearby early- and late-types galaxies are presented and are used to study the physical conditions of the gas within different morphological structures. The CO Tully-Fisher relation is also constructed for a sample of star-forming galaxies at z = 0:05 - 0:3, probing their mass and size evolution.
First, using single-dish observations of multiple locations within the nearby spiral galaxy NGC 6946, extensive CO ladders are generated. The molecular line ratios reveal a large variety of physical conditions across the molecular gas complexes, depending primarily on the presence of current or recent star formation, itself compared with that in the centre of the galaxy and other galaxies.
Second, interferometric observations of CO and high density molecular tracers in the nearby edge-on early-type galaxies NGC 4710 and NGC 5866 are presented. The gas kinematics reveals that the galaxies are barred, with most of the gas contained within a nuclear disc and a distinct inner ring. Using the molecular line ratios to probe the physical conditions of the gas, the nuclear discs appear to have a more diffuse and hotter molecular medium than the inner rings, with more embedded dense clumps. This suggests that the conditions in the nuclear discs are similar to those in photo-dissociation regions, with intense UV radiation from young stars and few cosmic rays. Indeed, the observed molecular line ratios are also intermediate between those of spiral galaxies and starbursts, with even milder star formation in the inner rings.
Third, homogeneously measuring the line widths in the CO spectra of star-forming disc galaxies at z = 0:05 - 0:3, their Ks-band CO Tully-Fisher relation is constructed. A comparison to local star-forming galaxy TFRs from the literature provides mild evidence that our sample galaxies are ≈ 0:89 mag brighter than local ones at a given rotational velocity, a result entirely consistent with our stellar mass TFR, suggesting that our sample galaxies are more massive than local ones by ≈ 0:35 dex. While they deserve further scrutiny, we suspect that these results are due to our sample galaxies being more heavily star-forming (and thus brighter at a given mass) than the comparison sample galaxies.