Bayesian hybrid algorithms and models : implementation and associated issues

This thesis addresses computational challenges arising from Bayesian analysis of complex real-world problems. Many of the models and algorithms designed for such analysis are ‘hybrid’ in nature, in that they are a composition of components for which their individual properties may be easily described but the performance of the model or algorithm as a whole is less well understood. The aim of this research project is to after a better understanding of the performance of hybrid models and algorithms. The goal of this thesis is to analyse the computational aspects of hybrid models and hybrid algorithms in the Bayesian context. The first objective of the research focuses on computational aspects of hybrid models, notably a continuous finite mixture of t-distributions. In the mixture model, an inference of interest is the number of components, as this may relate to both the quality of model fit to data and the computational workload. The analysis of t-mixtures using Markov chain Monte Carlo (MCMC) is described and the model is compared to the Normal case based on the goodness of fit. Through simulation studies, it is demonstrated that the t-mixture model can be more flexible and more parsimonious in terms of number of components, particularly for skewed and heavytailed data. The study also reveals important computational issues associated with the use of t-mixtures, which have not been adequately considered in the literature. The second objective of the research focuses on computational aspects of hybrid algorithms for Bayesian analysis. Two approaches will be considered: a formal comparison of the performance of a range of hybrid algorithms and a theoretical investigation of the performance of one of these algorithms in high dimensions. For the first approach, the delayed rejection algorithm, the pinball sampler, the Metropolis adjusted Langevin algorithm, and the hybrid version of the population Monte Carlo (PMC) algorithm are selected as a set of examples of hybrid algorithms. Statistical literature shows how statistical efficiency is often the only criteria for an efficient algorithm. In this thesis the algorithms are also considered and compared from a more practical perspective. This extends to the study of how individual algorithms contribute to the overall efficiency of hybrid algorithms, and highlights weaknesses that may be introduced by the combination process of these components in a single algorithm. The second approach to considering computational aspects of hybrid algorithms involves an investigation of the performance of the PMC in high dimensions. It is well known that as a model becomes more complex, computation may become increasingly difficult in real time. In particular the importance sampling based algorithms, including the PMC, are known to be unstable in high dimensions. This thesis examines the PMC algorithm in a simplified setting, a single step of the general sampling, and explores a fundamental problem that occurs in applying importance sampling to a high-dimensional problem. The precision of the computed estimate from the simplified setting is measured by the asymptotic variance of the estimate under conditions on the importance function. Additionally, the exponential growth of the asymptotic variance with the dimension is demonstrated and we illustrates that the optimal covariance matrix for the importance function can be estimated in a special case.

Culture independent analysis of greyback canegrub-associated microflora and microbial community comparison using subtractive hybridisation

Greyback canegrubs cost the Australian sugarcane industry around $13 million per annum in damage and control. A novel and cost effective biocontrol bacterium could play an important role in the integrated pest management program currently in place to reduce damage and control associated costs. During the course of this project, terminal restriction fragment length polymorphism (TRFLP), 16-S rDNA cloning, suppressive subtractive hybridisation (SSH) and entomopathogen-specific PCR screening were used to investigate the little studied canegrub-associated microflora in an attempt to discover novel pathogens from putatively-diseased specimens. Microflora associated with these soil-dwelling insects was found to be both highly diverse and divergent between individual specimens. Dominant members detected in live specimens were predominantly from taxa of known insect symbionts while dominant sequences amplified from dead grubs were homologous to putativelysaprophytic bacteria and bacteria able to grow during refrigeration. A number of entomopathogenic bacteria were identified such as Photorhabdus luminescens and Pseudomonas fluorescens. Dead canegrubs prior to decomposition need to be analysed if these bacteria are to be isolated. Novel strategies to enrich putative pathogen-associated sequences (SSH and PCR screening) were shown to be promising approaches for pathogen discovery and the investigation of canegrubsassociated microflora. However, due to inter- and intra-grub-associated community diversity, dead grub decomposition and PCR-specific methodological limitations (PCR bias, primer specificity, BLAST database restrictions, 16-S gene copy number and heterogeneity), recommendations have been made to improve the efficiency of such techniques. Improved specimen collection procedures and utilisation of emerging high-throughput sequencing technologies may be required to examine these complex communities in more detail. This is the first study to perform a whole-grub analysis and comparison of greyback canegrub-associated microbial communities. This work also describes the development of a novel V3-PCR based SSH technique. This was the first SSH technique to use V3-PCR products as a starting material and specifically compare bacterial species present in a complex community.

Evaluating sewage associated JCV and BKV polyomaviruses for sourcing human fecal pollution in a coastal river in Southeast Queensland Australia

In this study, the host-sensitivity and -specificity of JCV and BKV polyomaviruses were evaluated by testing wastewater/fecal samples from nine host groups in Southeast Queensland, Australia. The JCV and BKV polyomaviruses were detected in 48 human wastewater samples collected from the primary and secondary effluent suggesting high sensitivity of these viruses in human wastewater. Of the 81 animal wastewater/fecal samples tested, 80 were PCR negative for this marker. Only one sample from pig wastewater was positive. Nonetheless, the overall host-specificity of these viruses to differentiate between human and animal wastewater/fecal samples was 0.99. To our knowledge, this is the first study in Australia that reports the high specificity of JCV and BKV polyomaviruses. To evaluate the field application of these viruses to detect human fecal pollution, 20 environmental samples were collected from a coastal river. Of the 20 samples tested, 15% and 70% samples exceeded the regulatory guidelines for E. coli and enterococci levels for marine waters. In all, 5 (25%) samples were PCR positive for JCV and BKV indicated the presence of human fecal pollution in the studied river. The results suggest that JCV and BKV detection using PCR could be a useful tool for the identification of human sourced fecal pollution in coastal waters.

Managing illegal street racing and associated risky driving behaviour : An Australian perspective

Illegal street racing has received increased attention in recent years from the media, governments and road safety professionals. At the same time, there has been a shift from treating illegal street racing as a public nuisance issue to a road safety problem in Australia, as this behaviour now attracts a penalty of increased periods of vehicle impoundment leading to permanent vehicle forfeiture for repeat offences. This severe vehicle sanction is typically applied to repeat drink driving offenders and drivers who breach suspensions and disqualifications in North American jurisdictions, but was first introduced in Australia to deal with illegal street racing and associated risky driving behaviours, grouped together under the label of ‘hooning’ in Australian jurisdictions. This paper describes how Australian jurisdictions are dealing with this issue. The research described in this paper drew on multiple data sources to explore illegal street racing and the management of this issue in Australia. First, the paper reviews the relevant legislation in each Australian state to describe the cross-jurisdictional similarities and differences in approaches. It also describes some results from focus group discussions and a quantitative online survey with drivers who self-report engaging in illegal street racing and associated behaviours in Queensland, Australia. It was found that approaches to dealing with illegal street racing and associated risky driving behaviours in each Australian state are similar, with increasing periods of vehicle impoundment (leading to vehicle forfeiture) applied to repeat hooning offences within prescribed periods. Participants in the focus groups and respondents to the questionnaire generally felt these penalty periods were severe, with perceptions of severity increasing with the length of the penalty period. It was concluded that there is a need for each jurisdiction to objectively evaluate the effectiveness of their vehicle impoundment and forfeiture programs for hooning. These evaluations should compare the relative costs of these programs (e.g., enforcement, unrecovered towing and storage fees, and court costs) to the observed benefits (e.g., reduction in target behaviours, reduction in community complaints, and reduction in the number and severity of associated crashes).

Low fat loss response after medium-term supervised exercise in obese is associated with exercise-induced increase in food reward

Objective: To examine exercise-induced changes in the reward value of food during medium-term supervised exercise in obese individuals. ---------- Subjects/Methods: The study was a 12-week supervised exercise intervention prescribed to expend 500 kcal/day, 5 d/week. 34 sedentary obese males and females were identified as responders (R) or non-responders (NR) to the intervention according to changes in body composition relative to measured energy expended during exercise. Food reward (ratings of liking and wanting, and relative preference by forced choice pairs) for an array of food images was assessed before and after an acute exercise bout. ---------- Results. 20 responders and 14 non-responders were identified. R lost 5.2 kg±2.4 of total fat mass and NR lost 1.7 kg±1.4. After acute exercise, liking for all foods increased in NR compared to no change in R. Furthermore, NR showed an increase in wanting and relative preference for high-fat sweet foods. These differences were independent of 12-weeks regular exercise and weight loss. ---------- Conclusion. Individuals who showed an immediate post-exercise increase in liking and increased wanting and preference for high-fat sweet foods displayed a smaller reduction in fat mass with exercise. For some individuals, exercise increases the reward value of food and diminishes the impact of exercise on fat loss.

The stewardship paradigm : an enquiry into the ethical obligation associated with being in control of resorces

The resource allocation and utilization discourse is dominated by debates about rights particularly individual property rights and ownership. This is due largely to the philosophic foundations provided by Hobbes and Locke and adopted by Bentham. In our community, though, resources come not merely with rights embedded but also obligations. The relevant laws and equitable principles which give shape to our shared rights and obligations with respect to resources take cognizance not merely of the title to the resource (the proprietary right) but the particular context in which the right is exercised. Moral philosophy regarding resource utilisation has from ancient times taken cognizance of obligations but with ascendance of modernity, the agenda of moral philosophy regarding resources, has been dominated, at least since John Locke, by a preoccupation with property rights; the ethical obligations associated with resource management have been largely ignored. The particular social context has also been ignored. Exploring this applied ethical terrain regarding resource utilisation, this thesis: (1) Revisits the justifications for modem property rights (and in that the exclusion of obligations); (2) Identifies major deficiencies in these justifications and reasons for this; (3) Traces the concept of stewardship as understood in classical Greek writing and in the New Testament, and considers its application in the Patristic period and by Medieval and reformist writers, before turning to investigate its influence on legal and equitable concepts through to the current day; 4) Discusses the nature of the stewardship obligation,maps it and offers a schematic for applying the Stewardship Paradigm to problems arising in daily life; and, (5) Discusses the way in which the Stewardship Paradigm may be applied by, and assists in resolving issues arising from within four dominant philosophic world views: (a) Rawls' social contract theory; (b) Utilitarianism as discussed by Peter Singer; (c) Christianity with particular focus on the theology of Douglas Hall; (d) Feminism particularly as expressed in the ethics of care of Carol Gilligan; and, offers some more general comments about stewardship in the context of an ethically plural community.