Using Bayesian methods for the estimation of uncertainty in complex statistical models

The research objectives of this thesis were to contribute to Bayesian statistical methodology by contributing to risk assessment statistical methodology, and to spatial and spatio-temporal methodology, by modelling error structures using complex hierarchical models. Specifically, I hoped to consider two applied areas, and use these applications as a springboard for developing new statistical methods as well as undertaking analyses which might give answers to particular applied questions. Thus, this thesis considers a series of models, firstly in the context of risk assessments for recycled water, and secondly in the context of water usage by crops. The research objective was to model error structures using hierarchical models in two problems, namely risk assessment analyses for wastewater, and secondly, in a four dimensional dataset, assessing differences between cropping systems over time and over three spatial dimensions. The aim was to use the simplicity and insight afforded by Bayesian networks to develop appropriate models for risk scenarios, and again to use Bayesian hierarchical models to explore the necessarily complex modelling of four dimensional agricultural data. The specific objectives of the research were to develop a method for the calculation of credible intervals for the point estimates of Bayesian networks; to develop a model structure to incorporate all the experimental uncertainty associated with various constants thereby allowing the calculation of more credible credible intervals for a risk assessment; to model a single day’s data from the agricultural dataset which satisfactorily captured the complexities of the data; to build a model for several days’ data, in order to consider how the full data might be modelled; and finally to build a model for the full four dimensional dataset and to consider the timevarying nature of the contrast of interest, having satisfactorily accounted for possible spatial and temporal autocorrelations. This work forms five papers, two of which have been published, with two submitted, and the final paper still in draft. The first two objectives were met by recasting the risk assessments as directed, acyclic graphs (DAGs). In the first case, we elicited uncertainty for the conditional probabilities needed by the Bayesian net, incorporated these into a corresponding DAG, and used Markov chain Monte Carlo (MCMC) to find credible intervals, for all the scenarios and outcomes of interest. In the second case, we incorporated the experimental data underlying the risk assessment constants into the DAG, and also treated some of that data as needing to be modelled as an ‘errors-invariables’ problem [Fuller, 1987]. This illustrated a simple method for the incorporation of experimental error into risk assessments. In considering one day of the three-dimensional agricultural data, it became clear that geostatistical models or conditional autoregressive (CAR) models over the three dimensions were not the best way to approach the data. Instead CAR models are used with neighbours only in the same depth layer. This gave flexibility to the model, allowing both the spatially structured and non-structured variances to differ at all depths. We call this model the CAR layered model. Given the experimental design, the fixed part of the model could have been modelled as a set of means by treatment and by depth, but doing so allows little insight into how the treatment effects vary with depth. Hence, a number of essentially non-parametric approaches were taken to see the effects of depth on treatment, with the model of choice incorporating an errors-in-variables approach for depth in addition to a non-parametric smooth. The statistical contribution here was the introduction of the CAR layered model, the applied contribution the analysis of moisture over depth and estimation of the contrast of interest together with its credible intervals. These models were fitted using WinBUGS [Lunn et al., 2000]. The work in the fifth paper deals with the fact that with large datasets, the use of WinBUGS becomes more problematic because of its highly correlated term by term updating. In this work, we introduce a Gibbs sampler with block updating for the CAR layered model. The Gibbs sampler was implemented by Chris Strickland using pyMCMC [Strickland, 2010]. This framework is then used to consider five days data, and we show that moisture in the soil for all the various treatments reaches levels particular to each treatment at a depth of 200 cm and thereafter stays constant, albeit with increasing variances with depth. In an analysis across three spatial dimensions and across time, there are many interactions of time and the spatial dimensions to be considered. Hence, we chose to use a daily model and to repeat the analysis at all time points, effectively creating an interaction model of time by the daily model. Such an approach allows great flexibility. However, this approach does not allow insight into the way in which the parameter of interest varies over time. Hence, a two-stage approach was also used, with estimates from the first-stage being analysed as a set of time series. We see this spatio-temporal interaction model as being a useful approach to data measured across three spatial dimensions and time, since it does not assume additivity of the random spatial or temporal effects.

A Regularization Approach to Metrical Task Systems

We address the problem of constructing randomized online algorithms for the Metrical Task Systems (MTS) problem on a metric δ against an oblivious adversary. Restricting our attention to the class of “work-based” algorithms, we provide a framework for designing algorithms that uses the technique of regularization. For the case when δ is a uniform metric, we exhibit two algorithms that arise from this framework, and we prove a bound on the competitive ratio of each. We show that the second of these algorithms is ln n + O(loglogn) competitive, which is the current state-of-the art for the uniform MTS problem.

A task-oriented approach to search engine usability studies

Usability is a multi-dimensional characteristic of a computer system. This paper focuses on usability as a measurement of interaction between the user and the system. The research employs a task-oriented approach to evaluate the usability of a meta search engine. This engine encourages and accepts queries of unlimited size expressed in natural language. A variety of conventional metrics developed by academic and industrial research, including ISO standards,, are applied to the information retrieval process consisting of sequential tasks. Tasks range from formulating (long) queries to interpreting and retaining search results. Results of the evaluation and analysis of the operation log indicate that obtaining advanced search engine results can be accomplished simultaneously with enhancing the usability of the interactive process. In conclusion, we discuss implications for interactive information retrieval system design and directions for future usability research. © 2008 Academy Publisher.

Bayesian mixtures for modelling complex medical data : a case study in Parkinson’s disease

Mixture models are a flexible tool for unsupervised clustering that have found popularity in a vast array of research areas. In studies of medicine, the use of mixtures holds the potential to greatly enhance our understanding of patient responses through the identification of clinically meaningful clusters that, given the complexity of many data sources, may otherwise by intangible. Furthermore, when developed in the Bayesian framework, mixture models provide a natural means for capturing and propagating uncertainty in different aspects of a clustering solution, arguably resulting in richer analyses of the population under study. This thesis aims to investigate the use of Bayesian mixture models in analysing varied and detailed sources of patient information collected in the study of complex disease. The first aim of this thesis is to showcase the flexibility of mixture models in modelling markedly different types of data. In particular, we examine three common variants on the mixture model, namely, finite mixtures, Dirichlet Process mixtures and hidden Markov models. Beyond the development and application of these models to different sources of data, this thesis also focuses on modelling different aspects relating to uncertainty in clustering. Examples of clustering uncertainty considered are uncertainty in a patient’s true cluster membership and accounting for uncertainty in the true number of clusters present. Finally, this thesis aims to address and propose solutions to the task of comparing clustering solutions, whether this be comparing patients or observations assigned to different subgroups or comparing clustering solutions over multiple datasets. To address these aims, we consider a case study in Parkinson’s disease (PD), a complex and commonly diagnosed neurodegenerative disorder. In particular, two commonly collected sources of patient information are considered. The first source of data are on symptoms associated with PD, recorded using the Unified Parkinson’s Disease Rating Scale (UPDRS) and constitutes the first half of this thesis. The second half of this thesis is dedicated to the analysis of microelectrode recordings collected during Deep Brain Stimulation (DBS), a popular palliative treatment for advanced PD. Analysis of this second source of data centers on the problems of unsupervised detection and sorting of action potentials or "spikes" in recordings of multiple cell activity, providing valuable information on real time neural activity in the brain.

Strategic project evaluation for open pit mining ventures using real options and allied econometric techniques

Open pit mine operations are complex businesses that demand a constant assessment of risk. This is because the value of a mine project is typically influenced by many underlying economic and physical uncertainties, such as metal prices, metal grades, costs, schedules, quantities, and environmental issues, among others, which are not known with much certainty at the beginning of the project. Hence, mining projects present a considerable challenge to those involved in associated investment decisions, such as the owners of the mine and other stakeholders. In general terms, when an option exists to acquire a new or operating mining project, , the owners and stock holders of the mine project need to know the value of the mining project, which is the fundamental criterion for making final decisions about going ahead with the venture capital. However, obtaining the mine project’s value is not an easy task. The reason for this is that sophisticated valuation and mine optimisation techniques, which combine advanced theories in geostatistics, statistics, engineering, economics and finance, among others, need to be used by the mine analyst or mine planner in order to assess and quantify the existing uncertainty and, consequently, the risk involved in the project investment. Furthermore, current valuation and mine optimisation techniques do not complement each other. That is valuation techniques based on real options (RO) analysis assume an expected (constant) metal grade and ore tonnage during a specified period, while mine optimisation (MO) techniques assume expected (constant) metal prices and mining costs. These assumptions are not totally correct since both sources of uncertainty—that of the orebody (metal grade and reserves of mineral), and that about the future behaviour of metal prices and mining costs—are the ones that have great impact on the value of any mining project. Consequently, the key objective of this thesis is twofold. The first objective consists of analysing and understanding the main sources of uncertainty in an open pit mining project, such as the orebody (in situ metal grade), mining costs and metal price uncertainties, and their effect on the final project value. The second objective consists of breaking down the wall of isolation between economic valuation and mine optimisation techniques in order to generate a novel open pit mine evaluation framework called the ―Integrated Valuation / Optimisation Framework (IVOF)‖. One important characteristic of this new framework is that it incorporates the RO and MO valuation techniques into a single integrated process that quantifies and describes uncertainty and risk in a mine project evaluation process, giving a more realistic estimate of the project’s value. To achieve this, novel and advanced engineering and econometric methods are used to integrate financial and geological uncertainty into dynamic risk forecasting measures. The proposed mine valuation/optimisation technique is then applied to a real gold disseminated open pit mine deposit to estimate its value in the face of orebody, mining costs and metal price uncertainties.

Civil applications in the Magistrates Court are often set down for hearing by a judicial registrar, but there is now some uncertainty on the limitation of this practice

The decision of the District Court of Queensland in Mark Treherne & Associates -v- Murray David Hopkins [2010] QDC 36 will have particular relevance for early career lawyers. This decision raises questions about the limits of the jurisdiction of judicial registrars in the Magistrates Court.

Effect of topic domain and task type on Web image searching

Many user studies in Web information searching have found the significant effect of task types on search strategies. However, little attention was given to Web image searching strategies, especially the query reformulation activity despite that this is a crucial part in Web image searching. In this study, we investigated the effects of topic domains and task types on user’s image searching behavior and query reformulation strategies. Some significant differences in user’s tasks specificity and initial concepts were identified among the task domains. Task types are also found to influence participant’s result reviewing behavior and query reformulation strategies.

Effect of soil parameter uncertainty on seismic response of buried segmented pipeline

Pipelines are important lifeline facilities spread over a large area and they generally encounter a range of seismic hazards and different soil conditions. The seismic response of a buried segmented pipe depends on various parameters such as the type of buried pipe material and joints, end restraint conditions, soil characteristics, burial depths, and earthquake ground motion, etc. This study highlights the effect of the variation of geotechnical properties of the surrounding soil on seismic response of a buried pipeline. The variations of the properties of the surrounding soil along the pipe are described by sampling them from predefined probability distribution. The soil-pipe interaction model is developed in OpenSEES. Nonlinear earthquake time-history analysis is performed to study the effect of soil parameters variability on the response of pipeline. Based on the results, it is found that uncertainty in soil parameters may result in significant response variability of the pipeline.

Overview of the NTCIR-9 crosslink task : cross-lingual link discovery

This paper presents an overview of NTCIR-9 Cross-lingual Link Discovery (Crosslink) task. The overview includes: the motivation of cross-lingual link discovery; the Crosslink task definition; the run submission specification; the assessment and evaluation framework; the evaluation metrics; and the evaluation results of submitted runs. Cross-lingual link discovery (CLLD) is a way of automatically finding potential links between documents in different languages. The goal of this task is to create a reusable resource for evaluating automated CLLD approaches. The results of this research can be used in building and refining systems for automated link discovery. The task is focused on linking between English source documents and Chinese, Korean, and Japanese target documents.

(Un)doing gender : ways of being in an age of uncertainty

Children’s literature has conventionally and historically been concerned with identity and the often tortuous journey to becoming a subject who is generally older and wiser, a journey typically characterised by mishap, adventure, and detours. Narrative closure in children’s and young adult novels and films typically provides a point of self-realisation or self-actualisation, whereby the struggles of finding one’s “true” identity have been overcome. In this familiar coming-of-age narrative, there is often an underlying premise of an essential self that will emerge or be uncovered. This kind of narrative resolution provides readers with a reassurance that things will work for the best in the end, which is an enduring feature of children’s literature, and part of liberal-humanism’s project of harmonious individuality. However, uncertainty is a constant that has always characterised the ways lives are lived, regardless of best-laid plans. Children’s literature provides a field of narrative knowledge whereby readers gain impressions of childhood and adolescence, or more specifically, knowledge of ways of being at a time in life, which is marked by uncertainty. Despite the prevalence of children’s texts which continue to offer normative ways of being, in particular, normative forms of gender behaviour, there are texts which resist the pull for characters to be “like everyone else” by exploring alternative subjectivities. Fiction, however, cannot be regarded as a source of evidence about the material realities of life, as its strength lies in its affective and imaginative dimensions, which nevertheless can offer readers moments of reflection, recognition, or, in some cases, reality lessons. As a form of cultural production, contemporary children’s literature is highly responsive to social change and political debates, and is crucially implicated in shaping the values, attitudes and behaviours of children and young people.

Risk, uncertainty and complexity in science education

Increasingly societies and their governments are facing important social issues that have science and technology as key features. A number of these socio-scientific issues have two features that distinguish them from the restricted contexts in which school science has traditionally been presented. Some of their science is uncertain and scientific knowledge is not the only knowledge involved. As a result, the concepts of uncertainty, risk and complexity become essential aspects of the science underlying these issues. In this chapter we discuss the nature and role of these concepts in the public understanding of science and consider their links with school science. We argue that these same concepts and their role in contemporary scientific knowledge need to be addressed in school science curricula. The new features for content, pedagogy and assessment of this urgent challenge for science educators are outlined. These will be essential if the goal of science education for citizenship is to be achieved with our students, who will increasingly be required to make personal and collective decisions on issues involving science and technology.

Accounting for calibration uncertainty in phylogenetic estimation of evolutionary divergence times

The estimation of phylogenetic divergence times from sequence data is an important component of many molecular evolutionary studies. There is now a general appreciation that the procedure of divergence dating is considerably more complex than that initially described in the 1960s by Zuckerkandl and Pauling (1962, 1965). In particular, there has been much critical attention toward the assumption of a global molecular clock, resulting in the development of increasingly sophisticated techniques for inferring divergence times from sequence data. In response to the documentation of widespread departures from clocklike behavior, a variety of local- and relaxed-clock methods have been proposed and implemented. Local-clock methods permit different molecular clocks in different parts of the phylogenetic tree, thereby retaining the advantages of the classical molecular clock while casting off the restrictive assumption of a single, global rate of substitution (Rambaut and Bromham 1998; Yoder and Yang 2000).

Quadcopter see and avoid using a fuzzy controller

Unmanned Aerial Vehicles (UAVs) industry is a fast growing sector. Nowadays, the market offers numerous possibilities for off-the-shelf UAVs such as quadrotors or fixed-wings. Until UAVs demonstrate advance capabilities such as autonomous collision avoidance they will be segregated and restricted to flight in controlled environments. This work presents a visual fuzzy servoing system for obstacle avoidance using UAVs. To accomplish this task we used the visual information from the front camera. Images are processed off-board and the result send to the Fuzzy Logic controller which then send commands to modify the orientation of the aircraft. Results from flight test are presented with a commercial off-the-shelf platform.

Leveraging innovation for sustainable construction, proceedings of the CIB Task Group 58: Clients and Construction Innovation Workshop

This publication consists of a volume of papers presented at the workshop of the CIB Task Group 58: Clients and Construction Innovation, held on May 18- 19, 2009 at the University of Alberta in Edmonton, Canada. The workshop theme, “Leveraging Innovation for Sustainable Construction”, reflects a growing concern among clients for perspectives, approaches, and tools that will secure the practice of construction economically, socially, and environmentally. This collection encompasses some of the most incisive assessments of the challenges facing the construction industry today from a range of researchers and industry practitioners who are leading the way for tomorrow’s innovations. It provides a useful documentation of the ongoing conversation regarding innovation and sustainability issues and a foundation of knowledge for future research and development. The papers contained in this volume explore the workshop’s overarching theme of how to leverage innovation to increase the sustainability of the construction process and product. Participants sought to generate discussion on the topics of innovation and sustainability within the construction field, to share international examples of innovation from the research community and from industry, and to establish a point of reference for ongoing enquiry. In particular, our contributors have noted the value of learning through practice in order to orient research based on real-world industry experience. Chapters two and three present complementary models of sustainable research programs through the three parts collaboration of government, industry, and academia. Chapters four and five explore new tools and forms of technological innovation as they are deployed to improve construction project management and set the direction for advances in research. Chapters six, seven, and eight closely study practical examples of innovation in large-scale construction projects, showing with concrete results the impact of applying creative methods and best practices to the field. Innovation and sustainability in construction are truly global efforts; these papers illustrate how we can draw on international examples and cooperative organizations to address these important issues for long-term benefit of the industry.