Addressing issues in sparseness, ecological bias and formulation of the adjacency matrix in Bayesian spatio-temporal analysis of disease counts

The main objective of this PhD was to further develop Bayesian spatio-temporal models (specifically the Conditional Autoregressive (CAR) class of models), for the analysis of sparse disease outcomes such as birth defects. The motivation for the thesis arose from problems encountered when analyzing a large birth defect registry in New South Wales. The specific components and related research objectives of the thesis were developed from gaps in the literature on current formulations of the CAR model, and health service planning requirements. Data from a large probabilistically-linked database from 1990 to 2004, consisting of fields from two separate registries: the Birth Defect Registry (BDR) and Midwives Data Collection (MDC) were used in the analyses in this thesis. The main objective was split into smaller goals. The first goal was to determine how the specification of the neighbourhood weight matrix will affect the smoothing properties of the CAR model, and this is the focus of chapter 6. Secondly, I hoped to evaluate the usefulness of incorporating a zero-inflated Poisson (ZIP) component as well as a shared-component model in terms of modeling a sparse outcome, and this is carried out in chapter 7. The third goal was to identify optimal sampling and sample size schemes designed to select individual level data for a hybrid ecological spatial model, and this is done in chapter 8. Finally, I wanted to put together the earlier improvements to the CAR model, and along with demographic projections, provide forecasts for birth defects at the SLA level. Chapter 9 describes how this is done. For the first objective, I examined a series of neighbourhood weight matrices, and showed how smoothing the relative risk estimates according to similarity by an important covariate (i.e. maternal age) helped improve the model’s ability to recover the underlying risk, as compared to the traditional adjacency (specifically the Queen) method of applying weights. Next, to address the sparseness and excess zeros commonly encountered in the analysis of rare outcomes such as birth defects, I compared a few models, including an extension of the usual Poisson model to encompass excess zeros in the data. This was achieved via a mixture model, which also encompassed the shared component model to improve on the estimation of sparse counts through borrowing strength across a shared component (e.g. latent risk factor/s) with the referent outcome (caesarean section was used in this example). Using the Deviance Information Criteria (DIC), I showed how the proposed model performed better than the usual models, but only when both outcomes shared a strong spatial correlation. The next objective involved identifying the optimal sampling and sample size strategy for incorporating individual-level data with areal covariates in a hybrid study design. I performed extensive simulation studies, evaluating thirteen different sampling schemes along with variations in sample size. This was done in the context of an ecological regression model that incorporated spatial correlation in the outcomes, as well as accommodating both individual and areal measures of covariates. Using the Average Mean Squared Error (AMSE), I showed how a simple random sample of 20% of the SLAs, followed by selecting all cases in the SLAs chosen, along with an equal number of controls, provided the lowest AMSE. The final objective involved combining the improved spatio-temporal CAR model with population (i.e. women) forecasts, to provide 30-year annual estimates of birth defects at the Statistical Local Area (SLA) level in New South Wales, Australia. The projections were illustrated using sixteen different SLAs, representing the various areal measures of socio-economic status and remoteness. A sensitivity analysis of the assumptions used in the projection was also undertaken. By the end of the thesis, I will show how challenges in the spatial analysis of rare diseases such as birth defects can be addressed, by specifically formulating the neighbourhood weight matrix to smooth according to a key covariate (i.e. maternal age), incorporating a ZIP component to model excess zeros in outcomes and borrowing strength from a referent outcome (i.e. caesarean counts). An efficient strategy to sample individual-level data and sample size considerations for rare disease will also be presented. Finally, projections in birth defect categories at the SLA level will be made.

Integrated Bayesian network frameworks for modelling complex ecological issues

Ecological problems are typically multi faceted and need to be addressed from a scientific and a management perspective. There is a wealth of modelling and simulation software available, each designed to address a particular aspect of the issue of concern. Choosing the appropriate tool, making sense of the disparate outputs, and taking decisions when little or no empirical data is available, are everyday challenges facing the ecologist and environmental manager. Bayesian Networks provide a statistical modelling framework that enables analysis and integration of information in its own right as well as integration of a variety of models addressing different aspects of a common overall problem. There has been increased interest in the use of BNs to model environmental systems and issues of concern. However, the development of more sophisticated BNs, utilising dynamic and object oriented (OO) features, is still at the frontier of ecological research. Such features are particularly appealing in an ecological context, since the underlying facts are often spatial and temporal in nature. This thesis focuses on an integrated BN approach which facilitates OO modelling. Our research devises a new heuristic method, the Iterative Bayesian Network Development Cycle (IBNDC), for the development of BN models within a multi-field and multi-expert context. Expert elicitation is a popular method used to quantify BNs when data is sparse, but expert knowledge is abundant. The resulting BNs need to be substantiated and validated taking this uncertainty into account. Our research demonstrates the application of the IBNDC approach to support these aspects of BN modelling. The complex nature of environmental issues makes them ideal case studies for the proposed integrated approach to modelling. Moreover, they lend themselves to a series of integrated sub-networks describing different scientific components, combining scientific and management perspectives, or pooling similar contributions developed in different locations by different research groups. In southern Africa the two largest free-ranging cheetah (Acinonyx jubatus) populations are in Namibia and Botswana, where the majority of cheetahs are located outside protected areas. Consequently, cheetah conservation in these two countries is focussed primarily on the free-ranging populations as well as the mitigation of conflict between humans and cheetahs. In contrast, in neighbouring South Africa, the majority of cheetahs are found in fenced reserves. Nonetheless, conflict between humans and cheetahs remains an issue here. Conservation effort in South Africa is also focussed on managing the geographically isolated cheetah populations as one large meta-population. Relocation is one option among a suite of tools used to resolve human-cheetah conflict in southern Africa. Successfully relocating captured problem cheetahs, and maintaining a viable free-ranging cheetah population, are two environmental issues in cheetah conservation forming the first case study in this thesis. The second case study involves the initiation of blooms of Lyngbya majuscula, a blue-green algae, in Deception Bay, Australia. L. majuscula is a toxic algal bloom which has severe health, ecological and economic impacts on the community located in the vicinity of this algal bloom. Deception Bay is an important tourist destination with its proximity to Brisbane, Australia’s third largest city. Lyngbya is one of several algae considered to be a Harmful Algal Bloom (HAB). This group of algae includes other widespread blooms such as red tides. The occurrence of Lyngbya blooms is not a local phenomenon, but blooms of this toxic weed occur in coastal waters worldwide. With the increase in frequency and extent of these HAB blooms, it is important to gain a better understanding of the underlying factors contributing to the initiation and sustenance of these blooms. This knowledge will contribute to better management practices and the identification of those management actions which could prevent or diminish the severity of these blooms.

Bayesian models for longitudinal data

Longitudinal data, where data are repeatedly observed or measured on a temporal basis of time or age provides the foundation of the analysis of processes which evolve over time, and these can be referred to as growth or trajectory models. One of the traditional ways of looking at growth models is to employ either linear or polynomial functional forms to model trajectory shape, and account for variation around an overall mean trend with the inclusion of random eects or individual variation on the functional shape parameters. The identification of distinct subgroups or sub-classes (latent classes) within these trajectory models which are not based on some pre-existing individual classification provides an important methodology with substantive implications. The identification of subgroups or classes has a wide application in the medical arena where responder/non-responder identification based on distinctly diering trajectories delivers further information for clinical processes. This thesis develops Bayesian statistical models and techniques for the identification of subgroups in the analysis of longitudinal data where the number of time intervals is limited. These models are then applied to a single case study which investigates the neuropsychological cognition for early stage breast cancer patients undergoing adjuvant chemotherapy treatment from the Cognition in Breast Cancer Study undertaken by the Wesley Research Institute of Brisbane, Queensland. Alternative formulations to the linear or polynomial approach are taken which use piecewise linear models with a single turning point, change-point or knot at a known time point and latent basis models for the non-linear trajectories found for the verbal memory domain of cognitive function before and after chemotherapy treatment. Hierarchical Bayesian random eects models are used as a starting point for the latent class modelling process and are extended with the incorporation of covariates in the trajectory profiles and as predictors of class membership. The Bayesian latent basis models enable the degree of recovery post-chemotherapy to be estimated for short and long-term followup occasions, and the distinct class trajectories assist in the identification of breast cancer patients who maybe at risk of long-term verbal memory impairment.

Feasibility of "subjective" engineering assessments of road safety improvements : Bayesian analysis development

Regional safety program managers face a daunting challenge in the attempt to reduce deaths, injuries, and economic losses that result from motor vehicle crashes. This difficult mission is complicated by the combination of a large perceived need, small budget, and uncertainty about how effective each proposed countermeasure would be if implemented. A manager can turn to the research record for insight, but the measured effect of a single countermeasure often varies widely from study to study and across jurisdictions. The challenge of converting widespread and conflicting research results into a regionally meaningful conclusion can be addressed by incorporating "subjective" information into a Bayesian analysis framework. Engineering evaluations of crashes provide the subjective input on countermeasure effectiveness in the proposed Bayesian analysis framework. Empirical Bayes approaches are widely used in before-and-after studies and "hot-spot" identification; however, in these cases, the prior information was typically obtained from the data (empirically), not subjective sources. The power and advantages of Bayesian methods for assessing countermeasure effectiveness are presented. Also, an engineering evaluation approach developed at the Georgia Institute of Technology is described. Results are presented from an experiment conducted to assess the repeatability and objectivity of subjective engineering evaluations. In particular, the focus is on the importance, methodology, and feasibility of the subjective engineering evaluation for assessing countermeasures.

Privacy and trust management for electronic health records

Establishing a nationwide Electronic Health Record system has become a primary objective for many countries around the world, including Australia, in order to improve the quality of healthcare while at the same time decreasing its cost. Doing so will require federating the large number of patient data repositories currently in use throughout the country. However, implementation of EHR systems is being hindered by several obstacles, among them concerns about data privacy and trustworthiness. Current IT solutions fail to satisfy patients’ privacy desires and do not provide a trustworthiness measure for medical data. This thesis starts with the observation that existing EHR system proposals suer from six serious shortcomings that aect patients’ privacy and safety, and medical practitioners’ trust in EHR data: accuracy and privacy concerns over linking patients’ existing medical records; the inability of patients to have control over who accesses their private data; the inability to protect against inferences about patients’ sensitive data; the lack of a mechanism for evaluating the trustworthiness of medical data; and the failure of current healthcare workflow processes to capture and enforce patient’s privacy desires. Following an action research method, this thesis addresses the above shortcomings by firstly proposing an architecture for linking electronic medical records in an accurate and private way where patients are given control over what information can be revealed about them. This is accomplished by extending the structure and protocols introduced in federated identity management to link a patient’s EHR to his existing medical records by using pseudonym identifiers. Secondly, a privacy-aware access control model is developed to satisfy patients’ privacy requirements. The model is developed by integrating three standard access control models in a way that gives patients access control over their private data and ensures that legitimate uses of EHRs are not hindered. Thirdly, a probabilistic approach for detecting and restricting inference channels resulting from publicly-available medical data is developed to guard against indirect accesses to a patient’s private data. This approach is based upon a Bayesian network and the causal probabilistic relations that exist between medical data fields. The resulting definitions and algorithms show how an inference channel can be detected and restricted to satisfy patients’ expressed privacy goals. Fourthly, a medical data trustworthiness assessment model is developed to evaluate the quality of medical data by assessing the trustworthiness of its sources (e.g. a healthcare provider or medical practitioner). In this model, Beta and Dirichlet reputation systems are used to collect reputation scores about medical data sources and these are used to compute the trustworthiness of medical data via subjective logic. Finally, an extension is made to healthcare workflow management processes to capture and enforce patients’ privacy policies. This is accomplished by developing a conceptual model that introduces new workflow notions to make the workflow management system aware of a patient’s privacy requirements. These extensions are then implemented in the YAWL workflow management system.

Bayesian methodology incorporating expert judgment for ranking countermeasure effectiveness under uncertainty: Example applied to at grade railroad crossings in Korea

This paper describes the formalization and application of a methodology to evaluate the safety benefit of countermeasures in the face of uncertainty. To illustrate the methodology, 18 countermeasures for improving safety of at grade railroad crossings (AGRXs) in the Republic of Korea are considered. Akin to “stated preference” methods in travel survey research, the methodology applies random selection and laws of large numbers to derive accident modification factor (AMF) densities from expert opinions. In a full Bayesian analysis framework, the collective opinions in the form of AMF densities (data likelihood) are combined with prior knowledge (AMF density priors) for the 18 countermeasures to obtain ‘best’ estimates of AMFs (AMF posterior credible intervals). The countermeasures are then compared and recommended based on the largest safety returns with minimum risk (uncertainty). To the author's knowledge the complete methodology is new and has not previously been applied or reported in the literature. The results demonstrate that the methodology is able to discern anticipated safety benefit differences across candidate countermeasures. For the 18 at grade railroad crossings considered in this analysis, it was found that the top three performing countermeasures for reducing crashes are in-vehicle warning systems, obstacle detection systems, and constant warning time systems.

Bayesian spatiotemporal analysis of socio-ecologic drivers of Ross River Virus transmission in Queensland, Australia

This study aims to examine the impact of socio-ecologic factors on the transmission of Ross River virus (RRV) infection and to identify areas prone to social and ecologic-driven epidemics in Queensland, Australia. We used a Bayesian spatiotemporal conditional autoregressive model to quantify the relationship between monthly variation of RRV incidence and socio-ecologic factors and to determine spatiotemporal patterns. Our results show that the average increase in monthly RRV incidence was 2.4% (95% credible interval (CrI): 0.1–4.5%) and 2.0% (95% CrI: 1.6–2.3%) for a 1°C increase in monthly average maximum temperature and a 10 mm increase in monthly average rainfall, respectively. A significant spatiotemporal variation and interactive effect between temperature and rainfall on RRV incidence were found. No association between Socio-economic Index for Areas (SEIFA) and RRV was observed. The transmission of RRV in Queensland, Australia appeared to be primarily driven by ecologic variables rather than social factors.

Bayesian filtering over compressed appearance states

This paper presents a framework for performing real-time recursive estimation of landmarks’ visual appearance. Imaging data in its original high dimensional space is probabilistically mapped to a compressed low dimensional space through the definition of likelihood functions. The likelihoods are subsequently fused with prior information using a Bayesian update. This process produces a probabilistic estimate of the low dimensional representation of the landmark visual appearance. The overall filtering provides information complementary to the conventional position estimates which is used to enhance data association. In addition to robotics observations, the filter integrates human observations in the appearance estimates. The appearance tracks as computed by the filter allow landmark classification. The set of labels involved in the classification task is thought of as an observation space where human observations are made by selecting a label. The low dimensional appearance estimates returned by the filter allow for low cost communication in low bandwidth sensor networks. Deployment of the filter in such a network is demonstrated in an outdoor mapping application involving a human operator, a ground and an air vehicle.

Learning articulated motion structures with Bayesian Networks

This paper presents a general methodology for learning articulated motions that, despite having non-linear correlations, are cyclical and have a defined pattern of behavior Using conventional algorithms to extract features from images, a Bayesian classifier is applied to cluster and classify features of the moving object. Clusters are then associated in different frames and structure learning algorithms for Bayesian networks are used to recover the structure of the motion. This framework is applied to the human gait analysis and tracking but applications include any coordinated movement such as multi-robots behavior analysis.