Bayesian algorithms with applications

Advances in algorithms for approximate sampling from a multivariable target function have led to solutions to challenging statistical inference problems that would otherwise not be considered by the applied scientist. Such sampling algorithms are particularly relevant to Bayesian statistics, since the target function is the posterior distribution of the unobservables given the observables. In this thesis we develop, adapt and apply Bayesian algorithms, whilst addressing substantive applied problems in biology and medicine as well as other applications. For an increasing number of high-impact research problems, the primary models of interest are often sufficiently complex that the likelihood function is computationally intractable. Rather than discard these models in favour of inferior alternatives, a class of Bayesian "likelihoodfree" techniques (often termed approximate Bayesian computation (ABC)) has emerged in the last few years, which avoids direct likelihood computation through repeated sampling of data from the model and comparing observed and simulated summary statistics. In Part I of this thesis we utilise sequential Monte Carlo (SMC) methodology to develop new algorithms for ABC that are more efficient in terms of the number of model simulations required and are almost black-box since very little algorithmic tuning is required. In addition, we address the issue of deriving appropriate summary statistics to use within ABC via a goodness-of-fit statistic and indirect inference. Another important problem in statistics is the design of experiments. That is, how one should select the values of the controllable variables in order to achieve some design goal. The presences of parameter and/or model uncertainty are computational obstacles when designing experiments but can lead to inefficient designs if not accounted for correctly. The Bayesian framework accommodates such uncertainties in a coherent way. If the amount of uncertainty is substantial, it can be of interest to perform adaptive designs in order to accrue information to make better decisions about future design points. This is of particular interest if the data can be collected sequentially. In a sense, the current posterior distribution becomes the new prior distribution for the next design decision. Part II of this thesis creates new algorithms for Bayesian sequential design to accommodate parameter and model uncertainty using SMC. The algorithms are substantially faster than previous approaches allowing the simulation properties of various design utilities to be investigated in a more timely manner. Furthermore the approach offers convenient estimation of Bayesian utilities and other quantities that are particularly relevant in the presence of model uncertainty. Finally, Part III of this thesis tackles a substantive medical problem. A neurological disorder known as motor neuron disease (MND) progressively causes motor neurons to no longer have the ability to innervate the muscle fibres, causing the muscles to eventually waste away. When this occurs the motor unit effectively ‘dies’. There is no cure for MND, and fatality often results from a lack of muscle strength to breathe. The prognosis for many forms of MND (particularly amyotrophic lateral sclerosis (ALS)) is particularly poor, with patients usually only surviving a small number of years after the initial onset of disease. Measuring the progress of diseases of the motor units, such as ALS, is a challenge for clinical neurologists. Motor unit number estimation (MUNE) is an attempt to directly assess underlying motor unit loss rather than indirect techniques such as muscle strength assessment, which generally is unable to detect progressions due to the body’s natural attempts at compensation. Part III of this thesis builds upon a previous Bayesian technique, which develops a sophisticated statistical model that takes into account physiological information about motor unit activation and various sources of uncertainties. More specifically, we develop a more reliable MUNE method by applying marginalisation over latent variables in order to improve the performance of a previously developed reversible jump Markov chain Monte Carlo sampler. We make other subtle changes to the model and algorithm to improve the robustness of the approach.

Graph-based concept weighting for medical information retrieval

This paper presents a graph-based method to weight medical concepts in documents for the purposes of information retrieval. Medical concepts are extracted from free-text documents using a state-of-the-art technique that maps n-grams to concepts from the SNOMED CT medical ontology. In our graph-based concept representation, concepts are vertices in a graph built from a document, edges represent associations between concepts. This representation naturally captures dependencies between concepts, an important requirement for interpreting medical text, and a feature lacking in bag-of-words representations. We apply existing graph-based term weighting methods to weight medical concepts. Using concepts rather than terms addresses vocabulary mismatch as well as encapsulates terms belonging to a single medical entity into a single concept. In addition, we further extend previous graph-based approaches by injecting domain knowledge that estimates the importance of a concept within the global medical domain. Retrieval experiments on the TREC Medical Records collection show our method outperforms both term and concept baselines. More generally, this work provides a means of integrating background knowledge contained in medical ontologies into data-driven information retrieval approaches.

Understanding QC and EQA : an authentic learning model for undergraduate students (Conference Abstract)

Introduction QC and EQA are integral to good pathology laboratory practice. Medical Laboratory Science students undertake a project exploring internal QC and EQA procedures used in chemical pathology laboratories. Each student represents an individual lab and the class group represents the peer group of labs performing the same assay using the same method. Methods Using a manual BCG assay for serum albumin, normal and abnormal controls are run with a patient sample over 7 weeks. The QC results are assessed each week using calculated z-scores and both 2S & 3S control rules to determine whether a run is ‘in control’. At the end of the 7 weeks a completed LJ chart is assessed using the Westgard Multirules. Students investigate causes of error and the implications for both lab practice and patient care if runs are not ‘in control’. Twice in the 7 weeks two EQA samples (with target values unknown) are assayed alongside the weekly QC and patient samples. Results from each student are collated and form the basis of an EQA program. ALP are provided and students complete a Youden Plot, which is used to analyse the performance of each ‘lab’ and the method to identify bias. Students explore the concept of possible clinical implications of a biased method and address the actions that should be taken if a lab is not in consensus with the peer group. Conclusion This project is a model of ‘real world’ practice in which student demonstrate an understanding of the importance of QC procedures in a pathology laboratory, apply and interpret statistics and QC rules and charts, apply critical thinking and analytical skills to quality performance data to make recommendations for further practice and improve their technical competence and confidence.

A prospective window into medical device-related pressure ulcers in intensive care

Objective: To determine the prevalence, severity, location, etiology, treatment, and healing of medical device-related pressure ulcers in intensive care patients for up to 7 days. Design: Prospective repeated measures study. Setting and participants: Patients in 6 intensive care units of 2 major medical centers, one each in Australia and the United States, were screened 1 day per month for 6 months. Those with device-related ulcers were followed daily up to 7 days. Outcome measures: Device-related ulcer prevalence, pain, infection, treatment, healing. Results: 15/483 patients had device-related ulcers and 9/15 with 11 ulcers were followed beyond screening. Their mean age was 60.5 years, most were men, over-weight, and at increased pressure ulcer risk. Endotracheal and nasogastric tubes were the cause of most device-related ulcers. Repositioning was the most frequent treatment. 4/11 ulcers healed within the 7 day observation period. Conclusion: Device-related ulcer prevalence was 3.1%, similar to that reported in the limited literature available, indicating an ongoing problem. Systematic assessment and repositioning of devices are the mainstays of care. We recommend continued prevalence determination and that nurses remain vigilant to prevent device-related ulcers, especially in patients with nasogastric and endotracheal tubes.

Perceived barriers to healthy lifestyle activities in midlife and older Australian women with type 2 diabetes

Purpose: Type 2 diabetes is a leading cause of morbidity and mortality in midlife and older Australian women with known modifiable risk factors for type 2 diabetes including smoking, nutrition, physical activity and obesity. In Australia little research has been done to investigate the perceived barriers to healthy lifestyle activities in midlife and older women with type 2 diabetes. The primary aim of this study was to explore the level and type of perceived barriers to health promotion activities. The secondary aim was to explore the relationship of perceived barriers to smoking behaviour, fruit and vegetable intake, physical activity, and body mass index. Methods: The study was a cross sectional survey of women, aged over 45 with type 2 diabetes, attending metropolitan community health clinics (N = 41). Data was collected from self-report questionnaire and analysed using descriptive and inferential statistics. Results: Women in the study had average total barriers scores similar to those reported in the literature for women with a range of physical disabilities and illnesses. The leading barriers for this group of women were: lack of interest, concern about safety, too tired, lack of money and feeling what they do does not help. There was no association between total barriers scores and body mass index, physical activity, fruit and vegetable intake or socio-demographic variables. Conclusion: This study contributes to understanding the perceptions of midlife and older women with type 2 diabetes about the level and type of barriers to healthy lifestyle activities that they experience. Evidence from this study can be applied to inform health promotion for lifestyle risk factor reduction in women with type 2 diabetes.

What relationships exist between general self efficacy, locus of control and the nursing practice environment and caring efficacy and job satisfaction?

Research Question: What relationships exist between general self efficacy, locus of control and the nursing practice environment and caring efficacy and job satisfaction? Background: Important characteristics of current nursing practice include nurses having the ability to develop and continue therapeutic relationships with patients, nurses having autonomy and control over the practice environment and nurses having more involvement in decision making. In addition, employee satisfaction is enhanced when organisations offer access to authority. Despite this, nurses continue to complain of feeling powerless in their ability to make decisions. Sample: The study population and criteria for selection included Registered Nurses in Australia who were at the time members of an Australian professional and industrial organisation. Methods: A cross-sectional survey was undertaken. Data analysis was conducted using descriptive and bivariate statistics, and structural equation modeling. Results: The model fit the data well (χ² = 2.3594, χ²/df = 2.3594 and CFI = 0.9987). Twenty four percent of variation in caring efficacy (CE) can be accounted for by general self-efficacy (GSE); work locus of control (WLC) and practice environment (PE) and 62% of the variation in job satisfaction (JS) can be accounted for by GSE, WLC and PE. All pathways were found to be significant except PE to CE. GSE positively explained CE (β = 0.38). WLC was negatively related to CE i.e., as CE scores increased WLC scores decreased (β = -0.23). Further testing of the model found CE was positively related to GSE (βZ = 0.38, p < 0.001) and negatively related to WLC (βZ = - 0.23, p = 0.001). PE was not significantly associated with CE (βZ = - 0.01, p = 0.85). JS was explained by PE, which was positively related (βZ = 0.69, p = < 0.001); GSE which was negatively related (βZ - 0 .09, p < 0.001) and WLC, which was also negatively related (βZ = - 0.20, p < 0.001). Implications for Practice Nursing and organisational leaders should ensure the development of strategies for professional development and orientation programmes which may enhance nurses’ ability to develop caring relationships and express caring behaviours to their patients and as a result improve organisational and patient outcomes. Nursing shortages and turnover rates are associated with job satisfaction and the nursing practice environment. Improving the nursing environment can produce benefits to the health system such as better job satisfaction, improved workforce retention and better patient outcomes.

Examination of factors affecting caring efficacy, job satisfaction in Australian registered nurses

Research Question: What relationships exist between general self efficacy, locus of control and the nursing practice environment and caring efficacy and job satisfaction? Background: Important characteristics of current nursing practice include nurses having the ability to develop and continue therapeutic relationships with patients, nurses having autonomy and control over the practice environment and nurses having more involvement in decision making. In addition, employee satisfaction is enhanced when organisations offer access to authority. Despite this, nurses continue to complain of feeling powerless in their ability to make decisions. Sample: The study population and criteria for selection included Registered Nurses in Australia who were at the time members of an Australian professional and industrial organisation. Methods: A cross-sectional survey was undertaken. Data analysis was conducted using descriptive and bivariate statistics, and structural equation modelling. Results: The model fit the data well (χ² = 2.3594, χ²/df = 2.3594 and CFI = 0.9987). Twenty four percent of variation in caring efficacy (CE) can be accounted for by general self-efficacy (GSE); work locus of control (WLC) and practice environment (PE) and 62% of the variation in job satisfaction (JS) can be accounted for by GSE, WLC and PE. All pathways were found to be significant except PE to CE. GSE positively explained CE (β = 0.38). WLC was negatively related to CE i.e., as CE scores increased WLC scores decreased (β = -0.23). Further testing of the model found CE was positively related to GSE (βZ = 0.38, p < 0.001) and negatively related to WLC (βZ = - 0.23, p = 0.001). PE was not significantly associated with CE (βZ = - 0.01, p = 0.85). JS was explained by PE, which was positively related (βZ = 0.69, p = < 0.001); GSE which was negatively related (βZ - 0 .09, p < 0.001) and WLC, which was also negatively related (βZ = - 0.20, p < 0.001). Implications for Practice Nursing and organisational leaders should ensure the development of strategies for professional development and orientation programmes which may enhance nurses’ ability to develop caring relationships and express caring behaviours to their patients and as a result improve organisational and patient outcomes. Nursing shortages and turnover rates are associated with job satisfaction and the nursing practice environment. Improving the nursing environment can produce benefits to the health system such as better job satisfaction, improved workforce retention and better patient outcomes.

An evaluation of corpus-driven measures of medical concept similarity for information retrieval

Measures of semantic similarity between medical concepts are central to a number of techniques in medical informatics, including query expansion in medical information retrieval. Previous work has mainly considered thesaurus-based path measures of semantic similarity and has not compared different corpus-driven approaches in depth. We evaluate the effectiveness of eight common corpus-driven measures in capturing semantic relatedness and compare these against human judged concept pairs assessed by medical professionals. Our results show that certain corpus-driven measures correlate strongly (approx 0.8) with human judgements. An important finding is that performance was significantly affected by the choice of corpus used in priming the measure, i.e., used as evidence from which corpus-driven similarities are drawn. This paper provides guidelines for the implementation of semantic similarity measures for medical informatics and concludes with implications for medical information retrieval.

Gender and the capacity of women with NIDDM to implement medical advice

This qualitative study of women with non-insulin dependent diabetes mellitus (NIDDM) examined constructions of their diabetes management and socio-familial relationships as potential sources of support. Semi-structured interview data was collected from 16 women. The transcripts were analysed with the aim of examining the ways in which Sender relations structured women's accounts of health-related behaviours. Women talked about themselves as wives, mothers, being pregnant and parenting, and friends of other women in ways that demonstrated how caring for others impeded their capacity to care for themselves. Meeting the food preferences of husbands and dietary requirements of diabetic husbands were dominant themes in women's accounts of marriage, and in various ways women justified their husbands' lack of support. Furthermore, the care of others during pregnancy and parenting was also an obstacle to women caring for themselves. An awareness of the gender politics inherent within social and family contexts is crucial to improving the effectiveness of medical advice for diabetes management.

Support for patients with hepatitis C : An exploratory qualitative study of medical specialists’ perceptions

Objective: To explore the range of meanings about the role of support for patients with hepatitis C by examining medical specialists' perceptions. Method: The study employed a qualitative, open-ended interview design and was conducted in four major teaching hospitals in Adelaide, South Australia. Eight participants (three infectious disease physicians, four gastroenterologists, one hepatologist), selected through purposive sampling, were interviewed about general patient support, their role in support provision, the role of non-medical support and their reasons for not using support services. Results: Main themes included a focus on support as information provision and that patient education is best carried out by a medical specialist. The use of support services was defined as the patient's decision. Participants identified four key periods when patients would benefit from support; during diagnosis, failure to meet treatment criteria, during interferon treatment and following treatment failure. Conclusions: It was concluded that while barriers exist to the establishment of partnerships between specialists and other support services, this study has identified clear points at which future partnerships could be established. Implications: A partnership approach to developing support for patients with hepatitis C offers a systematic framework to facilitate the participation of health professionals and the community in an important area of public health.