Estimation of parameters for macroparasite population evolution using approximate Bayesian computation

We estimate the parameters of a stochastic process model for a macroparasite population within a host using approximate Bayesian computation (ABC). The immunity of the host is an unobserved model variable and only mature macroparasites at sacrifice of the host are counted. With very limited data, process rates are inferred reasonably precisely. Modeling involves a three variable Markov process for which the observed data likelihood is computationally intractable. ABC methods are particularly useful when the likelihood is analytically or computationally intractable. The ABC algorithm we present is based on sequential Monte Carlo, is adaptive in nature, and overcomes some drawbacks of previous approaches to ABC. The algorithm is validated on a test example involving simulated data from an autologistic model before being used to infer parameters of the Markov process model for experimental data. The fitted model explains the observed extra-binomial variation in terms of a zero-one immunity variable, which has a short-lived presence in the host.

Ontology-based image annotation

With regard to the long-standing problem of the semantic gap between low-level image features and high-level human knowledge, the image retrieval community has recently shifted its emphasis from low-level features analysis to high-level image semantics extrac- tion. User studies reveal that users tend to seek information using high-level semantics. Therefore, image semantics extraction is of great importance to content-based image retrieval because it allows the users to freely express what images they want. Semantic content annotation is the basis for semantic content retrieval. The aim of image anno- tation is to automatically obtain keywords that can be used to represent the content of images. The major research challenges in image semantic annotation are: what is the basic unit of semantic representation? how can the semantic unit be linked to high-level image knowledge? how can the contextual information be stored and utilized for image annotation? In this thesis, the Semantic Web technology (i.e. ontology) is introduced to the image semantic annotation problem. Semantic Web, the next generation web, aims at mak- ing the content of whatever type of media not only understandable to humans but also to machines. Due to the large amounts of multimedia data prevalent on the Web, re- searchers and industries are beginning to pay more attention to the Multimedia Semantic Web. The Semantic Web technology provides a new opportunity for multimedia-based applications, but the research in this area is still in its infancy. Whether ontology can be used to improve image annotation and how to best use ontology in semantic repre- sentation and extraction is still a worth-while investigation. This thesis deals with the problem of image semantic annotation using ontology and machine learning techniques in four phases as below. 1) Salient object extraction. A salient object servers as the basic unit in image semantic extraction as it captures the common visual property of the objects. Image segmen- tation is often used as the �rst step for detecting salient objects, but most segmenta- tion algorithms often fail to generate meaningful regions due to over-segmentation and under-segmentation. We develop a new salient object detection algorithm by combining multiple homogeneity criteria in a region merging framework. 2) Ontology construction. Since real-world objects tend to exist in a context within their environment, contextual information has been increasingly used for improving object recognition. In the ontology construction phase, visual-contextual ontologies are built from a large set of fully segmented and annotated images. The ontologies are composed of several types of concepts (i.e. mid-level and high-level concepts), and domain contextual knowledge. The visual-contextual ontologies stand as a user-friendly interface between low-level features and high-level concepts. 3) Image objects annotation. In this phase, each object is labelled with a mid-level concept in ontologies. First, a set of candidate labels are obtained by training Support Vectors Machines with features extracted from salient objects. After that, contextual knowledge contained in ontologies is used to obtain the �nal labels by removing the ambiguity concepts. 4) Scene semantic annotation. The scene semantic extraction phase is to get the scene type by using both mid-level concepts and domain contextual knowledge in ontologies. Domain contextual knowledge is used to create scene con�guration that describes which objects co-exist with which scene type more frequently. The scene con�guration is represented in a probabilistic graph model, and probabilistic inference is employed to calculate the scene type given an annotated image. To evaluate the proposed methods, a series of experiments have been conducted in a large set of fully annotated outdoor scene images. These include a subset of the Corel database, a subset of the LabelMe dataset, the evaluation dataset of localized semantics in images, the spatial context evaluation dataset, and the segmented and annotated IAPR TC-12 benchmark.

Multi-objective four-dimensional vehicle motion planning in large dynamic environments

This paper presents Multi-Step A* (MSA*), a search algorithm based on A* for multi-objective 4D vehicle motion planning (three spatial and one time dimension). The research is principally motivated by the need for offline and online motion planning for autonomous Unmanned Aerial Vehicles (UAVs). For UAVs operating in large, dynamic and uncertain 4D environments, the motion plan consists of a sequence of connected linear tracks (or trajectory segments). The track angle and velocity are important parameters that are often restricted by assumptions and grid geometry in conventional motion planners. Many existing planners also fail to incorporate multiple decision criteria and constraints such as wind, fuel, dynamic obstacles and the rules of the air. It is shown that MSA* finds a cost optimal solution using variable length, angle and velocity trajectory segments. These segments are approximated with a grid based cell sequence that provides an inherent tolerance to uncertainty. Computational efficiency is achieved by using variable successor operators to create a multi-resolution, memory efficient lattice sampling structure. Simulation studies on the UAV flight planning problem show that MSA* meets the time constraints of online replanning and finds paths of equivalent cost but in a quarter of the time (on average) of vector neighbourhood based A*.

Multivariate Markov Process Models for the transmission of methicillin-resistant Staphylococcus Aureus in a hospital ward

Methicillin-resistant Staphylococcus Aureus (MRSA) is a pathogen that continues to be of major concern in hospitals. We develop models and computational schemes based on observed weekly incidence data to estimate MRSA transmission parameters. We extend the deterministic model of McBryde, Pettitt, and McElwain (2007, Journal of Theoretical Biology 245, 470–481) involving an underlying population of MRSA colonized patients and health-care workers that describes, among other processes, transmission between uncolonized patients and colonized health-care workers and vice versa. We develop new bivariate and trivariate Markov models to include incidence so that estimated transmission rates can be based directly on new colonizations rather than indirectly on prevalence. Imperfect sensitivity of pathogen detection is modeled using a hidden Markov process. The advantages of our approach include (i) a discrete valued assumption for the number of colonized health-care workers, (ii) two transmission parameters can be incorporated into the likelihood, (iii) the likelihood depends on the number of new cases to improve precision of inference, (iv) individual patient records are not required, and (v) the possibility of imperfect detection of colonization is incorporated. We compare our approach with that used by McBryde et al. (2007) based on an approximation that eliminates the health-care workers from the model, uses Markov chain Monte Carlo and individual patient data. We apply these models to MRSA colonization data collected in a small intensive care unit at the Princess Alexandra Hospital, Brisbane, Australia.

Alcohol expectancy changes over a 12-week cognitive–behavioral therapy program are predictive of treatment success

This study examines if outcome expectancies (perceived consequences of engaging in certain behavior) and self- efficacy expectancies (confidence in personal capacity to regulate behavior) contribute to treatment outcome for alcohol dependence. Few clinical studies have examined these constructs. The Drinking Expectancy Profile (DEP), a psychometric measure of alcohol expectancy and drinking refusal selfefficacy, was administered to 298 alcohol-dependent patients (207 males) at assessment and on completion of a 12-week cognitive–behavioral therapy alcohol abstinence program. Baseline measures of expectancy and self-efficacy were not strong predictors of outcome. However, for the 164 patients who completed treatment, all alcohol expectancy and self-efficacy factors of the DEP showed change over time. The DEP scores approximated community norms at the end of treatment. Discriminant analysis indicated that change in social pressure drinking refusal self-efficacy, sexual enhancement expectancies, and assertion expectancies successfully discriminated those who successfully completed treatment from those who did not. Future research should examine the basis of expectancies related to social functioning as a possible mechanism of treatment response and a means to enhance treatment outcome.

Efficient simulation of unsaturated flow using exponential time integration

We assess the performance of an exponential integrator for advancing stiff, semidiscrete formulations of the unsaturated Richards equation in time. The scheme is of second order and explicit in nature but requires the action of the matrix function φ(A) where φ(z) = [exp(z) - 1]/z on a suitability defined vector v at each time step. When the matrix A is large and sparse, φ(A)v can be approximated by Krylov subspace methods that require only matrix-vector products with A. We prove that despite the use of this approximation the scheme remains second order. Furthermore, we provide a practical variable-stepsize implementation of the integrator by deriving an estimate of the local error that requires only a single additional function evaluation. Numerical experiments performed on two-dimensional test problems demonstrate that this implementation outperforms second-order, variable-stepsize implementations of the backward differentiation formulae.

Cancer-related symptom clusters for symptom management in outpatients after commencing adjuvant chemotherapy, at 6 months, and 12 months

Goals of work: The aim of this secondary data analysis was to investigate symptom clusters over time for symptom management of a patient group after commencing adjuvant chemotherapy. Materials and methods: A prospective longitudinal study of 219 cancer outpatients conducted within 1 month of commencing chemotherapy (T1), 6 months (T2), and 12 months (T3) later. Patients' distress levels were assessed for 42 physical symptoms on a clinician-modified Rotterdam Symptom Checklist. Symptom clusters were identified in exploratory factor analyses at each time. Symptom inclusion in clusters was determined from structure coefficients. Symptoms could be associated with multiple clusters. Stability over time was determined from symptom cluster composition and the proportion of symptoms in the initial symptom clusters replicated at later times. Main results Fatigue and daytime sleepiness were the most prevalent distressing symptoms over time. The median number of concurrent distressing symptoms approximated 7, over time. Five consistent clusters were identified at T1, 2, and T3. An additional two clusters were identified at 12 months, possibly due to less variation in distress levels. Weakness and fatigue were each associated with two, four, and five symptom clusters at T1, T2, and T3, respectively, potentially suggesting different causal mechanisms. Conclusion: Stability is a necessary attribute of symptom clusters, but definitional clarification is required. We propose that a core set of concurrent symptoms identifies each symptom cluster, signifying a common cause. Additional related symptoms may be included over time. Further longitudinal investigation is required to identify symptom clusters and the underlying causes.

Hierarchical Bayesian models for estimating the extent of plant pest invasions

Plant biosecurity requires statistical tools to interpret field surveillance data in order to manage pest incursions that threaten crop production and trade. Ultimately, management decisions need to be based on the probability that an area is infested or free of a pest. Current informal approaches to delimiting pest extent rely upon expert ecological interpretation of presence / absence data over space and time. Hierarchical Bayesian models provide a cohesive statistical framework that can formally integrate the available information on both pest ecology and data. The overarching method involves constructing an observation model for the surveillance data, conditional on the hidden extent of the pest and uncertain detection sensitivity. The extent of the pest is then modelled as a dynamic invasion process that includes uncertainty in ecological parameters. Modelling approaches to assimilate this information are explored through case studies on spiralling whitefly, Aleurodicus dispersus and red banded mango caterpillar, Deanolis sublimbalis. Markov chain Monte Carlo simulation is used to estimate the probable extent of pests, given the observation and process model conditioned by surveillance data. Statistical methods, based on time-to-event models, are developed to apply hierarchical Bayesian models to early detection programs and to demonstrate area freedom from pests. The value of early detection surveillance programs is demonstrated through an application to interpret surveillance data for exotic plant pests with uncertain spread rates. The model suggests that typical early detection programs provide a moderate reduction in the probability of an area being infested but a dramatic reduction in the expected area of incursions at a given time. Estimates of spiralling whitefly extent are examined at local, district and state-wide scales. The local model estimates the rate of natural spread and the influence of host architecture, host suitability and inspector efficiency. These parameter estimates can support the development of robust surveillance programs. Hierarchical Bayesian models for the human-mediated spread of spiralling whitefly are developed for the colonisation of discrete cells connected by a modified gravity model. By estimating dispersal parameters, the model can be used to predict the extent of the pest over time. An extended model predicts the climate restricted distribution of the pest in Queensland. These novel human-mediated movement models are well suited to demonstrating area freedom at coarse spatio-temporal scales. At finer scales, and in the presence of ecological complexity, exploratory models are developed to investigate the capacity for surveillance information to estimate the extent of red banded mango caterpillar. It is apparent that excessive uncertainty about observation and ecological parameters can impose limits on inference at the scales required for effective management of response programs. The thesis contributes novel statistical approaches to estimating the extent of pests and develops applications to assist decision-making across a range of plant biosecurity surveillance activities. Hierarchical Bayesian modelling is demonstrated as both a useful analytical tool for estimating pest extent and a natural investigative paradigm for developing and focussing biosecurity programs.

Improving accuracy and intelligibility of decisions

Intelligible and accurate risk-based decision-making requires a complex balance of information from different sources, appropriate statistical analysis of this information and consequent intelligent inference and decisions made on the basis of these analyses. Importantly, this requires an explicit acknowledgement of uncertainty in the inputs and outputs of the statistical model. The aim of this paper is to progress a discussion of these issues in the context of several motivating problems related to the wider scope of agricultural production. These problems include biosecurity surveillance design, pest incursion, environmental monitoring and import risk assessment. The information to be integrated includes observational and experimental data, remotely sensed data and expert information. We describe our efforts in addressing these problems using Bayesian models and Bayesian networks. These approaches provide a coherent and transparent framework for modelling complex systems, combining the different information sources, and allowing for uncertainty in inputs and outputs. While the theory underlying Bayesian modelling has a long and well established history, its application is only now becoming more possible for complex problems, due to increased availability of methodological and computational tools. Of course, there are still hurdles and constraints, which we also address through sharing our endeavours and experiences.

Reliable representations for association rules

Association rule mining has contributed to many advances in the area of knowledge discovery. However, the quality of the discovered association rules is a big concern and has drawn more and more attention recently. One problem with the quality of the discovered association rules is the huge size of the extracted rule set. Often for a dataset, a huge number of rules can be extracted, but many of them can be redundant to other rules and thus useless in practice. Mining non-redundant rules is a promising approach to solve this problem. In this paper, we first propose a definition for redundancy, then propose a concise representation, called a Reliable basis, for representing non-redundant association rules. The Reliable basis contains a set of non-redundant rules which are derived using frequent closed itemsets and their generators instead of using frequent itemsets that are usually used by traditional association rule mining approaches. An important contribution of this paper is that we propose to use the certainty factor as the criterion to measure the strength of the discovered association rules. Using this criterion, we can ensure the elimination of as many redundant rules as possible without reducing the inference capacity of the remaining extracted non-redundant rules. We prove that the redundancy elimination, based on the proposed Reliable basis, does not reduce the strength of belief in the extracted rules. We also prove that all association rules, their supports and confidences, can be retrieved from the Reliable basis without accessing the dataset. Therefore the Reliable basis is a lossless representation of association rules. Experimental results show that the proposed Reliable basis can significantly reduce the number of extracted rules. We also conduct experiments on the application of association rules to the area of product recommendation. The experimental results show that the non-redundant association rules extracted using the proposed method retain the same inference capacity as the entire rule set. This result indicates that using non-redundant rules only is sufficient to solve real problems needless using the entire rule set.

Adaptive Bayesian compound designs for dose finding studies

We consider the problem of how to efficiently and safely design dose finding studies. Both current and novel utility functions are explored using Bayesian adaptive design methodology for the estimation of a maximum tolerated dose (MTD). In particular, we explore widely adopted approaches such as the continual reassessment method and minimizing the variance of the estimate of an MTD. New utility functions are constructed in the Bayesian framework and are evaluated against current approaches. To reduce computing time, importance sampling is implemented to re-weight posterior samples thus avoiding the need to draw samples using Markov chain Monte Carlo techniques. Further, as such studies are generally first-in-man, the safety of patients is paramount. We therefore explore methods for the incorporation of safety considerations into utility functions to ensure that only safe and well-predicted doses are administered. The amalgamation of Bayesian methodology, adaptive design and compound utility functions is termed adaptive Bayesian compound design (ABCD). The performance of this amalgamation of methodology is investigated via the simulation of dose finding studies. The paper concludes with a discussion of results and extensions that could be included into our approach.

Multi-step ahead direct prediction for the machine condition prognosis using regression trees and neuro-fuzzy systems

This paper presents an approach to predict the operating conditions of machine based on classification and regression trees (CART) and adaptive neuro-fuzzy inference system (ANFIS) in association with direct prediction strategy for multi-step ahead prediction of time series techniques. In this study, the number of available observations and the number of predicted steps are initially determined by using false nearest neighbor method and auto mutual information technique, respectively. These values are subsequently utilized as inputs for prediction models to forecast the future values of the machines’ operating conditions. The performance of the proposed approach is then evaluated by using real trending data of low methane compressor. A comparative study of the predicted results obtained from CART and ANFIS models is also carried out to appraise the prediction capability of these models. The results show that the ANFIS prediction model can track the change in machine conditions and has the potential for using as a tool to machine fault prognosis.

The Foot Heath Status Questionnaire : correct scale score calculation

This letter is in response to the recently published article “Evaluation of two self-referent foot health instruments” by Robert Trevethan (RT) and is in regard to the scale scores he derived when using the quality of life measure, the Foot Health Status Questionnaire [1]. Unfortunately, the journal reviewers and editor did not identify, or address, a fundamental flaw in the methodology of this paper. Subsequently, the inference drawn from this paper could, in all reasonableness, mislead the reader

On the data consumption benefits of accepting increased uncertainty

In the context of learning paradigms of identification in the limit, we address the question: why is uncertainty sometimes desirable? We use mind change bounds on the output hypotheses as a measure of uncertainty and interpret ‘desirable’ as reduction in data memorization, also defined in terms of mind change bounds. The resulting model is closely related to iterative learning with bounded mind change complexity, but the dual use of mind change bounds — for hypotheses and for data — is a key distinctive feature of our approach. We show that situations exist where the more mind changes the learner is willing to accept, the less the amount of data it needs to remember in order to converge to the correct hypothesis. We also investigate relationships between our model and learning from good examples, set-driven, monotonic and strong-monotonic learners, as well as class-comprising versus class-preserving learnability.