Latent variable models in statistical genetics

Understanding the complexities that are involved in the genetics of multifactorial diseases is still a monumental task. In addition to environmental factors that can influence the risk of disease, there is also a number of other complicating factors. Genetic variants associated with age of disease onset may be different from those variants associated with overall risk of disease, and variants may be located in positions that are not consistent with the traditional protein coding genetic paradigm. Latent Variable Models are well suited for the analysis of genetic data. A latent variable is one that we do not directly observe, but which is believed to exist or is included for computational or analytic convenience in a model. This thesis presents a mixture of methodological developments utilising latent variables, and results from case studies in genetic epidemiology and comparative genomics. Epidemiological studies have identified a number of environmental risk factors for appendicitis, but the disease aetiology of this oft thought useless vestige remains largely a mystery. The effects of smoking on other gastrointestinal disorders are well documented, and in light of this, the thesis investigates the association between smoking and appendicitis through the use of latent variables. By utilising data from a large Australian twin study questionnaire as both cohort and case-control, evidence is found for the association between tobacco smoking and appendicitis. Twin and family studies have also found evidence for the role of heredity in the risk of appendicitis. Results from previous studies are extended here to estimate the heritability of age-at-onset and account for the eect of smoking. This thesis presents a novel approach for performing a genome-wide variance components linkage analysis on transformed residuals from a Cox regression. This method finds evidence for a dierent subset of genes responsible for variation in age at onset than those associated with overall risk of appendicitis. Motivated by increasing evidence of functional activity in regions of the genome once thought of as evolutionary graveyards, this thesis develops a generalisation to the Bayesian multiple changepoint model on aligned DNA sequences for more than two species. This sensitive technique is applied to evaluating the distributions of evolutionary rates, with the finding that they are much more complex than previously apparent. We show strong evidence for at least 9 well-resolved evolutionary rate classes in an alignment of four Drosophila species and at least 7 classes in an alignment of four mammals, including human. A pattern of enrichment and depletion of genic regions in the profiled segments suggests they are functionally significant, and most likely consist of various functional classes. Furthermore, a method of incorporating alignment characteristics representative of function such as GC content and type of mutation into the segmentation model is developed within this thesis. Evidence of fine-structured segmental variation is presented.

Efficient and accurate retrieval of business process models through indexing

Recent years have seen an increased uptake of business process management technology in industries. This has resulted in organizations trying to manage large collections of business process models. One of the challenges facing these organizations concerns the retrieval of models from large business process model repositories. For example, in some cases new process models may be derived from existing models, thus finding these models and adapting them may be more effective than developing them from scratch. As process model repositories may be large, query evaluation may be time consuming. Hence, we investigate the use of indexes to speed up this evaluation process. Experiments are conducted to demonstrate that our proposal achieves a significant reduction in query evaluation time.

Investigation of MEMS inertial sensors and aircraft dynamic models in global positioning system integrity monitoring for approaches with vertical guidance

An Approach with Vertical Guidance (APV) is an instrument approach procedure which provides horizontal and vertical guidance to a pilot on approach to landing in reduced visibility conditions. APV approaches can greatly reduce the safety risk to general aviation by improving the pilot’s situational awareness. In particular the incidence of Controlled Flight Into Terrain (CFIT) which has occurred in a number of fatal air crashes in general aviation over the past decade in Australia, can be reduced. APV approaches can also improve general aviation operations. If implemented at Australian airports, APV approach procedures are expected to bring a cost saving of millions of dollars to the economy due to fewer missed approaches, diversions and an increased safety benefit. The provision of accurate horizontal and vertical guidance is achievable using the Global Positioning System (GPS). Because aviation is a safety of life application, an aviation-certified GPS receiver must have integrity monitoring or augmentation to ensure that its navigation solution can be trusted. However, the difficulty with the current GPS satellite constellation alone meeting APV integrity requirements, the susceptibility of GPS to jamming or interference and the potential shortcomings of proposed augmentation solutions for Australia such as the Ground-based Regional Augmentation System (GRAS) justifies the investigation of Aircraft Based Augmentation Systems (ABAS) as an alternative integrity solution for general aviation. ABAS augments GPS with other sensors at the aircraft to help it meet the integrity requirements. Typical ABAS designs assume high quality inertial sensors to provide an accurate reference trajectory for Kalman filters. Unfortunately high-quality inertial sensors are too expensive for general aviation. In contrast to these approaches the purpose of this research is to investigate fusing GPS with lower-cost Micro-Electro-Mechanical System (MEMS) Inertial Measurement Units (IMU) and a mathematical model of aircraft dynamics, referred to as an Aircraft Dynamic Model (ADM) in this thesis. Using a model of aircraft dynamics in navigation systems has been studied before in the available literature and shown to be useful particularly for aiding inertial coasting or attitude determination. In contrast to these applications, this thesis investigates its use in ABAS. This thesis presents an ABAS architecture concept which makes use of a MEMS IMU and ADM, named the General Aviation GPS Integrity System (GAGIS) for convenience. GAGIS includes a GPS, MEMS IMU, ADM, a bank of Extended Kalman Filters (EKF) and uses the Normalized Solution Separation (NSS) method for fault detection. The GPS, IMU and ADM information is fused together in a tightly-coupled configuration, with frequent GPS updates applied to correct the IMU and ADM. The use of both IMU and ADM allows for a number of different possible configurations. Three are investigated in this thesis; a GPS-IMU EKF, a GPS-ADM EKF and a GPS-IMU-ADM EKF. The integrity monitoring performance of the GPS-IMU EKF, GPS-ADM EKF and GPS-IMU-ADM EKF architectures are compared against each other and against a stand-alone GPS architecture in a series of computer simulation tests of an APV approach. Typical GPS, IMU, ADM and environmental errors are simulated. The simulation results show the GPS integrity monitoring performance achievable by augmenting GPS with an ADM and low-cost IMU for a general aviation aircraft on an APV approach. A contribution to research is made in determining whether a low-cost IMU or ADM can provide improved integrity monitoring performance over stand-alone GPS. It is found that a reduction of approximately 50% in protection levels is possible using the GPS-IMU EKF or GPS-ADM EKF as well as faster detection of a slowly growing ramp fault on a GPS pseudorange measurement. A second contribution is made in determining how augmenting GPS with an ADM compares to using a low-cost IMU. By comparing the results for the GPS-ADM EKF against the GPS-IMU EKF it is found that protection levels for the GPS-ADM EKF were only approximately 2% higher. This indicates that the GPS-ADM EKF may potentially replace the GPS-IMU EKF for integrity monitoring should the IMU ever fail. In this way the ADM may contribute to the navigation system robustness and redundancy. To investigate this further, a third contribution is made in determining whether or not the ADM can function as an IMU replacement to improve navigation system redundancy by investigating the case of three IMU accelerometers failing. It is found that the failed IMU measurements may be supplemented by the ADM and adequate integrity monitoring performance achieved. Besides treating the IMU and ADM separately as in the GPS-IMU EKF and GPS-ADM EKF, a fourth contribution is made in investigating the possibility of fusing the IMU and ADM information together to achieve greater performance than either alone. This is investigated using the GPS-IMU-ADM EKF. It is found that the GPS-IMU-ADM EKF can achieve protection levels approximately 3% lower in the horizontal and 6% lower in the vertical than a GPS-IMU EKF. However this small improvement may not justify the complexity of fusing the IMU with an ADM in practical systems. Affordable ABAS in general aviation may enhance existing GPS-only fault detection solutions or help overcome any outages in augmentation systems such as the Ground-based Regional Augmentation System (GRAS). Countries such as Australia which currently do not have an augmentation solution for general aviation could especially benefit from the economic savings and safety benefits of satellite navigation-based APV approaches.

How environmental and organizational complexity affects opportunity recognition and exploitation in development projects

Principal Topic: Project structures are often created by entrepreneurs and large corporate organizations to develop new products. Since new product development projects (NPDP) are more often situated within a larger organization, intrapreneurship or corporate entrepreneurship plays an important role in bringing these projects to fruition. Since NPDP often involves the development of a new product using immature technology, we describe development of an immature technology. The Joint Strike Fighter (JSF) F-35 aircraft is being developed by the U.S. Department of Defense and eight allied nations. In 2001 Lockheed Martin won a $19 billion contract to develop an affordable, stealthy and supersonic all-weather strike fighter designed to replace a wide range of aging fighter aircraft. In this research we define a complex project as one that demonstrates a number of sources of uncertainty to a degree, or level of severity, that makes it extremely difficult to predict project outcomes, to control or manage project (Remington & Zolin, Forthcoming). Project complexity has been conceptualized by Remington and Pollock (2007) in terms of four major sources of complexity; temporal, directional, structural and technological complexity (See Figure 1). Temporal complexity exists when projects experience significant environmental change outside the direct influence or control of the project. The Global Economic Crisis of 2008 - 2009 is a good example of the type of environmental change that can make a project complex as, for example in the JSF project, where project managers attempt to respond to changes in interest rates, international currency exchange rates and commodity prices etc. Directional complexity exists in a project where stakeholders' goals are unclear or undefined, where progress is hindered by unknown political agendas, or where stakeholders disagree or misunderstand project goals. In the JSF project all the services and all non countries have to agree to the specifications of the three variants of the aircraft; Conventional Take Off and Landing (CTOL), Short Take Off/Vertical Landing (STOVL) and the Carrier Variant (CV). Because the Navy requires a plane that can take off and land on an aircraft carrier, that required a special variant of the aircraft design, adding complexity to the project. Technical complexity occurs in a project using technology that is immature or where design characteristics are unknown or untried. Developing a plane that can take off on a very short runway and land vertically created may highly interdependent technological challenges to correctly locate, direct and balance the lift fans, modulate the airflow and provide equivalent amount of thrust from the downward vectored rear exhaust to lift the aircraft and at the same time control engine temperatures. These technological challenges make costing and scheduling equally challenging. Structural complexity in a project comes from the sheer numbers of elements such as the number of people, teams or organizations involved, ambiguity regarding the elements, and the massive degree of interconnectedness between them. While Lockheed Martin is the prime contractor, they are assisted in major aspects of the JSF development by Northrop Grumman, BAE Systems, Pratt & Whitney and GE/Rolls-Royce Fighter Engineer Team and innumerable subcontractors. In addition to identifying opportunities to achieve project goals, complex projects also need to identify and exploit opportunities to increase agility in response to changing stakeholder demands or to reduce project risks. Complexity Leadership Theory contends that in complex environments adaptive and enabling leadership are needed (Uhl-Bien, Marion and McKelvey, 2007). Adaptive leadership facilitates creativity, learning and adaptability, while enabling leadership handles the conflicts that inevitably arise between adaptive leadership and traditional administrative leadership (Uhl-Bien and Marion, 2007). Hence, adaptive leadership involves the recognition and opportunities to adapt, while and enabling leadership involves the exploitation of these opportunities. Our research questions revolve around the type or source of complexity and its relationship to opportunity recognition and exploitation. For example, is it only external environmental complexity that creates the need for the entrepreneurial behaviours, such as opportunity recognition and opportunity exploitation? Do the internal dimensions of project complexity, such as technological and structural complexity, also create the need for opportunity recognition and opportunity exploitation? The Kropp, Zolin and Lindsay model (2009) describes a relationship between entrepreneurial orientation (EO), opportunity recognition (OR), and opportunity exploitation (OX) in complex projects, with environmental and organizational contextual variables as moderators. We extend their model by defining the affects of external complexity and internal complexity on OR and OX. ---------- Methodology/Key Propositions: When the environment complex EO is more likely to result in OR because project members will be actively looking for solutions to problems created by environmental change. But in projects that are technologically or structurally complex project leaders and members may try to make the minimum changes possible to reduce the risk of creating new problems due to delays or schedule changes. In projects with environmental or technological complexity project leaders who encourage the innovativeness dimension of EO will increase OR in complex projects. But projects with technical or structural complexity innovativeness will not necessarily result in the recognition and exploitation of opportunities due to the over-riding importance of maintaining stability in the highly intricate and interconnected project structure. We propose that in projects with environmental complexity creating the need for change and innovation project leaders, who are willing to accept and manage risk, are more likely to identify opportunities to increase project effectiveness and efficiency. In contrast in projects with internal complexity a much higher willingness to accept risk will be necessary to trigger opportunity recognition. In structurally complex projects we predict it will be less likely to find a relationship between risk taking and OP. When the environment is complex, and a project has autonomy, they will be motivated to execute opportunities to improve the project's performance. In contrast, when the project has high internal complexity, they will be more cautious in execution. When a project experiences high competitive aggressiveness and their environment is complex, project leaders will be motivated to execute opportunities to improve the project's performance. In contrast, when the project has high internal complexity, they will be more cautious in execution. This paper reports the first stage of a three year study into the behaviours of managers, leaders and team members of complex projects. We conduct a qualitative study involving a Group Discussion with experienced project leaders. The objective is to determine how leaders of large and potentially complex projects perceive that external and internal complexity will influence the affects of EO on OR. ---------- Results and Implications: These results will help identify and distinguish the impact of external and internal complexity on entrepreneurial behaviours in NPDP. Project managers will be better able to quickly decide how and when to respond to changes in the environment and internal project events.

Virtual Environment Visualisation of Executable Business Process Models

Business Process Modelling is a fast growing field in business and information technology, which uses visual grammars to model and execute the processes within an organisation. However, many analysts present such models in a 2D static and iconic manner that is difficult to understand by many stakeholders. Difficulties in understanding such grammars can impede the improvement of processes within an enterprise due to communication problems. In this chapter we present a novel framework for intuitively visualising animated business process models in interactive Virtual Environments. We also show that virtual environment visualisations can be performed with present 2D business process modelling technology, thus providing a low barrier to entry for business process practitioners. Two case studies are presented from film production and healthcare domains that illustrate the ease with which these visualisations can be created. This approach can be generalised to other executable workflow systems, for any application domain being modelled.

On the cognitive effectiveness of routing symbols in process modeling languages

Process models provide visual support for analyzing and improving complex organizational processes. In this paper, we discuss differences of process modeling languages using cognitive effectiveness considerations, to make statements about the ease of use and quality of user experience. Aspects of cognitive effectiveness are of importance for learning a modeling language, creating models, and understanding models. We identify the criteria representational clarity, perceptual discriminability, perceptual immediacy, visual expressiveness, and graphic parsimony to compare and assess the cognitive effectiveness of different modeling languages. We apply these criteria in an analysis of the routing elements of UML Activity Diagrams, YAWL, BPMN, and EPCs, to uncover their relative strengths and weaknesses from a quality of user experience perspective. We draw conclusions that are relevant to the usability of these languages in business process modeling projects.

Enablers and barriers to the organizational adoption of sustainable business practices

Individuals, organizations, and governments are increasingly becoming aware of the necessity of sustainability in living, organizing, performing, and managing work. In this context, “green IS” has become an established colloquial term, acknowledging that information technology, corporate information systems, and the surrounding practices are both a contributor to the sustainability challenge and a potential enabler for green and sustainable practices. To date, however, there are few reported studies on the role of information systems for the challenge, and solution, of sustainability. This paper presents results from a case study of a world-wide operating IT software solution provider that is engaged in the development and adoption of sustainable practices. Our study suggests that the adoption of sustainable practices comes along with a number of particularities. We found information technology to be a key enabler of transparency about the progress of sustainability operations. We further found personal, motivator factors as well as organizational factors such as business inclusion, strategy definition, and a dialectic top-management and bottom-up support, to play a role in enabling a company to manage their sustainability. We describe a set of conjectures forthcoming from our case analysis, and detail some implications for further research in this area.

Hippocampal models for simultaneous localisation and mapping on an autonomous robot

To navigate successfully in a novel environment a robot needs to be able to Simultaneously Localize And Map (SLAM) its surroundings. The most successful solutions to this problem so far have involved probabilistic algorithms, but there has been much promising work involving systems based on the workings of part of the rodent brain known as the hippocampus. In this paper we present a biologically plausible system called RatSLAM that uses competitive attractor networks to carry out SLAM in a probabilistic manner. The system can effectively perform parameter self-calibration and SLAM in one dimension. Tests in two dimensional environments revealed the inability of the RatSLAM system to maintain multiple pose hypotheses in the face of ambiguous visual input. These results support recent rat experimentation that suggest current competitive attractor models are not a complete solution to the hippocampal modelling problem.

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.

Next Generation ‘Filmmaking’: New Markets, New Methods and New Business Models

Digital production and distribution technologies may create new opportunities for filmmaking in Australia. A culture of new approaches to filmmaking is emerging driven by ‘next generation filmmakers’ who are willing to consider new business models: from online web series to short films produced for mobile phones. At the same time cultural representation itself is transforming within an interactive, social media driven environment. Yet there is very little research into next generation filmmaking. The aim of this paper is to scope and discuss three key aspects of next generation filmmaking, namely: digital trends in film distribution and marketing; processes and strategies of ‘next generation’ filmmakers; and case studies of viable next generation business models and filmmaking practices. We conclude with a brief examination of the implications for media and cultural policy which suggests the future possibility of a rapprochement between creative industries discourse and cultural policy.

Facilitating unlearning during implementation of new technology

Purpose – One of the critical issues for change management, particularly in relation to the implementation of new technologies, is the existence of prior knowledge and established mental models which may hinder change efforts. Understanding unlearning and how it might assist during organizational change is a way to address this resistance. The purpose of this paper is to present research designed to identify specific factors that facilitate unlearning. Design/methodology/approach – Drawing together issues identified as potential influencers of unlearning, a survey questionnaire was developed and administered in an Australian corporation undergoing large-scale change due to the implementation of an enterprise information system. The results were analyzed to identify specific factors that impact on unlearning. Findings – Findings from this paper identify factors that hinder or help the unlearning process during times of change including understanding the need for change, the level of organizational support and training, assessment of the change, positive experience and informal support, the organization's history of change, individual's prior outlooks, and individuals' feelings and expectations. Research limitations/implications – The use of only one organization does not allow for comparisons between organizations of different sizes, cultures or industries and therefore extension of this research is recommended. Practical implications – For practitioners, this paper provides specific elements at both the level of individuals and the organization that need to be considered for optimal unlearning during times of change. Originality/value – Previous literature on unlearning has been predominantly conceptual and theoretical. These empirical findings serve to further an earlier model based on qualitative research into potential influencers of unlearning.

Incorporating uncertainty in environmental models informed by imagery

In this thesis, the issue of incorporating uncertainty for environmental modelling informed by imagery is explored by considering uncertainty in deterministic modelling, measurement uncertainty and uncertainty in image composition. Incorporating uncertainty in deterministic modelling is extended for use with imagery using the Bayesian melding approach. In the application presented, slope steepness is shown to be the main contributor to total uncertainty in the Revised Universal Soil Loss Equation. A spatial sampling procedure is also proposed to assist in implementing Bayesian melding given the increased data size with models informed by imagery. Measurement error models are another approach to incorporating uncertainty when data is informed by imagery. These models for measurement uncertainty, considered in a Bayesian conditional independence framework, are applied to ecological data generated from imagery. The models are shown to be appropriate and useful in certain situations. Measurement uncertainty is also considered in the context of change detection when two images are not co-registered. An approach for detecting change in two successive images is proposed that is not affected by registration. The procedure uses the Kolmogorov-Smirnov test on homogeneous segments of an image to detect change, with the homogeneous segments determined using a Bayesian mixture model of pixel values. Using the mixture model to segment an image also allows for uncertainty in the composition of an image. This thesis concludes by comparing several different Bayesian image segmentation approaches that allow for uncertainty regarding the allocation of pixels to different ground components. Each segmentation approach is applied to a data set of chlorophyll values and shown to have different benefits and drawbacks depending on the aims of the analysis.

ERP systems implementation and organizational culture : the case of Jordan

Jordan is adopting Enterprise Resource Planning (ERP) systems in both its public and private sectors. Jordan's emerging private sector has historically close ties to the public sector; though a global market orientation requires a shift in its organizational culture. ERPs however embed business processes which do not necessarily fit with traditional cultural practices, and implementation success is not assured. This study looks at the perceptions of both public and private sector ERP implementations in Jordan and assesses these on various measures of success. There were few differences between public and private sectors, but the benefits actually realized in Jordanian ERPs fell short of claims made for the technology in other cultures.

Literacy models across nations : literacy and critical literacy in teacher training programs in India

The thrust towards constructivist learning and critical thinking in the National Curricular Framework (2005) of India implies shifts in pedagogical practices. In this context, drawing on grounded theory, focus group interviews were conducted with 40 preservice teachers to ascertain the contextual situation and the likely outcomes of applying critical literacy across the curriculum. Central themes that emerged in the discussion were: being teacher centred/ learner centred, and conformity/autonomy in teaching and learning. The paper argues that within the present Indian context, while there is scope for changes to pedagogy and learning styles, yet these must be adequately contextualised.