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.

A decision support system for sustainable urban development : the integrated land use and transportation indexing model

Broad, early definitions of sustainable development have caused confusion and hesitation among local authorities and planning professionals. This confusion has arisen because loosely defined principles of sustainable development have been employed when setting policies and planning projects, and when gauging the efficiencies of these policies in the light of designated sustainability goals. The question of how this theory-rhetoric-practice gap can be filled is the main focus of this chapter. It examines the triple bottom line approach–one of the sustainability accounting approaches widely employed by governmental organisations–and the applicability of this approach to sustainable urban development. The chapter introduces the ‘Integrated Land Use and Transportation Indexing Model’ that incorporates triple bottom line considerations with environmental impact assessment techniques via a geographic, information systems-based decision support system. This model helps decision-makers in selecting policy options according to their economic, environmental and social impacts. Its main purpose is to provide valuable knowledge about the spatial dimensions of sustainable development, and to provide fine detail outputs on the possible impacts of urban development proposals on sustainability levels. In order to embrace sustainable urban development policy considerations, the model is sensitive to the relationship between urban form, travel patterns and socio-economic attributes. Finally, the model is useful in picturing the holistic state of urban settings in terms of their sustainability levels, and in assessing the degree of compatibility of selected scenarios with the desired sustainable urban future.

Quantum Mechanics of Semantic Space

Presentation about information modelling and artificial intelligence, semantic structure, cognitive processing and quantum theory.

Calculating shades of meaning in semantic spaces

This thesis introduces the problem of conceptual ambiguity, or Shades of Meaning (SoM) that can exist around a term or entity. As an example consider President Ronald Reagan the ex-president of the USA, there are many aspects to him that are captured in text; the Russian missile deal, the Iran-contra deal and others. Simply finding documents with the word “Reagan” in them is going to return results that cover many different shades of meaning related to "Reagan". Instead it may be desirable to retrieve results around a specific shade of meaning of "Reagan", e.g., all documents relating to the Iran-contra scandal. This thesis investigates computational methods for identifying shades of meaning around a word, or concept. This problem is related to word sense ambiguity, but is more subtle and based less on the particular syntactic structures associated with or around an instance of the term and more with the semantic contexts around it. A particularly noteworthy difference from typical word sense disambiguation is that shades of a concept are not known in advance. It is up to the algorithm itself to ascertain these subtleties. It is the key hypothesis of this thesis that reducing the number of dimensions in the representation of concepts is a key part of reducing sparseness and thus also crucial in discovering their SoMwithin a given corpus.

Using the semantic grid to build bridges between museums and indigenous communities

In this paper we describe a Semantic Grid application designed to enable museums and indigenous communities in distributed locations, to collaboratively discuss, describe and annotate digital objects and documents in museums that originally belonged to or are of cultural or historical significance to indigenous groups. By extending and refining an existing application, Vannotea, we enable users on access grid nodes to collaboratively attach descriptive, rights and tribal care metadata and annotations to digital images, video or 3D representations. The aim is to deploy the software within museums to enable the traditional owners to describe and contextualize museum content in their own words and from their own perspectives. This sharing and exchange of knowledge will hopefully revitalize cultures eroded through colonization and globalization and repair and strengthen relationships between museums and indigenous communities.

Semantic search and inferencing in health informatics

Consider a person searching electronic health records, a search for the term ‘cracked skull’ should return documents that contain the term ‘cranium fracture’. A information retrieval systems is required that matches concepts, not just keywords. Further more, determining relevance of a query to a document requires inference – its not simply matching concepts. For example a document containing ‘dialysis machine’ should align with a query for ‘kidney disease’. Collectively we describe this problem as the ‘semantic gap’ – the difference between the raw medical data and the way a human interprets it. This paper presents an approach to semantic search of health records by combining two previous approaches: an ontological approach using the SNOMED CT medical ontology; and a distributional approach using semantic space vector space models. Our approach will be applied to a specific problem in health informatics: the matching of electronic patient records to clinical trials.

Examination of the latent structure of the psychological sense of school membership scale

Despite its widespread use, there has been limited examination of the underlying factor structure of the Psychological Sense of School Membership (PSSM) scale. The current study examined the psychometric properties of the PSSM to refine its utility for researchers and practitioners using a sample of 504 Australian high school students. Results from exploratory and confirmatory factor analyses indicated that the PSSM is a multidimensional instrument. Factor analysis procedures identified three factors representing related aspects of students’ perceptions of their school membership: caring relationships, acceptance, and rejection

Semantic oscillations : encoding context and structure in complex valued holographic vectors

In computational linguistics, information retrieval and applied cognition, words and concepts are often represented as vectors in high dimensional spaces computed from a corpus of text. These high dimensional spaces are often referred to as Semantic Spaces. We describe a novel and efficient approach to computing these semantic spaces via the use of complex valued vector representations. We report on the practical implementation of the proposed method and some associated experiments. We also briefly discuss how the proposed system relates to previous theoretical work in Information Retrieval and Quantum Mechanics and how the notions of probability, logic and geometry are integrated within a single Hilbert space representation. In this sense the proposed system has more general application and gives rise to a variety of opportunities for future research.

Towards defining semantic foundations for purpose-based privacy policies

We define a semantic model for purpose, based on which purpose-based privacy policies can be meaningfully expressed and enforced in a business system. The model is based on the intuition that the purpose of an action is determined by its situation among other inter-related actions. Actions and their relationships can be modeled in the form of an action graph which is based on the business processes in a system. Accordingly, a modal logic and the corresponding model checking algorithm are developed for formal expression of purpose-based policies and verifying whether a particular system complies with them. It is also shown through various examples, how various typical purpose-based policies as well as some new policy types can be expressed and checked using our model.

Utilising semantic tags in XML clustering

This paper presents an overview of the experiments conducted using Hybrid Clustering of XML documents using Constraints (HCXC) method for the clustering task in the INEX 2009 XML Mining track. This technique utilises frequent subtrees generated from the structure to extract the content for clustering the XML documents. It also presents the experimental study using several data representations such as the structure-only, content-only and using both the structure and the content of XML documents for the purpose of clustering them. Unlike previous years, this year the XML documents were marked up using the Wiki tags and contains categories derived by using the YAGO ontology. This paper also presents the results of studying the effect of these tags on XML clustering using the HCXC method.

Estimating the latent demand for rail transit : a case study in Perth, Western Australia

This paper presents a study on estimating the latent demand for rail transit in Australian context. Based on travel mode-choice modelling, a two-stage analysis approach is proposed, namely market population identification and mode share estimation. A case study is conducted on Midland-Fremantle rail transit corridor in Perth, Western Australia. The required data mainly include journey-to-work trip data from Australian Bureau of Statistics Census 2006 and work-purpose mode-choice model in Perth Strategic Transport Evaluation Model. The market profile is analysed, such as catchment areas, market population, mode shares, mode specific trip distributions and average trip distances. A numerical simulation is performed to test the sensitivity of the transit ridership to the change of fuel price. A corridor-level transit demand function of fuel price is thus obtained and its characteristics of elasticity are discussed. This study explores a viable approach to developing a decision-support tool for the assessment of short-term impacts of policy and operational adjustments on corridor-level demand for rail transit.

Latent degradation indicators estimation and prediction : a Monte Carlo approach

Asset health inspections can produce two types of indicators: (1) direct indicators (e.g. the thickness of a brake pad, and the crack depth on a gear) which directly relate to a failure mechanism; and (2) indirect indicators (e.g. the indicators extracted from vibration signals and oil analysis data) which can only partially reveal a failure mechanism. While direct indicators enable more precise references to asset health condition, they are often more difficult to obtain than indirect indicators. The state space model provides an efficient approach to estimating direct indicators by using indirect indicators. However, existing state space models to estimate direct indicators largely depend on assumptions such as, discrete time, discrete state, linearity, and Gaussianity. The discrete time assumption requires fixed inspection intervals. The discrete state assumption entails discretising continuous degradation indicators, which often introduces additional errors. The linear and Gaussian assumptions are not consistent with nonlinear and irreversible degradation processes in most engineering assets. This paper proposes a state space model without these assumptions. Monte Carlo-based algorithms are developed to estimate the model parameters and the remaining useful life. These algorithms are evaluated for performance using numerical simulations through MATLAB. The result shows that both the parameters and the remaining useful life are estimated accurately. Finally, the new state space model is used to process vibration and crack depth data from an accelerated test of a gearbox. During this application, the new state space model shows a better fitness result than the state space model with linear and Gaussian assumption.