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.

Framework for measuring corporate safety culture and its impact on construction safety performance

This paper presents the results of a structural equation model (SEM) that describes and quantifies the relationships between corporate culture and safety performance. The SEM is estimated using 196 individual questionnaire responses from three companies with better than average safety records. A multiattribute analysis of corporate safety culture characteristics resulted in a hierarchical description of corporate safety culture comprised of three major categories — people, process, and value. These three major categories were decomposed into 54 measurable questions and used to develop a questionnaire to quantify corporate safety culture. The SEM identified five latent variables that describe corporate safety culture: (1) a company’s safety commitment; (2) the safety incentives that are offered to field personal for safe performance; (3) the subcontractor involvement in the company culture; (4) the field safety accountability and dedication; and (5) the disincentives for unsafe behaviors. These characteristics of company safety culture serve as indicators for a company’s safety performance. Based on the findings from this limited sample of three companies, this paper proposes a list of practices that companies may consider to improve corporate safety culture and safety performance. A more comprehensive study based on a larger sample is recommended to corroborate the findings of this study.

Understanding the impact of strategic alignment on the operational performance of post implemented technological innovations

Purpose – The purpose of this paper is to examine the role of three strategies - organisational, business and information system – in post implementation of technological innovations. The findings reported in the paper are that improvements in operational performance can only be achieved by aligning technological innovation effectiveness with operational effectiveness. Design/methodology/approach – A combination of qualitative and quantitative methods was used to apply a two-stage methodological approach. Unstructured and semi structured interviews, based on the findings of the literature, were used to identify key factors used in the survey instrument design. Confirmatory factor analysis (CFA) was used to examine structural relationships between the set of observed variables and the set of continuous latent variables. Findings – Initial findings suggest that organisations looking for improvements in operational performance through adoption of technological innovations need to align with operational strategies of the firm. Impact of operational effectiveness and technological innovation effectiveness are related directly and significantly to improved operational performance. Perception of increase of operational effectiveness is positively and significantly correlated with improved operational performance. The findings suggest that technological innovation effectiveness is also positively correlated with improved operational performance. However, the study found that there is no direct influence of strategiesorganisational, business and information systems (IS) - on improvement of operational performance. Improved operational performance is the result of interactions between the implementation of strategies and related outcomes of both technological innovation and operational effectiveness. Practical implications – Some organisations are using technological innovations such as enterprise information systems to innovate through improvements in operational performance. However, they often focus strategically only on effectiveness of technological innovation or on operational effectiveness. Such a focus will be detrimental in the long-term of the enterprise. This research demonstrated that it is not possible to achieve maximum returns through technological innovations as dimensions of operational effectiveness need to be aligned with technological innovations to improve their operational performance. Originality/value – No single technological innovation implementation can deliver a sustained competitive advantage; rather, an advantage is obtained through the capacity of an organisation to exploit technological innovations’ functionality on a continuous basis. To achieve sustainable results, technology strategy must be aligned with organisational and operational strategies. This research proposes the key performance objectives and dimensions that organisations should focus to achieve a strategic alignment. Research limitations/implications – The principal limitation of this study is that the findings are based on investigation of small sample size. There is a need to explore the appropriateness of influence of scale prior to generalizing the results of this study.

Overcoming the complexity of diagnostic problems due to sensor network architecture

In fault detection and diagnostics, limitations coming from the sensor network architecture are one of the main challenges in evaluating a system’s health status. Usually the design of the sensor network architecture is not solely based on diagnostic purposes, other factors like controls, financial constraints, and practical limitations are also involved. As a result, it quite common to have one sensor (or one set of sensors) monitoring the behaviour of two or more components. This can significantly extend the complexity of diagnostic problems. In this paper a systematic approach is presented to deal with such complexities. It is shown how the problem can be formulated as a Bayesian network based diagnostic mechanism with latent variables. The developed approach is also applied to the problem of fault diagnosis in HVAC systems, an application area with considerable modeling and measurement constraints.

Utilizing industry-led innovation capacity to enhance supply chain performance : an empirical study

A fundamental principle of the resource-based (RBV) of the firm is that the basis for a competitive advantage lies primarily in the application of bundles of valuable strategic capabilities and resources at a firm’s or supply chain’s disposal. These capabilities enact research activities and outputs produced by industry funded R&D bodies. Such industry lead innovations are seen as strategic industry resources, because effective utilization of industry innovation capacity by sectors such as the Australian beef industry are critical, if productivity levels are to increase. Academics and practitioners often maintain that dynamic supply chains and innovation capacity are the mechanisms most likely to deliver performance improvements in national industries.. Yet many industries are still failing to capitalise on these strategic resources. In this research, we draw on the resource-based view (RBV) and embryonic research into strategic supply chain capabilities. We investigate how two strategic supply chain capabilities (supply chain performance differential capability and supply chain dynamic capability) influence industry-led innovation capacity utilization and provide superior performance enhancements to the supply chain. In addition, we examine the influence of size of the supply chain operative as a control variable. Results indicate that both small and large supply chain operatives in this industry believe these strategic capabilities influence and function as second-order latent variables of this strategic supply chain resource. Additionally respondents acknowledge size does impacts both the amount of influence these strategic capabilities have and the level of performance enhancement expected by supply chain operatives from utilizing industry-led innovation capacity. Results however also indicate contradiction in this industry and in relation to existing literature when it comes to utilizing such e-resources.

Educational stress scale for adolescents : development, validity, and reliability with Chinese students

This article describes the development and initial validation of a new instrument to measure academic stress—the Educational Stress Scale for Adolescents (ESSA). A series of cross-sectional questionnaire surveys were conducted with more than 2,000 Chinese adolescents to examine the psychometric properties. The final 16-item ESSA contains five latent variables: Pressure from study, Workload, Worry about grades, Self-expectation, and Despondency, which together explain 64% of the total item variance. Scale scores showed adequate internal consistency, 2-week test–retest reliability, and satisfactory concurrent validity. A confirmatory factor analysis suggested the proposed factor model fits well in a different sample. For researchers who have a particular interest in academic stress among adolescents, the ESSA promises to be a useful tool.

A proposed validation framework for expert elicited Bayesian Networks

The popularity of Bayesian Network modelling of complex domains using expert elicitation has raised questions of how one might validate such a model given that no objective dataset exists for the model. Past attempts at delineating a set of tests for establishing confidence in an entirely expert-elicited model have focused on single types of validity stemming from individual sources of uncertainty within the model. This paper seeks to extend the frameworks proposed by earlier researchers by drawing upon other disciplines where measuring latent variables is also an issue. We demonstrate that even in cases where no data exist at all there is a broad range of validity tests that can be used to establish confidence in the validity of a Bayesian Belief Network.

Marginal reversible jump Markov chain Monte Carlo with application to motor unit number estimation

Motor unit number estimation (MUNE) is a method which aims to provide a quantitative indicator of progression of diseases that lead to loss of motor units, such as motor neurone disease. However the development of a reliable, repeatable and fast real-time MUNE method has proved elusive hitherto. Ridall et al. (2007) implement a reversible jump Markov chain Monte Carlo (RJMCMC) algorithm to produce a posterior distribution for the number of motor units using a Bayesian hierarchical model that takes into account biological information about motor unit activation. However we find that the approach can be unreliable for some datasets since it can suffer from poor cross-dimensional mixing. Here we focus on improved inference by marginalising over latent variables to create the likelihood. In particular we explore how this can improve the RJMCMC mixing and investigate alternative approaches that utilise the likelihood (e.g. DIC (Spiegelhalter et al., 2002)). For this model the marginalisation is over latent variables which, for a larger number of motor units, is an intractable summation over all combinations of a set of latent binary variables whose joint sample space increases exponentially with the number of motor units. We provide a tractable and accurate approximation for this quantity and also investigate simulation approaches incorporated into RJMCMC using results of Andrieu and Roberts (2009).

On the commonly accepted assumptions regarding observed motor vehicle crash counts at transport system locations

Readily accepted knowledge regarding crash causation is consistently omitted from efforts to model and subsequently understand motor vehicle crash occurrence and their contributing factors. For instance, distracted and impaired driving accounts for a significant proportion of crash occurrence, yet is rarely modeled explicitly. In addition, spatially allocated influences such as local law enforcement efforts, proximity to bars and schools, and roadside chronic distractions (advertising, pedestrians, etc.) play a role in contributing to crash occurrence and yet are routinely absent from crash models. By and large, these well-established omitted effects are simply assumed to contribute to model error, with predominant focus on modeling the engineering and operational effects of transportation facilities (e.g. AADT, number of lanes, speed limits, width of lanes, etc.) The typical analytical approach—with a variety of statistical enhancements—has been to model crashes that occur at system locations as negative binomial (NB) distributed events that arise from a singular, underlying crash generating process. These models and their statistical kin dominate the literature; however, it is argued in this paper that these models fail to capture the underlying complexity of motor vehicle crash causes, and thus thwart deeper insights regarding crash causation and prevention. This paper first describes hypothetical scenarios that collectively illustrate why current models mislead highway safety researchers and engineers. It is argued that current model shortcomings are significant, and will lead to poor decision-making. Exploiting our current state of knowledge of crash causation, crash counts are postulated to arise from three processes: observed network features, unobserved spatial effects, and ‘apparent’ random influences that reflect largely behavioral influences of drivers. It is argued; furthermore, that these three processes in theory can be modeled separately to gain deeper insight into crash causes, and that the model represents a more realistic depiction of reality than the state of practice NB regression. An admittedly imperfect empirical model that mixes three independent crash occurrence processes is shown to outperform the classical NB model. The questioning of current modeling assumptions and implications of the latent mixture model to current practice are the most important contributions of this paper, with an initial but rather vulnerable attempt to model the latent mixtures as a secondary contribution.

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.

Technological innovation and operational effectiveness : their role in achieving performance improvements

The purpose of this article is to examine the role of the alignment between technological innovation effectiveness and operational effectiveness after the implementation of enterprise information systems, and the impact of this alignment on the improvement in operational performance. Confirmatory factor analysis was used to examine structural relationships between the set of observed variables and the set of continuous latent variables. The findings from this research suggest that the dimensions stemming from technological innovation effectiveness such as system quality, information quality, service quality, user satisfaction and the performance objectives stemming from operational effectiveness such as cost, quality, reliability, flexibility and speed are important and significantly well-correlated factors. These factors promote the alignment between technological innovation effectiveness and operational effectiveness and should be the focus for managers in achieving effective implementation of technological innovations. In addition, there is a significant and direct influence of this alignment on the improvement of operational performance. The principal limitation of this study is that the findings are based on investigation of small sample size.

Pseudo-marginal algorithms with multiple CPUs

The emergence of pseudo-marginal algorithms has led to improved computational efficiency for dealing with complex Bayesian models with latent variables. Here an unbiased estimator of the likelihood replaces the true likelihood in order to produce a Bayesian algorithm that remains on the marginal space of the model parameter (with latent variables integrated out), with a target distribution that is still the correct posterior distribution. Very efficient proposal distributions can be developed on the marginal space relative to the joint space of model parameter and latent variables. Thus psuedo-marginal algorithms tend to have substantially better mixing properties. However, for pseudo-marginal approaches to perform well, the likelihood has to be estimated rather precisely. This can be difficult to achieve in complex applications. In this paper we propose to take advantage of multiple central processing units (CPUs), that are readily available on most standard desktop computers. Here the likelihood is estimated independently on the multiple CPUs, with the ultimate estimate of the likelihood being the average of the estimates obtained from the multiple CPUs. The estimate remains unbiased, but the variability is reduced. We compare and contrast two different technologies that allow the implementation of this idea, both of which require a negligible amount of extra programming effort. The superior performance of this idea over the standard approach is demonstrated on simulated data from a stochastic volatility model.

An investigation of schizotypy in injecting amphetamine users

A fully dimensional view of psychiatric disorder conceptualises schizotypy as both a continuous personality trait and an underlying vulnerability to the development of psychotic illness. Such a model would predict that the structure of schizotypal traits would closely parallel the structure of schizophrenia or psychosis. This was investigated in injecting amphetamine users (N = 322), a clinical population who have high rates of acute psychotic episodes and subclinical schizotypal experiences. Schizotypy was assessed using the Oxford-Liverpool Inventory of Feelings and Experiences (O-LIFE), and psychotic symptoms were assessed using the Brief Psychiatric Rating Scale (BPRS). Using confirmatory factor analysis, O-LIFE subscale scores were mapped onto latent variables with their more clinical counterparts from the BPRS. A four-factor model comprising positive schizotypy, disorganisation, negative schizotypy, and disinhibition provided the best model fit, consistent with prior research into the structure of schizotypy. The model provided a good fit to the data, lending support to the theory that schizotypy and psychotic symptoms map onto common underlying dimensions.

Alternate destinies for survey items destined for the island of misfit toys: An analysis of teachers' perceptions of NAPLAN

This is a methodological paper describing when and how manifest items dropped from a latent construct measurement model (e.g., factor analysis) can be retained for additional analysis. Presented are protocols for assessment for retention in the measurement model, evaluation of dropped items as potential items separate from the latent construct, and post hoc analyses that can be conducted using all retained (manifest or latent) variables. The protocols are then applied to data relating to the impact of the NAPLAN test. The variables examined are teachers’ achievement goal orientations and teachers’ perceptions of the impact of the test on curriculum and pedagogy. It is suggested that five attributes be considered before retaining dropped manifest items for additional analyses. (1) Items can be retained when employed in service of an established or hypothesized theoretical model. (2) Items should only be retained if sufficient variance is present in the data set. (3) Items can be retained when they provide a rational segregation of the data set into subsamples (e.g., a consensus measure). (4) The value of retaining items can be assessed using latent class analysis or latent mean analysis. (5) Items should be retained only when post hoc analyses with these items produced significant and substantive results. These suggested exploratory strategies are presented so that other researchers using survey instruments might explore their data in similar and more innovative ways. Finally, suggestions for future use are provided.