A sequential Monte Carlo algorithm to incorporate model uncertainty in Bayesian sequential design

Here we present a sequential Monte Carlo (SMC) algorithm that can be used for any one-at-a-time Bayesian sequential design problem in the presence of model uncertainty where discrete data are encountered. Our focus is on adaptive design for model discrimination but the methodology is applicable if one has a different design objective such as parameter estimation or prediction. An SMC algorithm is run in parallel for each model and the algorithm relies on a convenient estimator of the evidence of each model which is essentially a function of importance sampling weights. Other methods for this task such as quadrature, often used in design, suffer from the curse of dimensionality. Approximating posterior model probabilities in this way allows us to use model discrimination utility functions derived from information theory that were previously difficult to compute except for conjugate models. A major benefit of the algorithm is that it requires very little problem specific tuning. We demonstrate the methodology on three applications, including discriminating between models for decline in motor neuron numbers in patients suffering from neurological diseases such as Motor Neuron disease.

What explains the association between socioeconomic status and depression among Vietnamese adults?

Background Depression is a major public health problem worldwide and is currently ranked second to heart disease for years lost due to disability. For many decades, international research has found that depressive symptoms occur more frequently among low socioeconomic (SES) individuals than their more-advantaged peers. However, the reasons as to why those of low socioeconomic groups suffer more depressive symptoms are not well understood. Studies investigating the prevalence of depression and its association with SES emanate largely from developed countries, with little research among developing countries. In particular, there is a serious dearth of research on depression and no investigation of its association with SES in Vietnam. The aims of the research presented in this Thesis are to: estimate the prevalence of depressive symptoms among Vietnamese adults, examine the nature and extent of the association between SES and depression and to elucidate causal pathways linking SES to depressive symptoms Methods The research was conducted between September 2008 and November 2009 in Hue city in central Vietnam and used a combination of qualitative (in-depth interviews) and quantitative (survey) data collection methods. The qualitative study contributed to the development of the theoretical model and to the refinement of culturally-appropriate data collection instruments for the quantitative study. The main survey comprised a cross-sectional population–based survey with randomised cluster sampling. A sample of 1976 respondents aged between 25-55 years from ten randomly-selected residential zones (quarters) of Hue city completed the questionnaire (response rate 95.5%). Measures SES was classified using three indicators: education, occupation and income. The Center for Epidemiologic Studies-Depression (CES-D) scale was used to measure depressive symptoms (range0-51, mean=11.0, SD=8.5). Three cut-off points for the CES-D scores were applied: ‘at risk for clinical depression’ (16 or above), ‘depressive symptoms’ (above 21) and ‘depression’ (above 25). Six psychosocial indicators: life time trauma, chronic stress, recent life events, social support, self esteem, and mastery were hypothesized to mediate the association between SES and depressive symptoms. Analyses The prevalence of depressive symptoms were analysed using bivariate analyses. The multivariable analytic phase comprised of ordinary least squares regression, in accordance with Baron and Kenny’s three-step framework for mediation modeling. All analyses were adjusted for a range of confounders, including age, marital status, smoking, drinking and chronic diseases and the mediation models were stratified by gender. Results Among these Vietnamese adults, 24.3% were at or above the cut-off for being ‘at risk for clinical depression’, 11.9% were classified as having depressive symptoms and 6.8% were categorised as having depression. SES was inversely related to depressive symptoms: the least educated those with low occupational status or with the lowest incomes reported more depressive symptoms. Socioeconomicallydisadvantaged individuals were more likely to report experiencing stress (life time trauma, chronic stress or recent life events), perceived less social support and reported fewer personal resources (self esteem and mastery) than their moreadvantaged counterparts. These psychosocial resources were all significantly associated with depressive symptoms independent of SES. Each psychosocial factor showed a significant mediating effect on the association between SES and depressive symptoms. This was found for all measures of SES, and for males and females. In particular, personal resources (mastery, self esteem) and chronic stress accounted for a substantial proportion of the variation in depressive symptoms between socioeconomic groups. Social support and recent life events contributed modestly to socioeconomic differences in depressive symptoms, whereas lifetime trauma contributed the least to these inequalities. Conclusion This is the first known study in Vietnam or any developing country to systematically examine the extent to which psychosocial factors mediate the relationship between SES and depression. The study contributes new evidence regarding the burden of depression in Vietnam. The findings have practical relevance for advocacy, for mental health promotion and health-care services, and point to the need for programs that focus on building a sense of personal mastery and self esteem. More broadly, the work presented in this Thesis contributes to the international scientific literature on the social determinants of depression.

Use of Bayesian MUNE to show differing rate of loss of motor units in subgroups of ALS

Objectives To evaluate differences among patients with different clinical features of ALS, we used our Bayesian method of motor unit number estimation (MUNE). Methods We performed serial MUNE studies on 42 subjects who fulfilled the diagnostic criteria for ALS during the course of their illness. Subjects were classified into three subgroups according to whether they had typical ALS (with upper and lower motor neurone signs) or had predominantly upper motor neurone weakness with only minor LMN signs, or predominantly lower motor neurone weakness with only minor UMN signs. In all subjects we calculated the half life of MUs, defined as the expected time for the number of MUs to halve, in one or more of the abductor digiti minimi (ADM), abductor pollicis brevis (APB) and extensor digitorum brevis (EDB) muscles. Results The mean half life of MUs was less in subjects who had typical ALS with both upper and lower motor neurone signs than in those with predominantly upper motor neurone weakness or predominantly lower motor neurone weakness. In 18 subjects we analysed the estimated size of the MUs and demonstrated the appearance of large MUs in subjects with upper or lower motor neurone predominant weakness. We found that the appearance of large MUs was correlated with the half life of MUs. Conclusions Patients with different clinical features of ALS have different rates of loss and different sizes of MUs. Significance: These findings could indicate differences in disease pathogenesis.

Reaction to point and counterpoint : bold adventure or missed opportunity

The draft of the first stage of the national curriculum has now been published. Its final form to be presented in December 2010 should be the centrepiece of Labor’s Educational Revolution. All the other aspects – personal computers, new school buildings, rebates for uniforms and even the MySchool report card – are marginal to the prescription of what is to be taught and learnt in schools. The seven authors in this journal’s Point and Counterpoint (Curriculum Perspectives, 30(1) 2010, pp.53-74) raise a number of both large and small issues in education as a whole, and in science education more particularly. Two of them (Groves and McGarry) make brief reference to earlier attempts to achieve national curriculum in Australia. Those writing from New Zealand and USA will be unaware of just how ambitious this project is for Australia - a bold and overdue educational adventure or a foolish political decision destined to failure, as happened in the later 1970s and the 1990s.

Severity of driver injury and vehicle damage in traffic crashes at intersections: A Bayesian hierarchical analysis

Most crash severity studies ignored severity correlations between driver-vehicle units involved in the same crashes. Models without accounting for these within-crash correlations will result in biased estimates in the factor effects. This study developed a Bayesian hierarchical binomial logistic model to identify the significant factors affecting the severity level of driver injury and vehicle damage in traffic crashes at signalized intersections. Crash data in Singapore were employed to calibrate the model. Model fitness assessment and comparison using Intra-class Correlation Coefficient (ICC) and Deviance Information Criterion (DIC) ensured the suitability of introducing the crash-level random effects. Crashes occurring in peak time, in good street lighting condition, involving pedestrian injuries are associated with a lower severity, while those in night time, at T/Y type intersections, on right-most lane, and installed with red light camera have larger odds of being severe. Moreover, heavy vehicles have a better resistance on severe crash, while crashes involving two-wheel vehicles, young or aged drivers, and the involvement of offending party are more likely to result in severe injuries.

Applying Bayesian hierarchical models to examine motorcycle crashes at signalized intersections

Motorcycles are overrepresented in road traffic crashes and particularly vulnerable at signalized intersections. The objective of this study is to identify causal factors affecting the motorcycle crashes at both four-legged and T signalized intersections. Treating the data in time-series cross-section panels, this study explores different Hierarchical Poisson models and found that the model allowing autoregressive lag 1 dependent specification in the error term is the most suitable. Results show that the number of lanes at the four-legged signalized intersections significantly increases motorcycle crashes largely because of the higher exposure resulting from higher motorcycle accumulation at the stop line. Furthermore, the presence of a wide median and an uncontrolled left-turn lane at major roadways of four-legged intersections exacerbate this potential hazard. For T signalized intersections, the presence of exclusive right-turn lane at both major and minor roadways and an uncontrolled left-turn lane at major roadways of T intersections increases motorcycle crashes. Motorcycle crashes increase on high-speed roadways because they are more vulnerable and less likely to react in time during conflicts. The presence of red light cameras reduces motorcycle crashes significantly for both four-legged and T intersections. With the red-light camera, motorcycles are less exposed to conflicts because it is observed that they are more disciplined in queuing at the stop line and less likely to jump start at the start of green.

An estimate of road accident costs in Singapore

An earlier study by the Asian Development Bank (ADB) showed that the annual cost of road traffic accidents in 2001 was S$699.36 million which was 0.5% of the annual GDP. This paper attempts to update of the cost estimates of road traffic accidents. More precise methods of computing the human cost, lost output and property damage are adopted which grew in an annual cost of S$610.3 million or 0.338% of the annual GDP in 2003. A more conservative estimate of S$878,000 for fatal accident is also obtained, compared to the earlier figure of S$1.4 million. This study has shown that it is necessary to update the annual traffic accident costs regularly, as the figures vary with the number of accidents which change with time.

Bayesian hierarchical analysis on crash prediction models

Traditional crash prediction models, such as generalized linear regression models, are incapable of taking into account the multilevel data structure, which extensively exists in crash data. Disregarding the possible within-group correlations can lead to the production of models giving unreliable and biased estimates of unknowns. This study innovatively proposes a -level hierarchy, viz. (Geographic region level – Traffic site level – Traffic crash level – Driver-vehicle unit level – Vehicle-occupant level) Time level, to establish a general form of multilevel data structure in traffic safety analysis. To properly model the potential cross-group heterogeneity due to the multilevel data structure, a framework of Bayesian hierarchical models that explicitly specify multilevel structure and correctly yield parameter estimates is introduced and recommended. The proposed method is illustrated in an individual-severity analysis of intersection crashes using the Singapore crash records. This study proved the importance of accounting for the within-group correlations and demonstrated the flexibilities and effectiveness of the Bayesian hierarchical method in modeling multilevel structure of traffic crash data.

Hotspot Identification: A Full Bayesian Hierarchical Modeling Approach

This study proposes a full Bayes (FB) hierarchical modeling approach in traffic crash hotspot identification. The FB approach is able to account for all uncertainties associated with crash risk and various risk factors by estimating a posterior distribution of the site safety on which various ranking criteria could be based. Moreover, by use of hierarchical model specification, FB approach is able to flexibly take into account various heterogeneities of crash occurrence due to spatiotemporal effects on traffic safety. Using Singapore intersection crash data(1997-2006), an empirical evaluate was conducted to compare the proposed FB approach to the state-of-the-art approaches. Results show that the Bayesian hierarchical models with accommodation for site specific effect and serial correlation have better goodness-of-fit than non hierarchical models. Furthermore, all model-based approaches perform significantly better in safety ranking than the naive approach using raw crash count. The FB hierarchical models were found to significantly outperform the standard EB approach in correctly identifying hotspots.

A novel quadratic Edge-based Smoothed Conforming Point Interpolation Method (ES-CPIM) for elasticity problems

his paper formulates an edge-based smoothed conforming point interpolation method (ES-CPIM) for solid mechanics using the triangular background cells. In the ES-CPIM, a technique for obtaining conforming PIM shape functions (CPIM) is used to create a continuous and piecewise quadratic displacement field over the whole problem domain. The smoothed strain field is then obtained through smoothing operation over each smoothing domain associated with edges of the triangular background cells. The generalized smoothed Galerkin weak form is then used to create the discretized system equations. Numerical studies have demonstrated that the ES-CPIM possesses the following good properties: (1) ES-CPIM creates conforming quadratic PIM shape functions, and can always pass the standard patch test; (2) ES-CPIM produces a quadratic displacement field without introducing any additional degrees of freedom; (3) The results of ES-CPIM are generally of very high accuracy.

FGFR2 point mutations in 466 Endometrioid Endometrial Tumors : relationship with MSI, KRAS, PIK3CA, CTNNB1 mutations and Clinicopathological features

Mutations in multiple oncogenes including KRAS, CTNNB1, PIK3CA and FGFR2 have been identified in endometrial cancer. The aim of this study was to provide insight into the clinicopathological features associated with patterns of mutation in these genes, a necessary step in planning targeted therapies for endometrial cancer. 466 endometrioid endometrial tumors were tested for mutations in FGFR2, KRAS, CTNNB1, and PIK3CA. The relationships between mutation status, tumor microsatellite instability (MSI) and clinicopathological features including overall survival (OS) and disease-free survival (DFS) were evaluated using Kaplan-Meier survival analysis and Cox proportional hazard models. Mutations were identified in FGFR2 (48/466); KRAS (87/464); CTNNB1 (88/454) and PIK3CA (104/464). KRAS and FGFR2 mutations were significantly more common, and CTNNB1 mutations less common, in MSI positive tumors. KRAS and FGFR2 occurred in a near mutually exclusive pattern (p = 0.05) and, surprisingly, mutations in KRAS and CTNNB1 also occurred in a near mutually exclusive pattern (p = 0.0002). Multivariate analysis revealed that mutation in KRAS and FGFR2 showed a trend (p = 0.06) towards longer and shorter DFS, respectively. In the 386 patients with early stage disease (stage I and II), FGFR2 mutation was significantly associated with shorter DFS (HR = 3.24; 95% confidence interval, CI, 1.35-7.77; p = 0.008) and OS (HR = 2.00; 95% CI 1.09-3.65; p = 0.025) and KRAS was associated with longer DFS (HR = 0.23; 95% CI 0.05-0.97; p = 0.045). In conclusion, although KRAS and FGFR2 mutations share similar activation of the MAPK pathway, our data suggest very different roles in tumor biology. This has implications for the implementation of anti-FGFR or anti-MEK biologic therapies.

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.