Optimal Bayesian experimental design for models with intractable likelihoods using indirect inference applied to biological process models

This paper addresses the problem of determining optimal designs for biological process models with intractable likelihoods, with the goal of parameter inference. The Bayesian approach is to choose a design that maximises the mean of a utility, and the utility is a function of the posterior distribution. Therefore, its estimation requires likelihood evaluations. However, many problems in experimental design involve models with intractable likelihoods, that is, likelihoods that are neither analytic nor can be computed in a reasonable amount of time. We propose a novel solution using indirect inference (II), a well established method in the literature, and the Markov chain Monte Carlo (MCMC) algorithm of Müller et al. (2004). Indirect inference employs an auxiliary model with a tractable likelihood in conjunction with the generative model, the assumed true model of interest, which has an intractable likelihood. Our approach is to estimate a map between the parameters of the generative and auxiliary models, using simulations from the generative model. An II posterior distribution is formed to expedite utility estimation. We also present a modification to the utility that allows the Müller algorithm to sample from a substantially sharpened utility surface, with little computational effort. Unlike competing methods, the II approach can handle complex design problems for models with intractable likelihoods on a continuous design space, with possible extension to many observations. The methodology is demonstrated using two stochastic models; a simple tractable death process used to validate the approach, and a motivating stochastic model for the population evolution of macroparasites.

The SEA-CALIPSO volcano imaging experiment at Montserrat : plans, campaigns at sea and on land, scientific results, and lessons learned

Since 1995 the eruption of the andesitic Soufrière Hills Volcano (SHV), Montserrat, has been studied in substantial detail. As an important contribution to this effort, the Seismic Experiment with Airgunsource-Caribbean Andesitic Lava Island Precision Seismo-geodetic Observatory (SEA-CALIPSO) experiment was devised to image the arc crust underlying Montserrat, and, if possible, the magma system at SHV using tomography and reflection seismology. Field operations were carried out in October–December 2007, with deployment of 238 seismometers on land supplementing seven volcano observatory stations, and with an array of 10 ocean-bottom seismometers deployed offshore. The RRS James Cook on NERC cruise JC19 towed a tuned airgun array plus a digital 48-channel streamer on encircling and radial tracks for 77 h about Montserrat during December 2007, firing 4414 airgun shots and yielding about 47 Gb of data. The main objecctives of the experiment were achieved. Preliminary analyses of these data published in 2010 generated images of heterogeneous high-velocity bodies representing the cores of volcanoes and subjacent intrusions, and shallow areas of low velocity on the flanks of the island that reflect volcaniclastic deposits and hydrothermal alteration. The resolution of this preliminary work did not extend beyond 5 km depth. An improved three-dimensional (3D) seismic velocity model was then obtained by inversion of 181 665 first-arrival travel times from a more-complete sampling of the dataset, yielding clear images to 7.5 km depth of a low-velocity volume that was interpreted as the magma chamber which feeds the current eruption, with an estimated volume 13 km3. Coupled thermal and seismic modelling revealed properties of the partly crystallized magma. Seismic reflection analyses aimed at imaging structures under southern Montserrat had limited success, and suggest subhorizontal layering interpreted as sills at a depth of between 6 and 19 km. Seismic reflection profiles collected offshore reveal deep fans of volcaniclastic debris and fault offsets, leading to new tectonic interpretations. This chapter presents the project goals and planning concepts, describes in detail the campaigns at sea and on land, summarizes the major results, and identifies the key lessons learned.

Analysis of two authorization protocols using Colored Petri Nets

To prevent unauthorized access to protected trusted platform module (TPM) objects, authorization protocols, such as the object-specific authorization protocol (OSAP), have been introduced by the trusted computing group (TCG). By using OSAP, processes trying to gain access to the protected TPM objects need to prove their knowledge of relevant authorization data before access to the objects can be granted. Chen and Ryan’s 2009 analysis has demonstrated OSAP’s authentication vulnerability in sessions with shared authorization data. They also proposed the Session Key Authorization Protocol (SKAP) with fewer stages as an alternative to OSAP. Chen and Ryan’s analysis of SKAP using ProVerif proves the authentication property. The purpose of this paper was to examine the usefulness of Colored Petri Nets (CPN) and CPN Tools for security analysis. Using OSAP and SKAP as case studies, we construct intruder and authentication property models in CPN. CPN Tools is used to verify the authentication property using a Dolev–Yao-based model. Verification of the authentication property in both models using the state space tool produces results consistent with those of Chen and Ryan.

A review of modern computational algorithms for Bayesian optimal design

Bayesian experimental design is a fast growing area of research with many real-world applications. As computational power has increased over the years, so has the development of simulation-based design methods, which involve a number of algorithms, such as Markov chain Monte Carlo, sequential Monte Carlo and approximate Bayes methods, facilitating more complex design problems to be solved. The Bayesian framework provides a unified approach for incorporating prior information and/or uncertainties regarding the statistical model with a utility function which describes the experimental aims. In this paper, we provide a general overview on the concepts involved in Bayesian experimental design, and focus on describing some of the more commonly used Bayesian utility functions and methods for their estimation, as well as a number of algorithms that are used to search over the design space to find the Bayesian optimal design. We also discuss other computational strategies for further research in Bayesian optimal design.

Spatial-temporal epidemiological analyses of two sympatric, co-endemic alphaviral diseases in Queensland, Australia

Background: The two most reported mosquito-borne diseases in Queensland, a northern state of Australia, are Ross River virus (RRV) disease and Barmah Forest virus (BFV) disease. Both diseases are endemic in Queensland and have similar clinical symptoms and comparable transmission cycles involving a complex inter-relationship between human hosts, various mosquito vectors, and a range of nonhuman vertebrate hosts, including marsupial mammals that are unique to the Australasian region. Although these viruses are thought to share similar vectors and vertebrate hosts, RRV is four times more prevalent than BFV in Queensland. Methods: We performed a retrospective analysis of BFV and RRV human disease notification data collected from 1995 to 2007 in Queensland to ascertain whether there were differences in the incidence patterns of RRV and BFV disease. In particular, we compared the temporal incidence and spatial distribution of both diseases and considered the relationship between their disease dynamics. We also investigated whether a peak in BFV incidence during spring was indicative of the following RRV and BFV transmission season incidence levels. Results: Although there were large differences in the notification rates of the two diseases, they had similar annual temporal patterns, but there were regional variations between the length and magnitude of the transmission seasons. During periods of increased disease activity, however, there was no association between the dynamics of the two diseases. Conclusions: The results from this study suggest that while RRV and BFV share similar mosquito vectors, there are significant differences in the ecology of these viruses that result in different epidemic patterns of disease incidence. Further investigation is required into the ecology of each virus to determine which factors are important in promoting RRV and BFV disease outbreaks.

Outbreak detection algorithms for seasonal disease data : a case study using Ross River virus disease

Background Detection of outbreaks is an important part of disease surveillance. Although many algorithms have been designed for detecting outbreaks, few have been specifically assessed against diseases that have distinct seasonal incidence patterns, such as those caused by vector-borne pathogens. Methods We applied five previously reported outbreak detection algorithms to Ross River virus (RRV) disease data (1991-2007) for the four local government areas (LGAs) of Brisbane, Emerald, Redland and Townsville in Queensland, Australia. The methods used were the Early Aberration Reporting System (EARS) C1, C2 and C3 methods, negative binomial cusum (NBC), historical limits method (HLM), Poisson outbreak detection (POD) method and the purely temporal SaTScan analysis. Seasonally-adjusted variants of the NBC and SaTScan methods were developed. Some of the algorithms were applied using a range of parameter values, resulting in 17 variants of the five algorithms. Results The 9,188 RRV disease notifications that occurred in the four selected regions over the study period showed marked seasonality, which adversely affected the performance of some of the outbreak detection algorithms. Most of the methods examined were able to detect the same major events. The exception was the seasonally-adjusted NBC methods that detected an excess of short signals. The NBC, POD and temporal SaTScan algorithms were the only methods that consistently had high true positive rates and low false positive and false negative rates across the four study areas. The timeliness of outbreak signals generated by each method was also compared but there was no consistency across outbreaks and LGAs. Conclusions This study has highlighted several issues associated with applying outbreak detection algorithms to seasonal disease data. In lieu of a true gold standard, a quantitative comparison is difficult and caution should be taken when interpreting the true positives, false positives, sensitivity and specificity.

Refining a teaching pattern: Reflection around artefacts

This book is about understanding the nature and application of reflection in higher education. It provides a theoretical model to guide the implementation of reflective learning and reflective practice across multiple disciplines and international contexts in higher education. The book presents research into the ways in which reflection is both considered and implemented in different ways across different professional disciplines, while maintaining a common purpose to transform and improve learning and/or practice. Chapter 13 'Refining a Teaching Pattern: Reflection Around Artefacts' explores reflective practices of an artefact, in this case fashion design garment samples.

Abundance and prevalence of Aedes aegypti immatures and relationships with household water storage in rural areas in southern Viet Nam

Since 2000, the Government of Viet Nam has committed to provide rural communities with increased access to safe water through a variety of household water supply schemes (wells, ferrocement tanks and jars) and piped water schemes. One possible, unintended consequence of these schemes is the concomitant increase in water containers that may serve as habitats for dengue mosquito immatures, principally Aedes aegypti. To assess these possible impacts we undertook detailed household surveys of Ae. aegypti immatures, water storage containers and various socioeconomic factors in three rural communes in southern Viet Nam. Positive relationships between the numbers of household water storage containers and the prevalence and abundance of Ae. aegypti immatures were found. Overall, water storage containers accounted for 92–97% and 93–96% of the standing crops of III/IV instars and pupae, respectively. Interestingly, households with higher socioeconomic levels had significantly higher numbers of water storage containers and therefore greater risk of Ae. aegypti infestation. Even after provision of piped water to houses, householders continued to store water in containers and there was no observed decrease in water storage container abundance in these houses, compared to those that relied entirely on stored water. These findings highlight the householders’ concerns about the limited availability of water and their strong behavoural patterns associated with storage of water. We conclude that household water storage container availability is a major risk factor for infestation with Ae. aegypti immatures, and that recent investment in rural water supply infrastructure are unlikely to mitigate this risk, at least in the short term.

Quality assurance of aerial applications of larvicides for mosquito control : effects of granule and catch tray size on field monitoring programs

Aerial applications of granular insecticides are preferable because they can effectively penetrate vegetation, there is less drift, and no loss of product due to evaporation. We aimed to 1) assess the field efficacy ofVectoBac G to control Aedes vigilax (Skuse) in saltmarsh pools, 2) develop a stochastic-modeling procedure to monitor application quality, and 3) assess the distribution of VectoBac G after an aerial application. Because ground-based studies with Ae. vigilax immatures found that VectoBac G provided effective control below the recommended label rate of 7 kg/ha, we trialed a nominated aerial rate of 5 kg/ha as a case study. Our distribution pattern modeling method indicated that the variability in the number of VectoBac G particles captured in catch-trays was greater than expected for 5 kg/ha and that the widely accepted contour mapping approach to visualize the deposition pattern provided spurious results and therefore was not statistically appropriate. Based on the results of distribution pattern modeling, we calculated the catch tray size required to analyze the distribution of aerially applied granular formulations. The minimum catch tray size for products with large granules was 4 m2 for Altosid pellets and 2 m2 for VectoBac G. In contrast, the minimum catch-tray size for Altosid XRG, Aquabac G, and Altosand, with smaller granule sizes, was 1 m2. Little gain in precision would be made by increasing the catch-tray size further, when the increased workload and infrastructure is considered. Our improved methods for monitoring the distribution pattern of aerially applied granular insecticides can be adapted for use by both public health and agricultural contractors.

Eccentric hamstring strength and hamstring injury risk in Australian footballers

Purpose Is eccentric hamstring strength and between limb imbalance in eccentric strength, measured during the Nordic hamstring exercise, a risk factor for hamstring strain injury (HSI)? Methods Elite Australian footballers (n=210) from five different teams participated. Eccentric hamstring strength during the Nordic was taken at the commencement and conclusion of preseason training and in season. Injury history and demographic data were also collected. Reports on prospectively occurring HSIs were completed by team medical staff. Relative risk (RR) was determined for univariate data and logistic regression was employed for multivariate data. Results Twenty-eight HSIs were recorded. Eccentric hamstring strength below 256N at the start of preseason and 279N at the end of preseason increased risk of future HSI 2.7 (relative risk, 2.7; 95% confidence interval, 1.3 to 5.5; p = 0.006) and 4.3 fold (relative risk, 4.3; 95% confidence interval, 1.7 to 11.0; p = 0.002) respectively. Between limb imbalance in strength of greater than 10% did not increase the risk of future HSI. Univariate analysis did not reveal a significantly greater relative risk for future HSI in athletes who had sustained a lower limb injury of any kind within the last 12 months. Logistic regression revealed interactions between both athlete age and history of HSI with eccentric hamstring strength, whereby the likelihood of future HSI in older athletes or athletes with a history of HSI was reduced if an athlete had high levels of eccentric strength. Conclusion Low levels of eccentric hamstring strength increased the risk of future HSI. Interaction effects suggest that the additional risk of future HSI associated with advancing age or previous injury was mitigated by higher levels of eccentric hamstring strength.

Antisocial behaviour orders : Unanticipated directions in social network site development

Abstract: Social network technologies, as we know them today have become a popular feature of everyday life for many people. As their name suggests, their underlying premise is to enable people to connect with each other for a variety of purposes. These purposes however, are generally thought of in a positive fashion. Based on a multi-method study of two online environments, Habbo Hotel and Second Life, which incorporate social networking functionality, we she light on forms of what can be conceptualized as antisocial behaviours and the rationales for these. Such behaviours included: scamming, racist/homophobic attacks, sim attacks, avatar attacks, non-conformance to contextual norms, counterfeiting and unneighbourly behaviour. The rationales for sub behaviours included: profit, fun, status building, network disruption, accidental acts and prejudice. Through our analysis we are able to comment upon the difficulties of defining antisocial behaviour in such environments, particularly when such environments are subject to interpretation vis their use and expected norms. We also point to the problems we face in conducting our public and private lives given the role ICTs are playing in the convergence of these two spaces and also the convergence of ICTs themselves.

An evaluation of crowd counting methods, features and regression models

Existing crowd counting algorithms rely on holistic, local or histogram based features to capture crowd properties. Regression is then employed to estimate the crowd size. Insufficient testing across multiple datasets has made it difficult to compare and contrast different methodologies. This paper presents an evaluation across multiple datasets to compare holistic, local and histogram based methods, and to compare various image features and regression models. A K-fold cross validation protocol is followed to evaluate the performance across five public datasets: UCSD, PETS 2009, Fudan, Mall and Grand Central datasets. Image features are categorised into five types: size, shape, edges, keypoints and textures. The regression models evaluated are: Gaussian process regression (GPR), linear regression, K nearest neighbours (KNN) and neural networks (NN). The results demonstrate that local features outperform equivalent holistic and histogram based features; optimal performance is observed using all image features except for textures; and that GPR outperforms linear, KNN and NN regression

Reflexive writers : re-thinking writing development and assessment in schools

Writing is a complex and highly individual activity, which is approached in different ways by different writers. Writers reflexively mediate subjective and objective conditions in specific and nuanced ways to produce a product in time and place. This paper uses a critical realist theory of reflexivity to argue that the teaching and assessment of writing must account for the different ways that students manage and make decisions in their writing. Data from linguistically and culturally diverse primary students in Australia are used to illustrate how four distinct reflexive modalities constitute the ways in which students approach writing. The paper offers a new approach to assessing writing for and of learning that considers writers as reflexive and agentic in different ways. It posits the importance of making visible and explicit the context and reflexive decision-making as writers shape a product for a purpose and audience.

Biceps femoris long-head architecture: A reliability and retrospective injury study

Purpose: To determine i) the reliability of two-dimensional ultrasonography for the assessment of biceps femoris long head (BFlh) architectural characteristics; ii) if limbs with a history of strain injury in the BFlh display different architecture and eccentric strength compared to uninjured limbs. Methods: This case-control study (control [n=20], injured group [n=16], males) assessed the BFlh architecture at rest and during graded isometric contractions using two-dimensional ultrasonography. The control group were assessed three times (>24hrs apart) to determine reliability. Previously injured individuals were evaluated once. Results The assessment of BFlh architecture was highly reliable (intraclass correlations >0.90). Fascicle length (p<0.001; d range: 0.67 to 1.34) and fascicle length relative to muscle thickness (p<0.001; d range: 0.58 to 0.85) of the previously injured BFlh were significantly less than the contralateral uninjured BFlh at all intensities. Pennation angle of the previously injured BFlh was significantly greater (p<0.001; d range: 0.62 to 0.88) than the contralateral uninjured BFlh at all intensities. Eccentric strength in the previously injured limb was significantly lower than the contralateral limb (-15.4%; -52.5N; 95% CI=-28.45 to -76.23; p<0.001, d=0.56). Conclusion These data indicate that two-dimensional ultrasonography is reliable for assessing BFlh architecture at rest and during graded isometric contractions. Fascicle length, fascicle length relative to muscle thickness and pennation angle are significantly different in previously injured BFlh compared to an uninjured contralateral BFlh. Eccentric strength of the previously injured limb is also significantly lower than the uninjured contralateral limb. These findings have implications for rehabilitation and injury prevention practices which should consider altered architectural characteristics.