An event-based approach to validating solar wind speed predictions: high-speed enhancements in the Wang-Sheeley-Arge model

One of the primary goals of the Center for Integrated Space Weather Modeling (CISM) effort is to assess and improve prediction of the solar wind conditions in near‐Earth space, arising from both quasi‐steady and transient structures. We compare 8 years of L1 in situ observations to predictions of the solar wind speed made by the Wang‐Sheeley‐Arge (WSA) empirical model. The mean‐square error (MSE) between the observed and model predictions is used to reach a number of useful conclusions: there is no systematic lag in the WSA predictions, the MSE is found to be highest at solar minimum and lowest during the rise to solar maximum, and the optimal lead time for 1 AU solar wind speed predictions is found to be 3 days. However, MSE is shown to frequently be an inadequate “figure of merit” for assessing solar wind speed predictions. A complementary, event‐based analysis technique is developed in which high‐speed enhancements (HSEs) are systematically selected and associated from observed and model time series. WSA model is validated using comparisons of the number of hit, missed, and false HSEs, along with the timing and speed magnitude errors between the forecasted and observed events. Morphological differences between the different HSE populations are investigated to aid interpretation of the results and improvements to the model. Finally, by defining discrete events in the time series, model predictions from above and below the ecliptic plane can be used to estimate an uncertainty in the predicted HSE arrival times.

Estimating the hidden number of scrapie affected holdings in great Britain using a simple, truncated count model allowing for heterogeneity.

None of the current surveillance streams monitoring the presence of scrapie in Great Britain provide a comprehensive and unbiased estimate of the prevalence of the disease at the holding level. Previous work to estimate the under-ascertainment adjusted prevalence of scrapie in Great Britain applied multiple-list capture–recapture methods. The enforcement of new control measures on scrapie-affected holdings in 2004 has stopped the overlapping between surveillance sources and, hence, the application of multiple-list capture–recapture models. Alternative methods, still under the capture–recapture methodology, relying on repeated entries in one single list have been suggested in these situations. In this article, we apply one-list capture–recapture approaches to data held on the Scrapie Notifications Database to estimate the undetected population of scrapie-affected holdings with clinical disease in Great Britain for the years 2002, 2003, and 2004. For doing so, we develop a new diagnostic tool for indication of heterogeneity as well as a new understanding of the Zelterman and Chao’s lower bound estimators to account for potential unobserved heterogeneity. We demonstrate that the Zelterman estimator can be viewed as a maximum likelihood estimator for a special, locally truncated Poisson likelihood equivalent to a binomial likelihood. This understanding allows the extension of the Zelterman approach by means of logistic regression to include observed heterogeneity in the form of covariates—in case studied here, the holding size and country of origin. Our results confirm the presence of substantial unobserved heterogeneity supporting the application of our two estimators. The total scrapie-affected holding population in Great Britain is around 300 holdings per year. None of the covariates appear to inform the model significantly.

A hierarchical Bayesian model for predicting the functional consequences of amino-acid polymorphisms

Genetic polymorphisms in deoxyribonucleic acid coding regions may have a phenotypic effect on the carrier, e.g. by influencing susceptibility to disease. Detection of deleterious mutations via association studies is hampered by the large number of candidate sites; therefore methods are needed to narrow down the search to the most promising sites. For this, a possible approach is to use structural and sequence-based information of the encoded protein to predict whether a mutation at a particular site is likely to disrupt the functionality of the protein itself. We propose a hierarchical Bayesian multivariate adaptive regression spline (BMARS) model for supervised learning in this context and assess its predictive performance by using data from mutagenesis experiments on lac repressor and lysozyme proteins. In these experiments, about 12 amino-acid substitutions were performed at each native amino-acid position and the effect on protein functionality was assessed. The training data thus consist of repeated observations at each position, which the hierarchical framework is needed to account for. The model is trained on the lac repressor data and tested on the lysozyme mutations and vice versa. In particular, we show that the hierarchical BMARS model, by allowing for the clustered nature of the data, yields lower out-of-sample misclassification rates compared with both a BMARS and a frequen-tist MARS model, a support vector machine classifier and an optimally pruned classification tree.

Evaluation of a predictive model for Mycosphaerella graminicola for economic and environmental benefits

A method was developed to evaluate crop disease predictive models for their economic and environmental benefits. Benefits were quantified as the value of a prediction measured by costs saved and fungicide dose saved. The value of prediction was defined as the net gain made by using predictions, measured as the difference between a scenario where predictions are available and used and a scenario without prediction. Comparable 'with' and 'without' scenarios were created with the use of risk levels. These risk levels were derived from a probability distribution fitted to observed disease severities. These distributions were used to calculate the probability that a certain disease induced economic loss was incurred. The method was exemplified by using it to evaluate a model developed for Mycosphaerella graminicola risk prediction. Based on the value of prediction, the tested model may have economic and environmental benefits to growers if used to guide treatment decisions on resistant cultivars. It is shown that the value of prediction measured by fungicide dose saved and costs saved is constant with the risk level. The model could also be used to evaluate similar crop disease predictive models.

A predictive model for early-warning of Septoria leaf blotch on winter wheat

Disease-weather relationships influencing Septoria leaf blotch (SLB) preceding growth stage (GS) 31 were identified using data from 12 sites in the UK covering 8 years. Based on these relationships, an early-warning predictive model for SLB on winter wheat was formulated to predict the occurrence of a damaging epidemic (defined as disease severity of 5% or > 5% on the top three leaf layers). The final model was based on accumulated rain > 3 mm in the 80-day period preceding GS 31 (roughly from early-February to the end of April) and accumulated minimum temperature with a 0A degrees C base in the 50-day period starting from 120 days preceding GS 31 (approximately January and February). The model was validated on an independent data set on which the prediction accuracy was influenced by cultivar resistance. Over all observations, the model had a true positive proportion of 0.61, a true negative proportion of 0.73, a sensitivity of 0.83, and a specificity of 0.18. True negative proportion increased to 0.85 for resistant cultivars and decreased to 0.50 for susceptible cultivars. Potential fungicide savings are most likely to be made with resistant cultivars, but such benefits would need to be identified with an in-depth evaluation.

Estimating the hidden number of scrapie affected holdings in great Britain using a simple, truncated count model allowing for heterogeneity

None of the current surveillance streams monitoring the presence of scrapie in Great Britain provide a comprehensive and unbiased estimate of the prevalence of the disease at the holding level. Previous work to estimate the under-ascertainment adjusted prevalence of scrapie in Great Britain applied multiple-list capture-recapture methods. The enforcement of new control measures on scrapie-affected holdings in 2004 has stopped the overlapping between surveillance sources and, hence, the application of multiple-list capture-recapture models. Alternative methods, still under the capture-recapture methodology, relying on repeated entries in one single list have been suggested in these situations. In this article, we apply one-list capture-recapture approaches to data held on the Scrapie Notifications Database to estimate the undetected population of scrapie-affected holdings with clinical disease in Great Britain for the years 2002, 2003, and 2004. For doing so, we develop a new diagnostic tool for indication of heterogeneity as well as a new understanding of the Zelterman and Chao's lower bound estimators to account for potential unobserved heterogeneity. We demonstrate that the Zelterman estimator can be viewed as a maximum likelihood estimator for a special, locally truncated Poisson likelihood equivalent to a binomial likelihood. This understanding allows the extension of the Zelterman approach by means of logistic regression to include observed heterogeneity in the form of covariates-in case studied here, the holding size and country of origin. Our results confirm the presence of substantial unobserved heterogeneity supporting the application of our two estimators. The total scrapie-affected holding population in Great Britain is around 300 holdings per year. None of the covariates appear to inform the model significantly.

A Bayesian approach for dose-escalation in a phase I clinical trial incorporating pharmacodynamic endpoints

Bayesian decision procedures have already been proposed for and implemented in Phase I dose-escalation studies in healthy volunteers. The procedures have been based on pharmacokinetic responses reflecting the concentration of the drug in blood plasma and are conducted to learn about the dose-response relationship while avoiding excessive concentrations. However, in many dose-escalation studies, pharmacodynamic endpoints such as heart rate or blood pressure are observed, and it is these that should be used to control dose-escalation. These endpoints introduce additional complexity into the modeling of the problem relative to pharmacokinetic responses. Firstly, there are responses available following placebo administrations. Secondly, the pharmacodynamic responses are related directly to measurable plasma concentrations, which in turn are related to dose. Motivated by experience of data from a real study conducted in a conventional manner, this paper presents and evaluates a Bayesian procedure devised for the simultaneous monitoring of pharmacodynamic and pharmacokinetic responses. Account is also taken of the incidence of adverse events. Following logarithmic transformations, a linear model is used to relate dose to the pharmacokinetic endpoint and a quadratic model to relate the latter to the pharmacodynamic endpoint. A logistic model is used to relate the pharmacokinetic endpoint to the risk of an adverse event.

A Monte Carlo Approach for the Cook -Torrance Model

In this work we consider the rendering equation derived from the illumination model called Cook-Torrance model. A Monte Carlo (MC) estimator for numerical treatment of the this equation, which is the Fredholm integral equation of second kind, is constructed and studied.

Hammerstein model identification algorithm using Bezier-Bernstein approximation

A new identification algorithm is introduced for the Hammerstein model consisting of a nonlinear static function followed by a linear dynamical model. The nonlinear static function is characterised by using the Bezier-Bernstein approximation. The identification method is based on a hybrid scheme including the applications of the inverse of de Casteljau's algorithm, the least squares algorithm and the Gauss-Newton algorithm subject to constraints. The related work and the extension of the proposed algorithm to multi-input multi-output systems are discussed. Numerical examples including systems with some hard nonlinearities are used to illustrate the efficacy of the proposed approach through comparisons with other approaches.