Extensions of Bayesian Reliability Analysis by Using Imprecise Dirichlet Model

Event Abstract Back to Event 2nd level modelling in fMRI analysis with a clinically depressed sample - Comparisons between classical and Bayesian methods Peter Goodin1, 2*, Joseph Ciorciari1, Susan Rossell1, 2, Matt Hughes1 and Richard Nibbs1 1 Swinburne University, BPsyC, Australia 2 Monash Alfred Psychiatric Research Centre, Australia The use of the Frequentist statistics in fMRI analysis has been the mainstay of the field for the last 25 years. Several other methods have been developed as alternatives, including those based on Bayesian statistics. Bayesian analysis methods have the benefit of allowing interrelation of data through effect size and confidence thresholds, can be more robust to outlier data and may negate the need for stringent multiple comparison correction. When examining functional differences in those with a mental illness , this can lead to detection of more subtle activation that may be of importance. Depression is a disorder that despite a common theme of symptoms is also characterised by functional heterogeneities between individuals, making inferences using Frequentist methods sometimes difficult. Utilising both Frequentist and Bayesian 2nd level analysis methods offered by SPM8 , we examined differences in activation between a healthy control sample and those with major depressive disorder during a novel emotional processing n-back task. Activation using classical methods showed small differences in more posterior visual regions however this was only detectable with liberal thresholding (p = .001 uncorrected, k = 0). In contrast Bayesian analysis (y = 0, 95% confidence) uncovered widespread differences (including overlap with those areas found with the Frequentist method) in multiple regions implicated with the disorder. This suggests that using Bayesian methods in fMRI analysis with a clinical population could be extremely useful in detecting responses that may otherwise go unnoticed or under-represented in more traditional methods, however determination of effect size importance is paramount. Keywords: Depression, fMRI, working memory, Bayesian, Frequentist Conference: XII International Conference on Cognitive Neuroscience (ICON-XII), Brisbane, Queensland, Australia, 27 Jul - 31 Jul, 2014. Presentation Type: Poster Topic: Methods Development Citation: Goodin P, Ciorciari J, Rossell S, Hughes M and Nibbs R (2015). 2nd level modelling in fMRI analysis with a clinically depressed sample - Comparisons between classical and Bayesian methods. Conference Abstract: XII International Conference on Cognitive Neuroscience (ICON-XII). doi: 10.3389/conf.fnhum.2015.217.00203 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 19 Feb 2015; Published Online: 24 Apr 2015. * Correspondence: Mr. Peter Goodin, Swinburne University, BPsyC, Hawthorn, Australia, peter@hitiq.com Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Peter Goodin Joseph Ciorciari Susan Rossell Matt Hughes Richard Nibbs Google Peter Goodin Joseph Ciorciari Susan Rossell Matt Hughes Richard Nibbs Google Scholar Peter Goodin Joseph Ciorciari Susan Rossell Matt Hughes Richard Nibbs PubMed Peter Goodin Joseph Ciorciari Susan Rossell Matt Hughes Richard Nibbs Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.

ObjectiveTo show how a simple Bayesian analysis method can be used to improve the evidence base in patient populations where recruitment and retention are challenging.MethodsA Bayesian conjugate analysis method was...

Bayesian reliability analysis (BRA) technique has been actively used in reliability assessment for engineered systems. However, there are two key controversies surrounding the BRA: the reasonableness of the prior and the consistency among all data sets. These issues have been debated in Bayesian analysis for many years. As we observed, they have not been resolved satisfactorily. These controversies have seriously hindered the applications of BRA as a useful reliability analysis tool to support engineering design. In this paper, a Bayesian reliability analysis methodology with a prior and data validation and adjustment scheme (PDVAS) is developed to address these issues. As the part of the PDVAS development, a consistency measure is first defined that judges the level of consistency among all data sets including the prior. The consistency measure is then used to adjust either the prior or the data or both to the extent that the prior and the data are statistically consistent. This prior and data validation and adjustment scheme is developed for Binomial sampling with Beta prior, called Beta-Binomial Bayesian model. The properties of the scheme are presented and discussed that provides some insights of PDVAS. Various forms of the adjustment formulas are shown, and a selection framework of a specific formula, based on engineering design and analysis knowledge, is established. Several illustrative examples are presented, which show the reasonableness, effectiveness, and usefulness of PDVAS. General discussion of the scheme is offered to enhance the Bayesian reliability analysis in engineering design for reliability assessment.

Bayesian statistics assumes that there are specific parameteric distributions for the unknown parameters. It fits the probability model of interest by incorporating prior information regarding the unknown parameters and the likelihood function of the observed data. Moreover, Bayesian statistics as well as non-Bayesian methods produce good asymptotic results. Using WinBUGS and R language, a binomial logistic regression model of voting choice in the 2002 Taipei mayoral election is developed. Adding the prior information from the first panel to the estimation of the second panel, the Bayesian model yields sharper estimates concerning the election outcome. Additionally, the replication of data provides a model check and the baseline of the new observations. The methodological contribution of this paper is the ability to fit a binary logistic regression model with the observed data using the Bayesian inference.

Comparison of Bayesian survival analysis and Cox regression analysis in simulated and breast cancer data sets

Previous research showed that employing results from meta-analyses of relevant previous fMRI studies can improve the performance of voxelwise Bayesian second-level fMRI analysis. In this process, prior distributions for Bayesian analysis can be determined by information acquired from the meta-analyses. However, only image-based meta-analysis, which is not widely accessible to fMRI researchers due to the lack of shared statistical images, was tested in the previous study, so the applicability of the prior determination method proposed by the previous study might be limited. In the present study, whether determining prior distributions based on coordinate-based meta-analysis, which is widely accessible to researchers, can also improve the performance of Bayesian analysis, was examined. Three different types of coordinate-based meta-analyses, BrainMap and Ginger ALE, and NeuroQuery, were tested as information sources for prior determination. Five different datasets addressing three task conditions, i.e., working memory, speech, and face processing, were analyzed via Bayesian analysis with a meta-analysis informed prior distribution, Bayesian analysis with a default Cauchy prior adjusted for multiple comparisons, and frequentist analysis with familywise error correction. The findings from the aforementioned analyses suggest that use of coordinate-based meta-analysis also significantly enhanced performance of Bayesian analysis as did image-based meta-analysis.

Strange bayes indeed: uniform topological priors imply non-uniform clade priors

At the start of new operation, a production process is commonly unstable. Then, a process condition is into being stable gradually over time. For the purpose of shifting to mass production, the stability in a process should be evaluated. This paper proposes a method of evaluating the process stability based on Bayesian statistics and information theory. In Bayesian statistics, the knowledge for a process is renewed by deriving posterior distribution based on current prior distribution and observations. Here, equivalency between prior and posterior distributions could be considered to be a criterion for the stability in a process. It is needed to define difference between prior and posterior distributions in order to evaluate the equivalency between prior and posterior distributions. We first formulate the relation between the prior distribution and the posterior distribution for process mean using Bayesian statistics. Secondly, we evaluate the difference between the both distributions based on Kullback‐Leibler (K‐L) divergence in information theory. Finally, some numerical examples in the method of evaluating the stability in process mean are illustrated. Also, we discuss about a decision rule for the stability in process mean through the numerical investigation.

A crucial decision in designing a spatial sample for soil survey is the number of sampling locations required to answer, with sufficient accuracy and precision, the questions posed by decision makers at different levels of geographic aggregation. In the Indian Soil Health Card (SHC) scheme, many thousands of locations are sampled per district. In this paper the SHC data are used to estimate the mean of a soil property within a defined study area, e.g., a district, or the areal fraction of the study area where some condition is satisfied, e.g., exceedence of a critical level. The central question is whether this large sample size is needed for this aim. The sample size required for a given maximum length of a confidence interval can be computed with formulas from classical sampling theory, using a prior estimate of the variance of the property of interest within the study area. Similarly, for the areal fraction a prior estimate of this fraction is required. In practice we are uncertain about these prior estimates, and our uncertainty is not accounted for in classical sample size determination (SSD). This deficiency can be overcome with a Bayesian approach, in which the prior estimate of the variance or areal fraction is replaced by a prior distribution. Once new data from the sample are available, this prior distribution is updated to a posterior distribution using Bayes’ rule. The apparent problem with a Bayesian approach prior to a sampling campaign is that the data are not yet available. This dilemma can be solved by computing, for a given sample size, the predictive distribution of the data, given a prior distribution on the population and design parameter. Thus we do not have a single vector with data values, but a finite or infinite set of possible data vectors. As a consequence, we have as many posterior distribution functions as we have data vectors. This leads to a probability distribution of lengths or coverages of Bayesian credible intervals, from which various criteria for SSD can be derived. Besides the fully Bayesian approach, a mixed Bayesian-likelihood approach for SSD is available. This is of interest when, after the data have been collected, we prefer to estimate the mean from these data only, using the frequentist approach, ignoring the prior distribution. The fully Bayesian and mixed Bayesian-likelihood approach are illustrated for estimating the mean of log-transformed Zn and the areal fraction with Zn-deficiency, defined as Zn concentration <0.9 mg kg −1, in the thirteen districts of Andhra Pradesh state. The SHC data from 2015–2017 are used to derive prior distributions. For all districts the Bayesian and mixed Bayesian-likelihood sample sizes are much smaller than the current sample sizes. The hyperparameters of the prior distributions have a strong effect on the sample sizes. We discuss methods to deal with this. Even at the mandal (sub-district) level the sample size can almost always be reduced substantially. Clearly SHC over-sampled, and here we show how to reduce the effort while still providing information required for decision-making. R scripts for SSD are provided as supplementary material.

Over the past 20years, there has been increasing interest in the use of Bayesian statistical methods for the analysis of clinical trials used to support regulatory decisions. Bayesian methods for the analysis of clinical trials are an attractive option when good prior information is available. Yet, in many cases, prior information is scarce and only tentative or proprietary prior information exists. In these situations, it is necessary to use noninformative type or skeptical-type priors. We undertook a systematic study of Bayesian methods and applied them to 13 randomized clinical trials in metastatic breast cancer submitted to the U.S. Food and Drug Administration for registrational purposes. Across all 13 studies, there were a total of 10,521 patients using 10 experimental agents. Our results demonstrated that Bayesian analyses with noninformative priors provided similar results to more traditional analyses. We also found that early interim looks at the study results can vary widely based upon the type of prior used. Finally, we found that pre-defined threshold stopping rules need to be relatively strong to prevent trials from stopping very early. Our results suggest that, when prior information is limited and a noninformative prior is used, there is little numerical difference between Bayesian methods and more traditional analysis methods. Bayesian methods, however, may provide additional summaries of the data that are more easily interpretable than means and confidence intervals.

Modern epidemiologic studies permit investigation of the complex pathways that mediate effects of social, behavioral, and molecular factors on health outcomes. Conventional analytical approaches struggle with high-dimensional data, leading to high likelihoods of both false-positive and false-negative inferences. Herein, we describe a novel Bayesian pathway analysis approach, the algorithm for learning pathway structure (ALPS), which addresses key limitations in existing approaches to complex data analysis. ALPS uses prior information about pathways in concert with empirical data to identify and quantify complex interactions within networks of factors that mediate an association between an exposure and an outcome. We illustrate ALPS through application to a complex gene-drug interaction analysis in the Predictors of Breast Cancer Recurrence (ProBe CaRe) Study, a Danish cohort study of premenopausal breast cancer patients (2002-2011), for which conventional analyses severely limit the quality of inference.

Prior information and elicitation are the prerequisite in Bayesian reliability inference. Multiple sources for priors such as probability fitting based on historical data and expert judgment are often available when estimating the reliability of complex systems. This paper investigates the integration of multiple priors in Bayesian reliability analysis. Specifically, methods for multiple priors' integration based on Bayesian Melding are investigated. The performance of the studied methods with different prior information integration algorithms such as the arithmetic and geometric averaging is investigated. The impacts of the prior misspecification and the pooling parameter selection for prior integration algorithms are also studied. In numerical examples, simulation methods are applied for posterior reliability inference under the proposed prior integration methods and the performance of the two methods are compared.

As an important reliability metric in disc drive industries, the annual failure rate (AFR), estimated from reliability demonstration tests (RDTs), is often used to make business decisions. Due to limited test sample size and short test duration, estimating the AFR from direct test data using Weibull distribution fit may result in a wide confidence interval, raising concerns regarding the uncertainty of the AFR estimate. To improve the confidence of the estimate, this article presents a Bayesian posterior analysis approach to estimate the AFR. Prior distributions of the Weibull distribution's shape and scale parameters are presented based on historic test data. An analysis of real RDT data demonstrates that the Bayesian posterior estimate of the AFR can produce a significantly narrower confidence interval than direct Weibull fitting, promoting higher confidence to accept the AFR estimate. To evaluate the significance of the prior distribution parameters on the AFR estimate, a sensitivity analysis is presented with respect to each individual parameter. The results indicate that the standard deviation value of either β or η has a more significant impact on the AFR estimate than the mean value.

Bayesian methods have been proposed as a way of synthesizing all available evidence to inform decision making. However, few practical applications of the use of Bayesian methods for combining patient-level data (i.e., trial) with additional evidence (e.g., literature) exist in the cost-effectiveness literature. The objective of this study was to compare a Bayesian cost-effectiveness analysis using informative priors to a standard non-Bayesian nonparametric method to assess the impact of incorporating additional information into a cost-effectiveness analysis. Patient-level data from a previously published nonrandomized study were analyzed using traditional nonparametric bootstrap techniques and bivariate normal Bayesian models with vague and informative priors. Two different types of informative priors were considered to reflect different valuations of the additional evidence relative to the patient-level data (i.e., "face value" and "skeptical"). The impact of using different distributions and valuations was assessed in a sensitivity analysis. Models were compared in terms of incremental net monetary benefit (INMB) and cost-effectiveness acceptability frontiers (CEAFs). The bootstrapping and Bayesian analyses using vague priors provided similar results. The most pronounced impact of incorporating the informative priors was the increase in estimated life years in the control arm relative to what was observed in the patient-level data alone. Consequently, the incremental difference in life years originally observed in the patient-level data was reduced, and the INMB and CEAF changed accordingly. The results of this study demonstrate the potential impact and importance of incorporating additional information into an analysis of patient-level data, suggesting this could alter decisions as to whether a treatment should be adopted and whether more information should be acquired.

The aging of large concrete structures such as Nuclear Containment Buildings (NCB) or bridges involves a continuous strain evolution in time, which may affect their durability, safety and the safety of their environment. Then, the evaluation of structural integrity requires an accurate assessment of the long-term strain level. When considering probabilistic analysis of the delayed mechanical behavior of large concrete structures, the prediction results may present large uncertainties, which do not provide clear indicators aiming at supporting decisions related to structures’ maintenance. In this context, Bayesian updating enables to reduce uncertainties, by combining a prior state of knowledge with noisy monitoring data of the structure response. It requires the definition of a prior probability distribution, which summarizes all available information before collecting monitoring data. In former work concerning Bayesian approaches applied to the analysis of delayed strains, the prior distribution is usually defined through expert judgement, which constitutes a quite subjective process which may have a significant influence on Bayesian updating results. Moreover, the previously cited work involved strong hypotheses related to observation noise, which is usually assumed to be perfectly known. The present contribution aims at evaluating the influence of prior distributions defined by expert judgement on Bayesian updating results, through an illustrative case study of a well instrumented 1:3 scale NCB. The present work proposes also a Bayesian framework suitable for cases where the observation noise of data is unknown. The influence of the amount of monitoring data on the uncertainty reduction provided by Bayesian updating is also studied. Results underline that the modeling choices of the analyst are of paramount importance in the framework of long-term strains predictions, regardless the quantity of available data. Furthermore, results also suggest that Bayesian updating is well suitable for providing significant uncertainty reduction, even in the case of structures which dispose of a limited amount of monitoring data.