Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A Simple Method for Comparing Complex Models: Bayesian Model Comparison for Hierarchical Multinomial Processing Tree Models Using Warp-III Bridge Sampling.

ABSTRACT: Multinomial processing trees (MPTs) are a popular class of cognitive models for categorical data. Typically, researchers compare several MPTs, each equipped with many parameters, especially when the models are implemented in a hierarchical framework. A Bayesian solution is to compute posterior model probabilities and Bayes factors. Both quantities, however, rely on the marginal likelihood, a high-dimensional integral that cannot be evaluated analytically. In this case study, we show how Warp-III bridge sampling can be used to compute the marginal likelihood for hierarchical MPTs. We illustrate the procedure with two published data sets and demonstrate how Warp-III facilitates Bayesian model averaging.

SUBMITTER: Gronau QF

PROVIDER: S-EPMC6684497 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A Simple Method for Comparing Complex Models: Bayesian Model Comparison for Hierarchical Multinomial Processing Tree Models Using Warp-III Bridge Sampling.

Gronau Quentin F QF Wagenmakers Eric-Jan EJ Heck Daniel W DW Matzke Dora D

Psychometrika 20181127 1

Multinomial processing trees (MPTs) are a popular class of cognitive models for categorical data. Typically, researchers compare several MPTs, each equipped with many parameters, especially when the models are implemented in a hierarchical framework. A Bayesian solution is to compute posterior model probabilities and Bayes factors. Both quantities, however, rely on the marginal likelihood, a high-dimensional integral that cannot be evaluated analytically. In this case study, we show how Warp-III ...[more]

PMID: 30483923

Similar Datasets

MicroBVS: Dirichlet-tree multinomial regression models with Bayesian variable selection - an R package.

Project description:BackgroundUnderstanding the relation between the human microbiome and modulating factors, such as diet, may help researchers design intervention strategies that promote and maintain healthy microbial communities. Numerous analytical tools are available to help identify these relations, oftentimes via automated variable selection methods. However, available tools frequently ignore evolutionary relations among microbial taxa, potential relations between modulating factors, as well as model selection uncertainty.ResultsWe present MicroBVS, an R package for Dirichlet-tree multinomial models with Bayesian variable selection, for the identification of covariates associated with microbial taxa abundance data. The underlying Bayesian model accommodates phylogenetic structure in the abundance data and various parameterizations of covariates' prior probabilities of inclusion.ConclusionWhile developed to study the human microbiome, our software can be employed in various research applications, where the aim is to generate insights into the relations between a set of covariates and compositional data with or without a known tree-like structure.

| S-EPMC7359232 | biostudies-literature

Testing Interactions in Multinomial Processing Tree Models.

Project description:Multinomial processing tree (MPT) models allow testing hypotheses on latent psychological processes that underlie human behavior. However, past applications of this model class have mainly been restricted to the analysis of main effects. In this paper, we adopt the interaction concept as defined in log-linear models and show why it is appropriate for MPT models. We then explain how to implement and test ordinal and disordinal two-way interaction hypotheses in MPT models. We also show how our method generalizes to higher-order interactions involving three or more factors. An empirical example from source memory and aging demonstrates the applicability of this method and allows for directly testing the associative deficit theory that age differences are larger in associative (e.g., source) memory as opposed to item memory. Throughout the paper, we explain how most analytic steps can be easily implemented in the freely available software multiTree.

| S-EPMC6837999 | biostudies-literature

The use of sampling weights in Bayesian hierarchical models for small area estimation.

Project description:Hierarchical modeling has been used extensively for small area estimation. However, design weights that are required to reflect complex surveys are rarely considered in these models. We develop computationally efficient, Bayesian spatial smoothing models that acknowledge the design weights. Computation is carried out using the integrated nested Laplace approximation, which is fast. An extensive simulation study is presented that considers the effects of non-response and non-random selection of individuals, allowing examination of the impact of ignoring the design weights and the benefits of spatial smoothing. The results show that, when compared with standard approaches, mean squared error can be greatly reduced with the proposed methods. Bias reduction occurs through the inclusion of the design weights, with variance reduction being achieved through hierarchical smoothing. We analyze data from the Washington State 2006 Behavioral Risk Factor Surveillance System. The models are easily and quickly fitted within the R environment, using existing packages.

| S-EPMC4357363 | biostudies-literature

Goodness-of-fit diagnostics for Bayesian hierarchical models.

Project description:This article proposes methodology for assessing goodness of fit in Bayesian hierarchical models. The methodology is based on comparing values of pivotal discrepancy measures (PDMs), computed using parameter values drawn from the posterior distribution, to known reference distributions. Because the resulting diagnostics can be calculated from standard output of Markov chain Monte Carlo algorithms, their computational costs are minimal. Several simulation studies are provided, each of which suggests that diagnostics based on PDMs have higher statistical power than comparable posterior-predictive diagnostic checks in detecting model departures. The proposed methodology is illustrated in a clinical application; an application to discrete data is described in supplementary material.

| S-EPMC3276744 | biostudies-literature

Bayesian Hierarchical Random Effects Models in Forensic Science.

Project description:Statistical modeling of the evaluation of evidence with the use of the likelihood ratio has a long history. It dates from the Dreyfus case at the end of the nineteenth century through the work at Bletchley Park in the Second World War to the present day. The development received a significant boost in 1977 with a seminal work by Dennis Lindley which introduced a Bayesian hierarchical random effects model for the evaluation of evidence with an example of refractive index measurements on fragments of glass. Many models have been developed since then. The methods have now been sufficiently well-developed and have become so widespread that it is timely to try and provide a software package to assist in their implementation. With that in mind, a project (SAILR: Software for the Analysis and Implementation of Likelihood Ratios) was funded by the European Network of Forensic Science Institutes through their Monopoly programme to develop a software package for use by forensic scientists world-wide that would assist in the statistical analysis and implementation of the approach based on likelihood ratios. It is the purpose of this document to provide a short review of a small part of this history. The review also provides a background, or landscape, for the development of some of the models within the SAILR package and references to SAILR as made as appropriate.

| S-EPMC5911710 | biostudies-literature

Estimating tree height-diameter models with the Bayesian method.

Project description:Six candidate height-diameter models were used to analyze the height-diameter relationships. The common methods for estimating the height-diameter models have taken the classical (frequentist) approach based on the frequency interpretation of probability, for example, the nonlinear least squares method (NLS) and the maximum likelihood method (ML). The Bayesian method has an exclusive advantage compared with classical method that the parameters to be estimated are regarded as random variables. In this study, the classical and Bayesian methods were used to estimate six height-diameter models, respectively. Both the classical method and Bayesian method showed that the Weibull model was the "best" model using data1. In addition, based on the Weibull model, data2 was used for comparing Bayesian method with informative priors with uninformative priors and classical method. The results showed that the improvement in prediction accuracy with Bayesian method led to narrower confidence bands of predicted value in comparison to that for the classical method, and the credible bands of parameters with informative priors were also narrower than uninformative priors and classical method. The estimated posterior distributions for parameters can be set as new priors in estimating the parameters using data2.

| S-EPMC3953559 | biostudies-other

Evaluating scaling models in biology using hierarchical Bayesian approaches.

Project description:Theoretical models for allometric relationships between organismal form and function are typically tested by comparing a single predicted relationship with empirical data. Several prominent models, however, predict more than one allometric relationship, and comparisons among alternative models have not taken this into account. Here we evaluate several different scaling models of plant morphology within a hierarchical Bayesian framework that simultaneously fits multiple scaling relationships to three large allometric datasets. The scaling models include: inflexible universal models derived from biophysical assumptions (e.g. elastic similarity or fractal networks), a flexible variation of a fractal network model, and a highly flexible model constrained only by basic algebraic relationships. We demonstrate that variation in intraspecific allometric scaling exponents is inconsistent with the universal models, and that more flexible approaches that allow for biological variability at the species level outperform universal models, even when accounting for relative increases in model complexity.

| S-EPMC2730548 | biostudies-literature

Bayesian hierarchical latent class models for estimating diagnostic accuracy.

Project description:The diagnostic accuracy of a test or rater has a crucial impact on clinical decision making. The assessment of diagnostic accuracy for multiple tests or raters also merits much attention. A Bayesian hierarchical conditional independence latent class model for estimating sensitivities and specificities for a large group of tests or raters is proposed, which is applicable to both with-gold-standard and without-gold-standard situations. Through the hierarchical structure, not only are the sensitivities and specificities of individual tests estimated, but also the diagnostic performance of the whole group of tests. For a small group of tests or raters, the proposed model is further extended by introducing pairwise covariances between tests to improve the fitting and to allow for more modeling flexibility. Correlation residual analysis is applied to detect any significant covariance between multiple tests. Just Another Gibbs Sampler (JAGS) implementation is efficiently adopted for both models. Three real data sets from literature are analyzed to explicitly illustrate the proposed methods.

| S-EPMC6884669 | biostudies-literature

Multinomial Models with Linear Inequality Constraints: Overview and Improvements of Computational Methods for Bayesian Inference.

Project description:Many psychological theories can be operationalized as linear inequality constraints on the parameters of multinomial distributions (e.g., discrete choice analysis). These constraints can be described in two equivalent ways: Either as the solution set to a system of linear inequalities or as the convex hull of a set of extremal points (vertices). For both representations, we describe a general Gibbs sampler for drawing posterior samples in order to carry out Bayesian analyses. We also summarize alternative sampling methods for estimating Bayes factors for these model representations using the encompassing Bayes factor method. We introduce the R package multinomineq, which provides an easily-accessible interface to a computationally efficient implementation of these techniques.

| S-EPMC6448806 | biostudies-literature

Hierarchical Bayesian modeling and Markov chain Monte Carlo sampling for tuning-curve analysis.

Project description:A central theme of systems neuroscience is to characterize the tuning of neural responses to sensory stimuli or the production of movement. Statistically, we often want to estimate the parameters of the tuning curve, such as preferred direction, as well as the associated degree of uncertainty, characterized by error bars. Here we present a new sampling-based, Bayesian method that allows the estimation of tuning-curve parameters, the estimation of error bars, and hypothesis testing. This method also provides a useful way of visualizing which tuning curves are compatible with the recorded data. We demonstrate the utility of this approach using recordings of orientation and direction tuning in primary visual cortex, direction of motion tuning in primary motor cortex, and simulated data.

| S-EPMC2807240 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data