Dataset Information

Bayesian Covariance Structure Modeling of Responses and Process Data.

ABSTRACT: A novel Bayesian modeling framework for response accuracy (RA), response times (RTs) and other process data is proposed. In a Bayesian covariance structure modeling approach, nested and crossed dependences within test-taker data (e.g., within a testlet, between RAs and RTs for an item) are explicitly modeled. The local dependences are modeled directly through covariance parameters in an additive covariance matrix. The inclusion of random effects (on person or group level) is not necessary, which allows constructing parsimonious models for responses and multiple types of process data. Bayesian Covariance Structure Models (BCSMs) are presented for various well-known dependence structures. Through truncated shifted inverse-gamma priors, closed-form expressions for the conditional posteriors of the covariance parameters are derived. The priors avoid boundary effects at zero, and ensure the positive definiteness of the additive covariance structure at any layer. Dependences of categorical outcome data are modeled through latent continuous variables. In a simulation study, a BCSM for RAs and RTs is compared to van der Linden's hierarchical model (LHM; van der Linden, 2007). Under the BCSM, the dependence structure is extended to allow variations in test-takers' working speed and ability and is estimated with a satisfying performance. Under the LHM, the assumption of local independence is violated, which results in a biased estimate of the variance of the ability distribution. Moreover, the BCSM provides insight in changes in the speed-accuracy trade-off. With an empirical example, the flexibility and relevance of the BCSM for complex dependence structures in a real-world setting are discussed.

SUBMITTER: Klotzke K

PROVIDER: S-EPMC6690231 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Publications

Bayesian Covariance Structure Modeling of Responses and Process Data.

Klotzke Konrad K Fox Jean-Paul JP

Frontiers in psychology 20190805

A novel Bayesian modeling framework for response accuracy (RA), response times (RTs) and other process data is proposed. In a Bayesian covariance structure modeling approach, nested and crossed dependences within test-taker data (e.g., within a testlet, between RAs and RTs for an item) are explicitly modeled. The local dependences are modeled directly through covariance parameters in an additive covariance matrix. The inclusion of random effects (on person or group level) is not necessary, which ...[more]

PMID: 31428007

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Project description:BackgroundStable Isotope Resolved Metabolomics (SIRM) is a new biological approach that uses stable isotope tracers such as uniformly [Formula: see text]-enriched glucose ([Formula: see text]-Glc) to trace metabolic pathways or networks at the atomic level in complex biological systems. Non-steady-state kinetic modeling based on SIRM data uses sets of simultaneous ordinary differential equations (ODEs) to quantitatively characterize the dynamic behavior of metabolic networks. It has been increasingly used to understand the regulation of normal metabolism and dysregulation in the development of diseases. However, fitting a kinetic model is challenging because there are usually multiple sets of parameter values that fit the data equally well, especially for large-scale kinetic models. In addition, there is a lack of statistically rigorous methods to compare kinetic model parameters between different experimental groups.ResultsWe propose a new Bayesian statistical framework to enhance parameter estimation and hypothesis testing for non-steady-state kinetic modeling of SIRM data. For estimating kinetic model parameters, we leverage the prior distribution not only to allow incorporation of experts' knowledge but also to provide robust parameter estimation. We also introduce a shrinkage approach for borrowing information across the ensemble of metabolites to stably estimate the variance of an individual isotopomer. In addition, we use a component-wise adaptive Metropolis algorithm with delayed rejection to perform efficient Monte Carlo sampling of the posterior distribution over high-dimensional parameter space. For comparing kinetic model parameters between experimental groups, we propose a new reparameterization method that converts the complex hypothesis testing problem into a more tractable parameter estimation problem. We also propose an inference procedure based on credible interval and credible value. Our method is freely available for academic use at https://github.com/xuzhang0131/MCMCFlux .ConclusionsOur new Bayesian framework provides robust estimation of kinetic model parameters and enables rigorous comparison of model parameters between experimental groups. Simulation studies and application to a lung cancer study demonstrate that our framework performs well for non-steady-state kinetic modeling of SIRM data.

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Bayesian Covariance Structure Modeling of Responses and Process Data.

Publications

Bayesian Covariance Structure Modeling of Responses and Process Data.

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