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Likelihood-free Bayesian analysis of memory models.

ABSTRACT: Many influential memory models are computational in the sense that their predictions are derived through simulation. This means that it is difficult or impossible to write down a probability distribution or likelihood that characterizes the random behavior of the data as a function of the model's parameters. In turn, the lack of a likelihood means that these models cannot be directly fitted to data using traditional techniques. In particular, standard Bayesian analyses of such models are impossible. In this article, we examine how a new procedure called approximate Bayesian computation (ABC), a method for Bayesian analysis that circumvents the evaluation of the likelihood, can be used to fit computational models to memory data. In particular, we investigate the bind cue decide model of episodic memory (Dennis & Humphreys, 2001) and the retrieving effectively from memory model (Shiffrin & Steyvers, 1997). We fit hierarchical versions of each model to the data of Dennis, Lee, and Kinnell (2008) and Kinnell and Dennis (2012). The ABC analysis permits us to explore the relationships between the parameters in each model as well as evaluate their relative fits to data-analyses that were not previously possible.

SUBMITTER: Turner BM

PROVIDER: S-EPMC4140406 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature

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Likelihood-free Bayesian analysis of memory models.

Turner Brandon M BM Dennis Simon S Van Zandt Trisha T

Psychological review 20130415 3

Many influential memory models are computational in the sense that their predictions are derived through simulation. This means that it is difficult or impossible to write down a probability distribution or likelihood that characterizes the random behavior of the data as a function of the model's parameters. In turn, the lack of a likelihood means that these models cannot be directly fitted to data using traditional techniques. In particular, standard Bayesian analyses of such models are impossi ...[more]

PMID: 23586446

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Project description:There is a paradigm shift from the traditional focus on the "average" individual towards the definition and analysis of trait variation within individual life-history and among individuals in populations. This is a result of increasing availability of individual phenotypic data. The shift allows the use of genetic and environment-driven variations to assess robustness to challenge, gain greater understanding of organismal biological processes, or deliver individual-targeted treatments or genetic selection. These consequences apply, in particular, to variation in ontogenetic growth. We propose an approach to parameterise mathematical models of individual traits (e.g., reaction norms, growth curves) that address two challenges: 1) Estimation of individual traits while making minimal assumptions about data distribution and correlation, addressed via Approximate Bayesian Computation (a form of nonparametric inference). We are motivated by the fact that available information on distribution of biological data is often less precise than assumed by conventional likelihood functions. 2) Scaling-up to population phenotype distributions while facilitating unbiased use of individual data; this is addressed via a probabilistic framework where population distributions build on separately-inferred individual distributions and individual-trait interpretability is preserved. The approach is tested against Bayesian likelihood-based inference, by fitting weight and energy intake growth models to animal data and normal- and skewed-distributed simulated data. i) Individual inferences were accurate and robust to changes in data distribution and sample size; in particular, median-based predictions were more robust than maximum- likelihood-based curves. These results suggest that the approach gives reliable inferences using few observations and monitoring resources. ii) At the population level, each individual contributed via a specific data distribution, and population phenotype estimates were not disproportionally influenced by outlier individuals. Indices measuring population phenotype variation can be derived for study comparisons. The approach offers an alternative for estimating trait variability in biological systems that may be reliable for various applications, for example, in genetics, health, and individualised nutrition, while using fewer assumptions and fewer empirical observations. In livestock breeding, the potentially greater accuracy of trait estimation (without specification of multitrait variance-covariance parameters) could lead to improved selection and to more decisive estimates of trait heritability.

Project description:BackgroundUncertainty in comparative analyses can come from at least two sources: a) phylogenetic uncertainty in the tree topology or branch lengths, and b) uncertainty due to intraspecific variation in trait values, either due to measurement error or natural individual variation. Most phylogenetic comparative methods do not account for such uncertainties. Not accounting for these sources of uncertainty leads to false perceptions of precision (confidence intervals will be too narrow) and inflated significance in hypothesis testing (e.g. p-values will be too small). Although there is some application-specific software for fitting Bayesian models accounting for phylogenetic error, more general and flexible software is desirable.MethodsWe developed models to directly incorporate phylogenetic uncertainty into a range of analyses that biologists commonly perform, using a Bayesian framework and Markov Chain Monte Carlo analyses.ResultsWe demonstrate applications in linear regression, quantification of phylogenetic signal, and measurement error models. Phylogenetic uncertainty was incorporated by applying a prior distribution for the phylogeny, where this distribution consisted of the posterior tree sets from Bayesian phylogenetic tree estimation programs. The models were analysed using simulated data sets, and applied to a real data set on plant traits, from rainforest plant species in Northern Australia. Analyses were performed using the free and open source software OpenBUGS and JAGS.ConclusionsIncorporating phylogenetic uncertainty through an empirical prior distribution of trees leads to more precise estimation of regression model parameters than using a single consensus tree and enables a more realistic estimation of confidence intervals. In addition, models incorporating measurement errors and/or individual variation, in one or both variables, are easily formulated in the Bayesian framework. We show that BUGS is a useful, flexible general purpose tool for phylogenetic comparative analyses, particularly for modelling in the face of phylogenetic uncertainty and accounting for measurement error or individual variation in explanatory variables. Code for all models is provided in the BUGS model description language.

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Likelihood-free Bayesian analysis of memory models.

Publications

Likelihood-free Bayesian analysis of memory models.

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