Gaussian process modelling in approximate Bayesian computation to estimate horizontal gene transfer in bacteria
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Publication:1728645
Abstract: Approximate Bayesian computation (ABC) can be used for model fitting when the likelihood function is intractable but simulating from the model is feasible. However, even a single evaluation of a complex model may take several hours, limiting the number of model evaluations available. Modelling the discrepancy between the simulated and observed data using a Gaussian process (GP) can be used to reduce the number of model evaluations required by ABC, but the sensitivity of this approach to a specific GP formulation has not yet been thoroughly investigated. We begin with a comprehensive empirical evaluation of using GPs in ABC, including various transformations of the discrepancies and two novel GP formulations. Our results indicate the choice of GP may significantly affect the accuracy of the estimated posterior distribution. Selection of an appropriate GP model is thus important. We formulate expected utility to measure the accuracy of classifying discrepancies below or above the ABC threshold, and show that it can be used to automate the GP model selection step. Finally, based on the understanding gained with toy examples, we fit a population genetic model for bacteria, providing insight into horizontal gene transfer events within the population and from external origins.
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Cites work
- A survey of Bayesian predictive methods for model assessment, selection and comparison
- A tutorial on approximate Bayesian computation
- Accelerating pseudo-marginal MCMC using Gaussian processes
- Adaptive approximate Bayesian computation
- Adaptive approximate Bayesian computation for complex models
- An adaptive sequential Monte Carlo method for approximate Bayesian computation
- Approximate Bayesian computation: a nonparametric perspective
- Approximate Bayesian computational methods
- Bayesian Model Assessment and Comparison Using Cross-Validation Predictive Densities
- Bayesian Synthetic Likelihood
- Bayesian indirect inference using a parametric auxiliary model
- Bayesian optimization for likelihood-free inference of simulator-based statistical models
- Constructing summary statistics for approximate Bayesian computation: semi-automatic approximate Bayesian computation. With discussion and authors' reply
- Efficient acquisition rules for model-based approximate Bayesian computation
- Estimation of parameters for macroparasite population evolution using approximate Bayesian computation
- GPstuff: Bayesian modeling with Gaussian processes
- Gaussian process modelling in approximate Bayesian computation to estimate horizontal gene transfer in bacteria
- Gaussian processes for machine learning.
- Nonparametric guidance of autoencoder representations using label information
- Sequential Monte Carlo without likelihoods
Cited in
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- New approximate Bayesian computation algorithm for censored data
- Adaptive approximate Bayesian computation tolerance selection
- Bayesian optimization of functional output in inverse problems
- Uncertainty quantification in deterministic parameterization of single diode model of a silicon solar cell
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