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Jean-Michel Marin
Publication date
2015
fields
Mathematical Statistics
and research's language is
English
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This document is an invited chapter covering the specificities of ABC model choice, intended for the incoming Handbook of ABC by Sisson, Fan, and Beaumont (2017). Beyond exposing the potential pitfalls of ABC based posterior probabilities, the review emphasizes mostly the solution proposed by Pudlo et al. (2016) on the use of random forests for aggregating summary statistics and and for estimating the posterior probability of the most likely model via a secondary random fores.
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A maximum likelihood methodology for the parameters of models with an intractable likelihood is introduced. We produce a likelihood-free version of the stochastic approximation expectation-maximization (SAEM) algorithm to maximize the likelihood function of model parameters. While SAEM is best suited for models having a tractable complete likelihood function, its application to moderately complex models is a difficult or even impossible task. We show how to construct a likelihood-free version of SAEM by using the synthetic likelihood paradigm. Our method is completely plug-and-play, requires almost no tuning and can be applied to both static and dynamic models. Four simulation studies illustrate the method, including a stochastic differential equation model, a stochastic Lotka-Volterra model and data from $g$-and-$k$ distributions. MATLAB code is available as supplementary material.
In Chib (1995), a method for approximating marginal densities in a Bayesian setting is proposed, with one proeminent application being the estimation of the number of components in a normal mixture. As pointed out in Neal (1999) and Fruhwirth-Schnatter (2004), the approximation often fails short of providing a proper approximation to the true marginal densities because of the well-known label switching problem (Celeux et al., 2000). While there exist other alternatives to the derivation of approximate marginal densities, we reconsider the original proposal here and show as in Berkhof et al. (2003) and Lee et al. (2008) that it truly approximates the marginal densities once the label switching issue has been solved.
A maximum likelihood methodology for a general class of models is presented, using an approximate Bayesian computation (ABC) approach. The typical target of ABC methods are models with intractable likelihoods, and we combine an ABC-MCMC sampler with so-called data cloning for maximum likelihood estimation. Accuracy of ABC methods relies on the use of a small threshold value for comparing simulations from the model and observed data. The proposed methodology shows how to use large threshold values, while the number of data-clones is increased to ease convergence towards an approximate maximum likelihood estimate. We show how to exploit the methodology to reduce the number of iterations of a standard ABC-MCMC algorithm and therefore reduce the computational effort, while obtaining reasonable point estimates. Simulation studies show the good performance of our approach on models with intractable likelihoods such as g-and-k distributions, stochastic differential equations and state-space models.
Let X_1, ..., X_n be independent and identically distributed random vectors with a log-concave (Lebesgue) density f. We first prove that, with probability one, there exists a unique maximum likelihood estimator of f. The use of this estimator is attractive because, unlike kernel density estimation, the method is fully automatic, with no smoothing parameters to choose. Although the existence proof is non-constructive, we are able to reformulate the issue of computation in terms of a non-differentiable convex optimisation problem, and thus combine techniques of computational geometry with Shors r-algorithm to produce a sequence that converges to the maximum likelihood estimate. For the moderate or large sample sizes in our simulations, the maximum likelihood estimator is shown to provide an improvement in performance compared with kernel-based methods, even when we allow the use of a theoretical, optimal fixed bandwidth for the kernel estimator that would not be available in practice. We also present a real data clustering example, which shows that our methodology can be used in conjunction with the Expectation--Maximisation (EM) algorithm to fit finite mixtures of log-concave densities. An R version of the algorithm is available in the package LogConcDEAD -- Log-Concave Density Estimation in Arbitrary Dimensions.
Nonlinear Mixed effects models are hidden variables models that are widely used in many field such as pharmacometrics. In such models, the distribution characteristics of hidden variables can be specified by including several parameters such as covariates or correlations which must be selected. Recent development of pharmacogenomics has brought averaged/high dimensional problems to the field of nonlinear mixed effects modeling for which standard covariates selection techniques like stepwise methods are not well suited. This work proposes to select covariates and correlation parameters using a penalized likelihood approach. The penalized likelihood problem is solved using a stochastic proximal gradient algorithm to avoid inner-outer iterations. Speed of convergence of the proximal gradient algorithm is improved by the use of component-wise adaptive gradient step sizes. The practical implementation and tuning of the proximal gradient algorithm is explored using simulations. Calibration of regularization parameters is performed by minimizing the Bayesian Information Criterion using particle swarm optimization, a zero order optimization procedure. The use of warm restart and parallelization allows to reduce significantly computing time. The performance of the proposed method compared to the traditional grid search strategy is explored using simulated data. Finally, an application to real data from two pharmacokinetics studies is provided, one studying an antifibrinolitic and the other studying an antibiotic.
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