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Jean-Michel Marin

Publications and source records attributed to Jean-Michel Marin.

At least 37 records · Page 2Linked to original sources
arXiv2011

Approximate Bayesian Computational methods

Also known as likelihood-free methods, approximate Bayesian computational (ABC) methods have appeared in the past ten years as the most satisfactory approach to untractable likelihood problems, first in genetics then in a broader spectrum of applications. However, these methods suffer to some degree from calibration difficulties that make them rather volatile in their implementation and thus render them suspicious to the users of more traditional Monte Carlo methods. In this survey, we study the various improvements and extensions made to the original ABC algorithm over the recent years.

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arXiv2011

Maximin design on non hypercube domain and kernel interpolation

In the paradigm of computer experiments, the choice of an experimental design is an important issue. When no information is available about the black-box function to be approximated, an exploratory design have to be used. In this context, two dispersion criteria are usually considered: the minimax and the maximin ones. In the case of a hypercube domain, a standard strategy consists of taking the maximin design within the class of Latin hypercube designs. However, in a non hypercube context, it does not make sense to use the Latin hypercube strategy. Moreover, whatever the design is, the black-box function is typically approximated thanks to kernel interpolation. Here, we first provide a theoretical justification to the maximin criterion with respect to kernel interpolations. Then, we propose simulated annealing algorithms to determine maximin designs in any bounded connected domain. We prove the convergence of the different schemes.

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arXiv2011

An empirical Bayes procedure for the selection of Gaussian graphical models

A new methodology for model determination in decomposable graphical Gaussian models is developed. The Bayesian paradigm is used and, for each given graph, a hyper inverse Wishart prior distribution on the covariance matrix is considered. This prior distribution depends on hyper-parameters. It is well-known that the models's posterior distribution is sensitive to the specification of these hyper-parameters and no completely satisfactory method is registered. In order to avoid this problem, we suggest adopting an empirical Bayes strategy, that is a strategy for which the values of the hyper-parameters are determined using the data. Typically, the hyper-parameters are fixed to their maximum likelihood estimations. In order to calculate these maximum likelihood estimations, we suggest a Markov chain Monte Carlo version of the Stochastic Approximation EM algorithm. Moreover, we introduce a new sampling scheme in the space of graphs that improves the add and delete proposal of Armstrong et al. (2009). We illustrate the efficiency of this new scheme on simulated and real datasets.

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arXiv2011

Why approximate Bayesian computational (ABC) methods cannot handle model choice problems

Approximate Bayesian computation (ABC), also known as likelihood-free methods, have become a favourite tool for the analysis of complex stochastic models, primarily in population genetics but also in financial analyses. We advocated in Grelaud et al. (2009) the use of ABC for Bayesian model choice in the specific case of Gibbs random fields (GRF), relying on a sufficiency property mainly enjoyed by GRFs to show that the approach was legitimate. Despite having previously suggested the use of ABC for model choice in a wider range of models in the DIY ABC software (Cornuet et al., 2008), we present theoretical evidence that the general use of ABC for model choice is fraught with danger in the sense that no amount of computation, however large, can guarantee a proper approximation of the posterior probabilities of the models under comparison.

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arXiv2010

On Particle Learning

This document is the aggregation of six discussions of Lopes et al. (2010) that we submitted to the proceedings of the Ninth Valencia Meeting, held in Benidorm, Spain, on June 3-8, 2010, in conjunction with Hedibert Lopes' talk at this meeting, and of a further discussion of the rejoinder by Lopes et al. (2010). The main point in those discussions is the potential for degeneracy in the particle learning methodology, related with the exponential forgetting of the past simulations. We illustrate in particular the resulting difficulties in the case of mixtures.

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arXiv2010

On resolving the Savage-Dickey paradox

The Savage-Dickey ratio is known as a specialised representation of the Bayes factor (O'Hagan and Forster, 2004) that allows for a functional plugging approximation of this quantity. We demonstrate here that the Savage-Dickey representation is in fact a generic representation of the Bayes factor that relies on specific measure-theoretic versions of the densities involved in the ratio, instead of a special identity imposing the above constraints on the prior distributions. We completely clarify the measure-theoretic foundations of the representation as well as the generalisation of Verdinelli and Wasserman (1995) and propose a comparison of this new approximation with their version, as well as with bridge sampling and Chib's approaches.

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arXiv2010

On computational tools for Bayesian data analysis

While Robert and Rousseau (2010) addressed the foundational aspects of Bayesian analysis, the current chapter details its practical aspects through a review of the computational methods available for approximating Bayesian procedures. Recent innovations like Monte Carlo Markov chain, sequential Monte Carlo methods and more recently Approximate Bayesian Computation techniques have considerably increased the potential for Bayesian applications and they have also opened new avenues for Bayesian inference, first and foremost Bayesian model choice.

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arXiv2010

Bayesian Inference

This chapter provides a overview of Bayesian inference, mostly emphasising that it is a universal method for summarising uncertainty and making estimates and predictions using probability statements conditional on observed data and an assumed model (Gelman 2008). The Bayesian perspective is thus applicable to all aspects of statistical inference, while being open to the incorporation of information items resulting from earlier experiments and from expert opinions. We provide here the basic elements of Bayesian analysis when considered for standard models, refering to Marin and Robert (2007) and to Robert (2007) for book-length entries.1 In the following, we refrain from embarking upon philosophical discussions about the nature of knowledge (see, e.g., Robert 2007, Chapter 10), opting instead for a mathematically sound presentation of an eminently practical statistical methodology. We indeed believe that the most convincing arguments for adopting a Bayesian version of data analyses are in the versatility of this tool and in the large range of existing applications, rather than in those polemical arguments.

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arXiv2009

Importance sampling methods for Bayesian discrimination between embedded models

This paper surveys some well-established approaches on the approximation of Bayes factors used in Bayesian model choice, mostly as covered in Chen et al. (2000). Our focus here is on methods that are based on importance sampling strategies rather than variable dimension techniques like reversible jump MCMC, including: crude Monte Carlo, maximum likelihood based importance sampling, bridge and harmonic mean sampling, as well as Chib's method based on the exploitation of a functional equality. We demonstrate in this survey how these different methods can be efficiently implemented for testing the significance of a predictive variable in a probit model. Finally, we compare their performances on a real dataset.

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arXiv2009

ABC likelihood-freee methods for model choice in Gibbs random fields

Gibbs random fields (GRF) are polymorphous statistical models that can be used to analyse different types of dependence, in particular for spatially correlated data. However, when those models are faced with the challenge of selecting a dependence structure from many, the use of standard model choice methods is hampered by the unavailability of the normalising constant in the Gibbs likelihood. In particular, from a Bayesian perspective, the computation of the posterior probabilities of the models under competition requires special likelihood-free simulation techniques like the Approximate Bayesian Computation (ABC) algorithm that is intensively used in population genetics. We show in this paper how to implement an ABC algorithm geared towards model choice in the general setting of Gibbs random fields, demonstrating in particular that there exists a sufficient statistic across models. The accuracy of the approximation to the posterior probabilities can be further improved by importance sampling on the distribution of the models. The practical aspects of the method are detailed through two applications, the test of an iid Bernoulli model versus a first-order Markov chain, and the choice of a folding structure for two proteins.

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arXiv2009

Adaptive approximate Bayesian computation

Sequential techniques can enhance the efficiency of the approximate Bayesian computation algorithm, as in Sisson et al.'s (2007) partial rejection control version. While this method is based upon the theoretical works of Del Moral et al. (2006), the application to approximate Bayesian computation results in a bias in the approximation to the posterior. An alternative version based on genuine importance sampling arguments bypasses this difficulty, in connection with the population Monte Carlo method of Cappe et al. (2004), and it includes an automatic scaling of the forward kernel. When applied to a population genetics example, it compares favourably with two other versions of the approximate algorithm.

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arXiv2008

Inferring population history with DIYABC: a user-friendly approach to Approximate Bayesian Computation

Genetic data obtained on population samples convey information about their evolutionary history. Inference methods can extract this information (at least partially) but they require sophisticated statistical techniques that have been made available to the biologist community (through computer programs) only for simple and standard situations typically involving a small number of samples. We propose here a computer program (DIYABC) for inference based on Approximate Bayesian Computation (ABC), in which scenarios can be customized by the user to fit many complex situations involving any number of populations and samples. Such scenarios involve any combination of population divergences, admixtures and stepwise population size changes. DIYABC can be used to compare competing scenarios, estimate parameters for one or more scenarios, and compute bias and precision measures for a given scenario and known values of parameters (the current version applies to unlinked microsatellite data). This article describes key methods used in the program and provides its main features. The analysis of one simulated and one real data set, both with complex evolutionary scenarios, illustrates the main possibilities of DIYABC

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arXiv2008

Online data processing: comparison of Bayesian regularized particle filters

The aim of this paper is to compare three regularized particle filters in an online data processing context. We carry out the comparison in terms of hidden states filtering and parameters estimation, considering a Bayesian paradigm and a univariate stochastic volatility model. We discuss the use of an improper prior distribution in the initialization of the filtering procedure and show that the regularized Auxiliary Particle Filter (APF) outperforms the regularized Sequential Importance Sampling (SIS) and the regularized Sampling Importance Resampling (SIR).

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arXiv2008

On some difficulties with a posterior probability approximation technique

In Scott (2002) and Congdon (2006), a new method is advanced to compute posterior probabilities of models under consideration. It is based solely on MCMC outputs restricted to single models, i.e., it is bypassing reversible jump and other model exploration techniques. While it is indeed possible to approximate posterior probabilities based solely on MCMC outputs from single models, as demonstrated by Gelfand and Dey (1994) and Bartolucci et al. (2006), we show that the proposals of Scott (2002) and Congdon (2006) are biased and advance several arguments towards this thesis, the primary one being the confusion between model-based posteriors and joint pseudo-posteriors. From a practical point of view, the bias in Scott's (2002) approximation appears to be much more severe than the one in Congdon's (2006), the later being often of the same magnitude as the posterior probability it approximates, although we also exhibit an example where the divergence from the true posterior probability is extreme.

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arXiv2008

Adaptive Importance Sampling in General Mixture Classes

In this paper, we propose an adaptive algorithm that iteratively updates both the weights and component parameters of a mixture importance sampling density so as to optimise the importance sampling performances, as measured by an entropy criterion. The method is shown to be applicable to a wide class of importance sampling densities, which includes in particular mixtures of multivariate Student t distributions. The performances of the proposed scheme are studied on both artificial and real examples, highlighting in particular the benefit of a novel Rao-Blackwellisation device which can be easily incorporated in the updating scheme.

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arXiv2008

Bayesian Inference on Mixtures of Distributions

This survey covers state-of-the-art Bayesian techniques for the estimation of mixtures. It complements the earlier Marin, Mengersen and Robert (2005) by studying new types of distributions, the multinomial, latent class and t distributions. It also exhibits closed form solutions for Bayesian inference in some discrete setups. Lastly, it sheds a new light on the computation of Bayes factors via the approximation of Chib (1995).

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