A moment-matching Ferguson and Klass algorithm

Completely random measures (CRM) represent the key building block of a wide variety of popular stochastic models and play a pivotal role in modern Bayesian Nonparametrics. A popular representation of CRMs as a random series with decreasing jumps is due to Ferguson and Klass (1972). This can immediately be turned into an algorithm for sampling realizations of CRMs or more elaborate models involving transformed CRMs. However, concrete implementation requires to truncate the random series at some threshold resulting in an approximation error. The goal of this paper is to quantify the quality of the approximation by a moment-matching criterion, which consists in evaluating a measure of discrepancy between actual moments and moments based on the simulation output. Seen as a function of the truncation level, the methodology can be used to determine the truncation level needed to reach a certain level of precision. The resulting moment-matching \FK algorithm is then implemented and illustrated on several popular Bayesian nonparametric models.Comment: 24 pages, 6 figures, 5 table

On the sub-Gaussianity of the Beta and Dirichlet distributions

We obtain the optimal proxy variance for the sub-Gaussianity of Beta distribution, thus proving upper bounds recently conjectured by Elder (2016). We provide different proof techniques for the symmetrical (around its mean) case and the non-symmetrical case. The technique in the latter case relies on studying the ordinary differential equation satisfied by the Beta moment-generating function known as the confluent hypergeometric function. As a consequence, we derive the optimal proxy variance for the Dirichlet distribution, which is apparently a novel result. We also provide a new proof of the optimal proxy variance for the Bernoulli distribution, and discuss in this context the proxy variance relation to log-Sobolev inequalities and transport inequalities.Comment: 13 pages, 2 figure

Approximating predictive probabilities of Gibbs-type priors

Gibbs-type random probability measures, or Gibbs-type priors, are arguably the most "natural" generalization of the celebrated Dirichlet prior. Among them the two parameter Poisson-Dirichlet prior certainly stands out for the mathematical tractability and interpretability of its predictive probabilities, which made it the natural candidate in several applications. Given a sample of size $n$, in this paper we show that the predictive probabilities of any Gibbs-type prior admit a large $n$ approximation, with an error term vanishing as $o(1/n)$, which maintains the same desirable features as the predictive probabilities of the two parameter Poisson-Dirichlet prior.Comment: 22 pages, 6 figures. Added posterior simulation study, corrected typo

Bayesian nonparametric dependent model for partially replicated data: the influence of fuel spills on species diversity

We introduce a dependent Bayesian nonparametric model for the probabilistic modeling of membership of subgroups in a community based on partially replicated data. The focus here is on species-by-site data, i.e. community data where observations at different sites are classified in distinct species. Our aim is to study the impact of additional covariates, for instance environmental variables, on the data structure, and in particular on the community diversity. To that purpose, we introduce dependence a priori across the covariates, and show that it improves posterior inference. We use a dependent version of the Griffiths-Engen-McCloskey distribution defined via the stick-breaking construction. This distribution is obtained by transforming a Gaussian process whose covariance function controls the desired dependence. The resulting posterior distribution is sampled by Markov chain Monte Carlo. We illustrate the application of our model to a soil microbial dataset acquired across a hydrocarbon contamination gradient at the site of a fuel spill in Antarctica. This method allows for inference on a number of quantities of interest in ecotoxicology, such as diversity or effective concentrations, and is broadly applicable to the general problem of communities response to environmental variables.Comment: Main Paper: 22 pages, 6 figures. Supplementary Material: 11 pages, 1 figur

Dirichlet process mixtures under affine transformations of the data

Location-scale Dirichlet process mixtures of Gaussians (DPM-G) have proved extremely useful in dealing with density estimation and clustering problems in a wide range of domains. Motivated by an astronomical application, in this work we address the robustness of DPM-G models to affine transformations of the data, a natural requirement for any sensible statistical method for density estimation and clustering. First, we devise a coherent prior specification of the model which makes posterior inference invariant with respect to affine transformations of the data. Second, we formalise the notion of asymptotic robustness under data transformation and show that mild assumptions on the true data generating process are sufficient to ensure that DPM-G models feature such a property. Our investigation is supported by an extensive simulation study and illustrated by the analysis of an astronomical dataset consisting of physical measurements of stars in the field of the globular cluster NGC 2419.Comment: 36 pages, 7 Figure

Bayesian optimal adaptive estimation using a sieve prior

We derive rates of contraction of posterior distributions on nonparametric models resulting from sieve priors. The aim of the paper is to provide general conditions to get posterior rates when the parameter space has a general structure, and rate adaptation when the parameter space is, e.g., a Sobolev class. The conditions employed, although standard in the literature, are combined in a different way. The results are applied to density, regression, nonlinear autoregression and Gaussian white noise models. In the latter we have also considered a loss function which is different from the usual l2 norm, namely the pointwise loss. In this case it is possible to prove that the adaptive Bayesian approach for the l2 loss is strongly suboptimal and we provide a lower bound on the rate.Comment: 33 pages, 2 figure

Sub-Weibull distributions: generalizing sub-Gaussian and sub-Exponential properties to heavier-tailed distributions

We propose the notion of sub-Weibull distributions, which are characterised by tails lighter than (or equally light as) the right tail of a Weibull distribution. This novel class generalises the sub-Gaussian and sub-Exponential families to potentially heavier-tailed distributions. Sub-Weibull distributions are parameterized by a positive tail index $\theta$ and reduce to sub-Gaussian distributions for $\theta=1/2$ and to sub-Exponential distributions for $\theta=1$. A characterisation of the sub-Weibull property based on moments and on the moment generating function is provided and properties of the class are studied. An estimation procedure for the tail parameter is proposed and is applied to an example stemming from Bayesian deep learning.Comment: 10 pages, 3 figure

The fine print on tempered posteriors

We conduct a detailed investigation of tempered posteriors and uncover a number of crucial and previously undiscussed points. Contrary to previous results, we first show that for realistic models and datasets and the tightly controlled case of the Laplace approximation to the posterior, stochasticity does not in general improve test accuracy. The coldest temperature is often optimal. One might think that Bayesian models with some stochasticity can at least obtain improvements in terms of calibration. However, we show empirically that when gains are obtained this comes at the cost of degradation in test accuracy. We then discuss how targeting Frequentist metrics using Bayesian models provides a simple explanation of the need for a temperature parameter $\lambda$ in the optimization objective. Contrary to prior works, we finally show through a PAC-Bayesian analysis that the temperature $\lambda$ cannot be seen as simply fixing a misspecified prior or likelihood

Clustering Milky Way's Globulars: a Bayesian Nonparametric Approach

International audienceThis chapter presents a Bayesian nonparametric approach to clustering , which is particularly relevant when the number of components in the clustering is unknown. The approach is illustrated with the Milky Way's glob-ulars, that are clouds of stars orbiting in our galaxy. Clustering globulars is key for better understanding the Milky Way's history. We define the Dirichlet process and illustrate some alternative definitions such as the Chinese restaurant process, the Pólya Urn, the Ewens sampling formula, the stick-breaking representation through some simple R code. The Dirichlet process mixture model is presented, as well as the R package BNPmix implementing Markov chain Monte Carlo sampling. Inference for the clustering is done with the variation of information loss function