arXiv subjects

Stefano Favaro

Publications and source records attributed to Stefano Favaro.

88 records · Page 5Linked to original sources

arXiv2017

Bayesian Nonparametric Ordination for the Analysis of Microbial Communities

Human microbiome studies use sequencing technologies to measure the abundance of bacterial species or Operational Taxonomic Units (OTUs) in samples of biological material. Typically the data are organized in contingency tables with OTU counts across heterogeneous biological samples. In the microbial ecology community, ordination methods are frequently used to investigate latent factors or clusters that capture and describe variations of OTU counts across biological samples. It remains important to evaluate how uncertainty in estimates of each biological sample's microbial distribution propagates to ordination analyses, including visualization of clusters and projections of biological samples on low dimensional spaces. We propose a Bayesian analysis for dependent distributions to endow frequently used ordinations with estimates of uncertainty. A Bayesian nonparametric prior for dependent normalized random measures is constructed, which is marginally equivalent to the normalized generalized Gamma process, a well-known prior for nonparametric analyses. In our prior the dependence and similarity between microbial distributions is represented by latent factors that concentrate in a low dimensional space. We use a shrinkage prior to tune the dimensionality of the latent factors. The resulting posterior samples of model parameters can be used to evaluate uncertainty in analyses routinely applied in microbiome studies. Specifically, by combining them with multivariate data analysis techniques we can visualize credible regions in ecological ordination plots. The characteristics of the proposed model are illustrated through a simulation study and applications in two microbiome datasets.

stat.ME↗

arXiv2016

Moderate deviations for Ewens-Pitman exchangeable random partitions

Consider a population of individuals belonging to an infinity number of types, and assume that type proportions follow the two-parameter Poisson-Dirichlet distribution. A sample of size n is selected from the population. The total number of different types and the number of types appearing in the sample with a fixed frequency are important statistics. In this paper we establish the moderate deviation principles for these quantities. The corresponding rate functions are explicitly identified, which help revealing a critical scale and understanding the exact role of the parameters. Conditional, or posterior, counterparts of moderate deviation principles are also established.

math.PR↗

arXiv2016

Frequency of Frequencies Distributions and Size Dependent Exchangeable Random Partitions

Motivated by the fundamental problem of modeling the frequency of frequencies (FoF) distribution, this paper introduces the concept of a cluster structure to define a probability function that governs the joint distribution of a random count and its exchangeable random partitions. A cluster structure, naturally arising from a completely random measure mixed Poisson process, allows the probability distribution of the random partitions of a subset of a population to be dependent on the population size, a distinct and motivated feature that makes it more flexible than a partition structure. This allows it to model an entire FoF distribution whose structural properties change as the population size varies. A FoF vector can be simulated by drawing an infinite number of Poisson random variables, or by a stick-breaking construction with a finite random number of steps. A generalized negative binomial process model is proposed to generate a cluster structure, where in the prior the number of clusters is finite and Poisson distributed, and the cluster sizes follow a truncated negative binomial distribution. We propose a simple Gibbs sampling algorithm to extrapolate the FoF vector of a population given the FoF vector of a sample taken without replacement from the population. We illustrate our results and demonstrate the advantages of the proposed models through the analysis of real text, genomic, and survey data.

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arXiv2016

A characterization of product-form exchangeable feature probability functions

We characterize the class of exchangeable feature allocations assigning probability $V_{n,k}\prod_{l=1}^{k}W_{m_{l}}U_{n-m_{l}}$ to a feature allocation of $n$ individuals, displaying $k$ features with counts $(m_{1},\ldots,m_{k})$ for these features. Each element of this class is parametrized by a countable matrix $V$ and two sequences $U$ and $W$ of non-negative weights. Moreover, a consistency condition is imposed to guarantee that the distribution for feature allocations of $n-1$ individuals is recovered from that of $n$ individuals, when the last individual is integrated out. In Theorem 1.1, we prove that the only members of this class satisfying the consistency condition are mixtures of the Indian Buffet Process over its mass parameter $γ$ and mixtures of the Beta--Bernoulli model over its dimensionality parameter $N$. Hence, we provide a characterization of these two models as the only, up to randomization of the parameters, consistent exchangeable feature allocations having the required product form.

math.PR↗

arXiv2016

Bayesian nonparametric inference for discovery probabilities: credible intervals and large sample asymptotics

Given a sample of size $n$ from a population of individuals belonging to different species with unknown proportions, a popular problem of practical interest consists in making inference on the probability $D_{n}(l)$ that the $(n+1)$-th draw coincides with a species with frequency $l$ in the sample, for any $l=0,1,\ldots,n$. This paper contributes to the methodology of Bayesian nonparametric inference for $D_{n}(l)$. Specifically, under the general framework of Gibbs-type priors we show how to derive credible intervals for a Bayesian nonparametric estimation of $D_{n}(l)$, and we investigate the large $n$ asymptotic behaviour of such an estimator. Of particular interest are special cases of our results obtained under the specification of the two parameter Poisson--Dirichlet prior and the normalized generalized Gamma prior, which are two of the most commonly used Gibbs-type priors. With respect to these two prior specifications, the proposed results are illustrated through a simulation study and a benchmark Expressed Sequence Tags dataset. To the best our knowledge, this illustration provides the first comparative study between the two parameter Poisson--Dirichlet prior and the normalized generalized Gamma prior in the context of Bayesian nonparemetric inference for $D_{n}(l)$.

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arXiv2015

A hybrid sampler for Poisson-Kingman mixture models

This paper concerns the introduction of a new Markov Chain Monte Carlo scheme for posterior sampling in Bayesian nonparametric mixture models with priors that belong to the general Poisson-Kingman class. We present a novel compact way of representing the infinite dimensional component of the model such that while explicitly representing this infinite component it has less memory and storage requirements than previous MCMC schemes. We describe comparative simulation results demonstrating the efficacy of the proposed MCMC algorithm against existing marginal and conditional MCMC samplers.

stat.CO↗

arXiv2015

A marginal sampler for $σ$-Stable Poisson-Kingman mixture models

We investigate the class of $σ$-stable Poisson-Kingman random probability measures (RPMs) in the context of Bayesian nonparametric mixture modeling. This is a large class of discrete RPMs which encompasses most of the the popular discrete RPMs used in Bayesian nonparametrics, such as the Dirichlet process, Pitman-Yor process, the normalized inverse Gaussian process and the normalized generalized Gamma process. We show how certain sampling properties and marginal characterizations of $σ$-stable Poisson-Kingman RPMs can be usefully exploited for devising a Markov chain Monte Carlo (MCMC) algorithm for making inference in Bayesian nonparametric mixture modeling. Specifically, we introduce a novel and efficient MCMC sampling scheme in an augmented space that has a fixed number of auxiliary variables per iteration. We apply our sampling scheme for a density estimation and clustering tasks with unidimensional and multidimensional datasets, and we compare it against competing sampling schemes.

stat.CO↗

arXiv2015

Rediscovery of Good-Turing estimators via Bayesian nonparametrics

The problem of estimating discovery probabilities originated in the context of statistical ecology, and in recent years it has become popular due to its frequent appearance in challenging applications arising in genetics, bioinformatics, linguistics, designs of experiments, machine learning, etc. A full range of statistical approaches, parametric and nonparametric as well as frequentist and Bayesian, has been proposed for estimating discovery probabilities. In this paper we investigate the relationships between the celebrated Good-Turing approach, which is a frequentist nonparametric approach developed in the 1940s, and a Bayesian nonparametric approach recently introduced in the literature. Specifically, under the assumption of a two parameter Poisson-Dirichlet prior, we show that Bayesian nonparametric estimators of discovery probabilities are asymptotically equivalent, for a large sample size, to suitably smoothed Good-Turing estimators. As a by-product of this result, we introduce and investigate a methodology for deriving exact and asymptotic credible intervals to be associated with the Bayesian nonparametric estimators of discovery probabilities. The proposed methodology is illustrated through a comprehensive simulation study and the analysis of Expressed Sequence Tags data generated by sequencing a benchmark complementary DNA library.

stat.ME↗

arXiv2015

Looking-backward probabilities for Gibbs-type exchangeable random partitions

Gibbs-type random probability measures and the exchangeable random partitions they induce represent the subject of a rich and active literature. They provide a probabilistic framework for a wide range of theoretical and applied problems that are typically referred to as species sampling problems. In this paper, we consider the class of looking-backward species sampling problems introduced in Lijoi et al. (Ann. Appl. Probab. 18 (2008) 1519-1547) in Bayesian nonparametrics. Specifically, given some information on the random partition induced by an initial sample from a Gibbs-type random probability measure, we study the conditional distributions of statistics related to the old species, namely those species detected in the initial sample and possibly re-observed in an additional sample. The proposed results contribute to the analysis of conditional properties of Gibbs-type exchangeable random partitions, so far focused mainly on statistics related to those species generated by the additional sample and not already detected in the initial sample.

math.ST↗

arXiv2014

Large deviation principles for the Ewens-Pitman sampling model

Let $M_{l,n}$ be the number of blocks with frequency $l$ in the exchangeable random partition induced by a sample of size $n$ from the Ewens-Pitman sampling model. We show that, as $n$ tends to infinity, $n^{-1}M_{l,n}$ satisfies a large deviation principle and we characterize the corresponding rate function. A conditional counterpart of this large deviation principle is also presented. Specifically, given an initial sample of size $n$ from the Ewens-Pitman sampling model, we consider an additional sample of size $m$. For any fixed $n$ and as $m$ tends to infinity, we establish a large deviation principle for the conditional number of blocks with frequency $l$ in the enlarged sample, given the initial sample. Interestingly, the conditional and unconditional large deviation principles coincide, namely there is no long lasting impact of the given initial sample. Potential applications of our results are discussed in the context of Bayesian nonparametric inference for discovery probabilities.

math.PR↗

arXiv2013

MCMC for Normalized Random Measure Mixture Models

This paper concerns the use of Markov chain Monte Carlo methods for posterior sampling in Bayesian nonparametric mixture models with normalized random measure priors. Making use of some recent posterior characterizations for the class of normalized random measures, we propose novel Markov chain Monte Carlo methods of both marginal type and conditional type. The proposed marginal samplers are generalizations of Neal's well-regarded Algorithm 8 for Dirichlet process mixture models, whereas the conditional sampler is a variation of those recently introduced in the literature. For both the marginal and conditional methods, we consider as a running example a mixture model with an underlying normalized generalized Gamma process prior, and describe comparative simulation results demonstrating the efficacies of the proposed methods.

stat.ME↗

arXiv2013

Conditional formulae for Gibbs-type exchangeable random partitions

Gibbs-type random probability measures and the exchangeable random partitions they induce represent an important framework both from a theoretical and applied point of view. In the present paper, motivated by species sampling problems, we investigate some properties concerning the conditional distribution of the number of blocks with a certain frequency generated by Gibbs-type random partitions. The general results are then specialized to three noteworthy examples yielding completely explicit expressions of their distributions, moments and asymptotic behaviors. Such expressions can be interpreted as Bayesian nonparametric estimators of the rare species variety and their performance is tested on some real genomic data.

math.PR↗

arXiv2013

Bayesian nonparametric analysis of reversible Markov chains

We introduce a three-parameter random walk with reinforcement, called the $(θ,α,β)$ scheme, which generalizes the linearly edge reinforced random walk to uncountable spaces. The parameter $β$ smoothly tunes the $(θ,α,β)$ scheme between this edge reinforced random walk and the classical exchangeable two-parameter Hoppe urn scheme, while the parameters $α$ and $θ$ modulate how many states are typically visited. Resorting to de Finetti's theorem for Markov chains, we use the $(θ,α,β)$ scheme to define a nonparametric prior for Bayesian analysis of reversible Markov chains. The prior is applied in Bayesian nonparametric inference for species sampling problems with data generated from a reversible Markov chain with an unknown transition kernel. As a real example, we analyze data from molecular dynamics simulations of protein folding.

math.ST↗

arXiv2013

Alpha-diversity processes and normalized inverse-Gaussian diffusions

The infinitely-many-neutral-alleles model has recently been extended to a class of diffusion processes associated with Gibbs partitions of two-parameter Poisson-Dirichlet type. This paper introduces a family of infinite-dimensional diffusions associated with a different subclass of Gibbs partitions, induced by normalized inverse-Gaussian random probability measures. Such diffusions describe the evolution of the frequencies of infinitely-many types together with the dynamics of the time-varying mutation rate, which is driven by an alpha-diversity diffusion. Constructed as a dynamic version, relative to this framework, of the corresponding notion for Gibbs partitions, the latter is explicitly derived from an underlying population model and shown to coincide, in a special case, with the diffusion approximation of a critical Galton-Watson branching process. The class of infinite-dimensional processes is characterized in terms of its infinitesimal generator on an appropriate domain, and shown to be the limit in distribution of a certain sequence of Feller diffusions with finitely-many types. Moreover, a discrete representation is provided by means of appropriately transformed Moran-type particle processes, where the particles are samples from a normalized inverse-Gaussian random probability measure. The relationship between the limit diffusion and the two-parameter model is also discussed.

math.PR↗

arXiv2012

Asymptotics for a Bayesian nonparametric estimator of species variety

In Bayesian nonparametric inference, random discrete probability measures are commonly used as priors within hierarchical mixture models for density estimation and for inference on the clustering of the data. Recently, it has been shown that they can also be exploited in species sampling problems: indeed they are natural tools for modeling the random proportions of species within a population thus allowing for inference on various quantities of statistical interest. For applications that involve large samples, the exact evaluation of the corresponding estimators becomes impracticable and, therefore, asymptotic approximations are sought. In the present paper, we study the limiting behaviour of the number of new species to be observed from further sampling, conditional on observed data, assuming the observations are exchangeable and directed by a normalized generalized gamma process prior. Such an asymptotic study highlights a connection between the normalized generalized gamma process and the two-parameter Poisson-Dirichlet process that was previously known only in the unconditional case.

math.ST↗

arXiv2012

A class of measure-valued Markov chains and Bayesian nonparametrics

Measure-valued Markov chains have raised interest in Bayesian nonparametrics since the seminal paper by (Math. Proc. Cambridge Philos. Soc. 105 (1989) 579--585) where a Markov chain having the law of the Dirichlet process as unique invariant measure has been introduced. In the present paper, we propose and investigate a new class of measure-valued Markov chains defined via exchangeable sequences of random variables. Asymptotic properties for this new class are derived and applications related to Bayesian nonparametric mixture modeling, and to a generalization of the Markov chain proposed by (Math. Proc. Cambridge Philos. Soc. 105 (1989) 579--585), are discussed. These results and their applications highlight once again the interplay between Bayesian nonparametrics and the theory of measure-valued Markov chains.

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