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Nested nonparametric processes are vectors of random probability measures widely used in the Bayesian literature to model the dependence across distinct, though related, groups of observations. These processes allow a two-level clustering, both at the observational and group levels. Several alternatives have been proposed starting from the nested Dirichlet process by Rodr\'iguez et al. (2008). However, most of the available models are neither computationally efficient or mathematically tractable. In the present paper, we aim to introduce a range of nested processes that are mathematically tractable, flexible, and computationally efficient. Our proposal builds upon Compound Random Measures, which are vectors of dependent random measures early introduced by Griffin and Leisen (2017). We provide a complete investigation of theoretical properties of our model. In particular, we prove a general posterior characterization for vectors of Compound Random Measures, which is interesting per se and still not available in the current literature. Based on our theoretical results and the available posterior representation, we develop the first Ferguson & Klass algorithm for nested nonparametric processes. We specialize our general theorems and algorithms in noteworthy examples. We finally test the model's performance on different simulated scenarios, and we exploit the construction to study air pollution in different provinces of an Italian region (Lombardy). We empirically show how nested processes based on Compound Random Measures outperform other Bayesian competitors.

Palm distributions are critical in the study of point processes. In the present paper we focus on a point process $\Phi$ defined as the superposition, i.e., sum, of two independent point processes, say $\Phi = \Phi_1 + \Phi_2$, and we characterize its Palm distribution. In particular, we show that the Palm distribution of $\Phi$ admits a simple mixture representation depending only on the Palm distribution of $\Phi_j$, as $j=1, 2$, and the associated moment measures. Extensions to the superposition of multiple point processes, and higher order Palm distributions, are treated analogously.

Feature allocation models are an extension of Bayesian nonparametric clustering models, where individuals can share multiple features. We study a broad class of models whose probability distribution has a product form, which includes the popular Indian buffet process. This class plays a prominent role among existing priors, and it shares structural characteristics with Gibbs-type priors in the species sampling framework. We develop a general theory for the entire class, obtaining closed form expressions for the predictive structure and the posterior law of the underlying stochastic process. Additionally, we describe the distribution for the number of features and the number of hitherto unseen features in a future sample, leading to the $\alpha$-diversity for feature models. We also examine notable novel examples, such as mixtures of Indian buffet processes and beta Bernoulli models, where the latter entails a finite random number of features. This methodology finds significant applications in ecology, allowing the estimation of species richness for incidence data, as we demonstrate by analyzing plant diversity in Danish forests and trees in Barro Colorado Island.

Statistical modelling in the presence of data organized in groups is a crucial task in Bayesian statistics. The present paper conceives a mixture model based on a novel family of Bayesian priors designed for multilevel data and obtained by normalizing a finite point process. In particular, the work extends the popular Mixture of Finite Mixture model to the hierarchical framework to capture heterogeneity within and between groups. A full distribution theory for this new family and the induced clustering is developed, including the marginal, posterior, and predictive distributions. Efficient marginal and conditional Gibbs samplers are designed to provide posterior inference. The proposed mixture model overcomes the Hierarchical Dirichlet Process, the utmost tool for handling multilevel data, in terms of analytical feasibility, clustering discovery, and computational time. The motivating application comes from the analysis of shot put data, which contains performance measurements of athletes across different seasons. In this setting, the proposed model is exploited to induce clustering of the observations across seasons and athletes. By linking clusters across seasons, similarities and differences in athletes' performances are identified.

The study of almost surely discrete random probability measures is an active line of research in Bayesian nonparametrics. The idea of assuming interaction across the atoms of the random probability measure has recently spurred significant interest in the context of Bayesian mixture models. This allows the definition of priors that encourage well-separated and interpretable clusters. In this work, we provide a unified framework for the construction and the Bayesian analysis of random probability measures with interacting atoms, encompassing both repulsive and attractive behaviours. Specifically, we derive closed-form expressions for the posterior distribution, the marginal and predictive distributions, which were not previously available except for the case of measures with i.i.d. atoms. We show how these quantities are fundamental both for prior elicitation and to develop new posterior simulation algorithms for hierarchical mixture models. Our results are obtained without any assumption on the finite point process that governs the atoms of the random measure. Their proofs rely on analytical tools borrowed from the Palm calculus theory, which might be of independent interest. We specialise our treatment to the classes of Poisson, Gibbs, and determinantal point processes, as well as in the case of shot-noise Cox processes. Finally, we illustrate the performance of different modelling strategies on simulated and real datasets.

Species-sampling problems (SSPs) refer to a vast class of statistical problems calling for the estimation of (discrete) functionals of the unknown species composition of an unobservable population. A common feature of SSPs is their invariance with respect to species labeling, which is at the core of the Bayesian nonparametric (BNP) approach to SSPs under the popular Pitman-Yor process (PYP) prior. In this paper, we develop a BNP approach to SSPs that are not "invariant" to species labeling, in the sense that an ordering or ranking is assigned to species' labels. Inspired by the population genetics literature on age-ordered alleles' compositions, we study the following SSP with ordering: given an observable sample from an unknown population of individuals belonging to species (alleles), with species' labels being ordered according to weights (ages), estimate the frequencies of the first $r$ order species' labels in an enlarged sample obtained by including additional unobservable samples. By relying on an ordered PYP prior, we obtain an explicit posterior distribution of the first $r$ order frequencies, with estimates being of easy implementation and computationally efficient. We apply our approach to the analysis of genetic variation, showing its effectiveness in estimating the frequency of the oldest allele, and then we discuss other potential applications.

Posterior contractions rates (PCRs) strengthen the notion of Bayesian consistency, quantifying the speed at which the posterior distribution concentrates on arbitrarily small neighborhoods of the true model, with probability tending to 1 or almost surely, as the sample size goes to infinity. Under the Bayesian nonparametric framework, a common assumption in the study of PCRs is that the model is dominated for the observations; that is, it is assumed that the posterior can be written through the Bayes formula. In this paper, we consider the problem of establishing PCRs in Bayesian nonparametric models where the posterior distribution is not available through the Bayes formula, and hence models that are non-dominated for the observations. By means of the Wasserstein distance and a suitable sieve construction, our main result establishes PCRs in Bayesian nonparametric models where the posterior is available through a more general disintegration than the Bayes formula. To the best of our knowledge, this is the first general approach to provide PCRs in non-dominated Bayesian nonparametric models, and it relies on minimal modeling assumptions and on a suitable continuity assumption for the posterior distribution. Some refinements of our result are presented under additional assumptions on the prior distribution, and applications are given with respect to the Dirichlet process prior and the normalized extended Gamma process prior., Comment: arXiv admin note: text overlap with arXiv:2011.14425

In the 1920's, the English philosopher W.E. Johnson introduced a characterization of the symmetric Dirichlet prior distribution in terms of its predictive distribution. This is typically referred to as Johnson's "sufficientness" postulate, and it has been the subject of many contributions in Bayesian statistics, leading to predictive characterization for infinite-dimensional generalizations of the Dirichlet distribution, i.e. species-sampling models. In this paper, we review "sufficientness" postulates for species-sampling models, and then investigate analogous predictive characterizations for the more general features-sampling models. In particular, we present a "sufficientness" postulate for a class of features-sampling models referred to as Scaled Processes (SPs), and then discuss analogous characterizations in the general setup of features-sampling models.

Gibbs-type priors are widely used as key components in several Bayesian nonparametric models. By virtue of their flexibility and mathematical tractability, they turn out to be predominant priors in species sampling problems, clustering and mixture modelling. We introduce a new family of processes which extend the Gibbs-type one, by including a contaminant component in the model to account for the presence of anomalies (outliers) or an excess of observations with frequency one. We first investigate the induced random partition, the associated predictive distribution and we characterize the asymptotic behaviour of the number of clusters. All the results we obtain are in closed form and easily interpretable, as a noteworthy example we focus on the contaminated version of the Pitman-Yor process. Finally we pinpoint the advantage of our construction in different applied problems: we show how the contaminant component helps to perform outlier detection for an astronomical clustering problem and to improve predictive inference in a species-related dataset, exhibiting a high number of species with frequency one., Comment: 43 pages, 14 figures, 10 tables

There is a growing interest in the estimation of the number of unseen features, mostly driven by biological applications. A recent work brought out a peculiar property of the popular completely random measures (CRMs) as prior models in Bayesian nonparametric (BNP) inference for the unseen-features problem: for fixed prior's parameters, they all lead to a Poisson posterior distribution for the number of unseen features, which depends on the sampling information only through the sample size. CRMs are thus not a flexible prior model for the unseen-features problem and, while the Poisson posterior distribution may be appealing for analytical tractability and ease of interpretability, its independence from the sampling information makes the BNP approach a questionable oversimplification, with posterior inferences being completely determined by the estimation of unknown prior's parameters. In this paper, we introduce the stable-Beta scaled process (SB-SP) prior, and we show that it allows to enrich the posterior distribution of the number of unseen features arising under CRM priors, while maintaining its analytical tractability and interpretability. That is, the SB-SP prior leads to a negative Binomial posterior distribution, which depends on the sampling information through the sample size and the number of distinct features, with corresponding estimates being simple, linear in the sampling information and computationally efficient. We apply our BNP approach to synthetic data and to real cancer genomic data, showing that: i) it outperforms the most popular parametric and nonparametric competitors in terms of estimation accuracy; ii) it provides improved coverage for the estimation with respect to a BNP approach under CRM priors.

Post Randomization Methods (PRAM) are among the most popular disclosure limitation techniques for both categorical and continuous data. In the categorical case, given a stochastic matrix $M$ and a specified variable, an individual belonging to category $i$ is changed to category $j$ with probability $M_{i,j}$. Every approach to choose the randomization matrix $M$ has to balance between two desiderata: 1) preserving as much statistical information from the raw data as possible; 2) guaranteeing the privacy of individuals in the dataset. This trade-off has generally been shown to be very challenging to solve. In this work, we use recent tools from the computer science literature and propose to choose $M$ as the solution of a constrained maximization problems. Specifically, $M$ is chosen as the solution of a constrained maximization problem, where we maximize the Mutual Information between raw and transformed data, given the constraint that the transformation satisfies the notion of Differential Privacy. For the general Categorical model, it is shown how this maximization problem reduces to a convex linear programming and can be therefore solved with known optimization algorithms.

The use of high-dimensional data for targeted therapeutic interventions requires new ways to characterize the heterogeneity observed across subgroups of a specific population. In particular, models for partially exchangeable data are needed for inference on nested datasets, where the observations are assumed to be organized in different units and some sharing of information is required to learn distinctive features of the units. In this manuscript, we propose a nested Common Atoms Model (CAM) that is particularly suited for the analysis of nested datasets where the distributions of the units are expected to differ only over a small fraction of the observations sampled from each unit. The proposed CAM allows a two-layered clustering at the distributional and observational level and is amenable to scalable posterior inference through the use of a computationally efficient nested slice-sampler algorithm. We further discuss how to extend the proposed modeling framework to handle discrete measurements, and we conduct posterior inference on a real microbiome dataset from a diet swap study to investigate how the alterations in intestinal microbiota composition are associated with different eating habits. We further investigate the performance of our model in capturing true distributional structures in the population by means of a simulation study.

While the cost of sequencing genomes has decreased dramatically in recent years, this expense often remains non-trivial. Under a fixed budget, then, scientists face a natural trade-off between quantity and quality; they can spend resources to sequence a greater number of genomes (quantity) or spend resources to sequence genomes with increased accuracy (quality). Our goal is to find the optimal allocation of resources between quantity and quality. Optimizing resource allocation promises to reveal as many new variations in the genome as possible, and thus as many new scientific insights as possible. In this paper, we consider the common setting where scientists have already conducted a pilot study to reveal variants in a genome and are contemplating a follow-up study. We introduce a Bayesian nonparametric methodology to predict the number of new variants in the follow-up study based on the pilot study. When experimental conditions are kept constant between the pilot and follow-up, we demonstrate on real data from the gnomAD project that our prediction is more accurate than three recent proposals, and competitive with a more classic proposal. Unlike existing methods, though, our method allows practitioners to change experimental conditions between the pilot and the follow-up. We demonstrate how this distinction allows our method to be used for (i) more realistic predictions and (ii) optimal allocation of a fixed budget between quality and quantity.

The problem of maximizing cell type discovery under budget constraints is a fundamental challenge for the collection and analysis of single-cell RNA-sequencing (scRNA-seq) data. In this paper, we introduce a simple, computationally efficient, and scalable Bayesian nonparametric sequential approach to optimize the budget allocation when designing a large scale experiment for the collection of scRNA-seq data for the purpose of, but not limited to, creating cell atlases. Our approach relies on the following tools: i) a hierarchical Pitman-Yor prior that recapitulates biological assumptions regarding cellular differentiation, and ii) a Thompson sampling multi-armed bandit strategy that balances exploitation and exploration to prioritize experiments across a sequence of trials. Posterior inference is performed by using a sequential Monte Carlo approach, which allows us to fully exploit the sequential nature of our species sampling problem. We empirically show that our approach outperforms state-of-the-art methods and achieves near-Oracle performance on simulated and scRNA-seq data alike. HPY-TS code is available at https://github.com/fedfer/HPYsinglecell.

Feature models are popular in machine learning and they have been recently used to solve many unsupervised learning problems. In these models every observation is endowed with a finite set of features, usually selected from an infinite collection $(F_{j})_{j\geq 1}$. Every observation can display feature $F_{j}$ with an unknown probability $p_{j}$. A statistical problem inherent to these models is how to estimate, given an initial sample, the conditional expected number of hitherto unseen features that will be displayed in a future observation. This problem is usually referred to as the missing mass problem. In this work we prove that, using a suitable multiplicative loss function and without imposing any assumptions on the parameters $p_{j}$, there does not exist any universally consistent estimator for the missing mass. In the second part of the paper, we focus on a special class of heavy-tailed probabilities $(p_{j})_{j\geq 1}$, which are common in many real applications, and we show that, within this restricted class of probabilities, the nonparametric estimator of the missing mass suggested by Ayed et al. (2017) is strongly consistent. As a byproduct result, we will derive concentration inequalities for the missing mass and the number of features observed with a specified frequency in a sample of size $n$.

Feature allocation models generalize species sampling models by allowing every observation to belong to more than one species, now called features. Under the popular Bernoulli product model for feature allocation, given $n$ samples, we study the problem of estimating the missing mass $M_{n}$, namely the expected number hitherto unseen features that would be observed if one additional individual was sampled. This is motivated by numerous applied problems where the sampling procedure is expensive, in terms of time and/or financial resources allocated, and further samples can be only motivated by the possibility of recording new unobserved features. We introduce a simple, robust and theoretically sound nonparametric estimator $\hat{M}_{n}$ of $M_{n}$. $\hat{M}_{n}$ turns out to have the same analytic form of the popular Good-Turing estimator of the missing mass in species sampling models, with the difference that the two estimators have different ranges. We show that $\hat{M}_{n}$ admits a natural interpretation both as a jackknife estimator and as a nonparametric empirical Bayes estimator, we give provable guarantees for the performance of $\hat{M}_{n}$ in terms of minimax rate optimality, and we provide with an interesting connection between $\hat{M}_{n}$ and the Good-Turing estimator for species sampling. Finally, we derive non-asymptotic confidence intervals for $\hat{M}_{n}$, which are easily computable and do not rely on any asymptotic approximation. Our approach is illustrated with synthetic data and SNP data from the ENCODE sequencing genome project.

Protection against disclosure is a legal and ethical obligation for agencies releasing microdata files for public use. Consider a microdata sample of size $n$ from a finite population of size $\bar{n}=n+\lambda n$, with $\lambda>0$, such that each record contains two disjoint types of information: identifying categorical information and sensitive information. Any decision about releasing data is supported by the estimation of measures of disclosure risk, which are functionals of the number of sample records with a unique combination of values of identifying variables. The most common measure is arguably the number $\tau_{1}$ of sample unique records that are population uniques. In this paper, we first study nonparametric estimation of $\tau_{1}$ under the Poisson abundance model for sample records. We introduce a class of linear estimators of $\tau_{1}$ that are simple, computationally efficient and scalable to massive datasets, and we give uniform theoretical guarantees for them. In particular, we show that they provably estimate $\tau_{1}$ all of the way up to the sampling fraction $(\lambda+1)^{-1}\propto (\log n)^{-1}$, with vanishing normalized mean-square error (NMSE) for large $n$. We then establish a lower bound for the minimax NMSE for the estimation of $\tau_{1}$, which allows us to show that: i) $(\lambda+1)^{-1}\propto (\log n)^{-1}$ is the smallest possible sampling fraction; ii) estimators' NMSE is near optimal, in the sense of matching the minimax lower bound, for large $n$. This is the main result of our paper, and it provides a precise answer to an open question about the feasibility of nonparametric estimation of $\tau_{1}$ under the Poisson abundance model and for a sampling fraction $(\lambda+1)^{-1}<1/2$.

Given $n$ samples from a population of individuals belonging to different types with unknown proportions, how do we estimate the probability of discovering a new type at the $(n+1)$-th draw? This is a classical problem in statistics, commonly referred to as the missing mass estimation problem. Recent results by Ohannessian and Dahleh \citet{Oha12} and Mossel and Ohannessian \citet{Mos15} showed: i) the impossibility of estimating (learning) the missing mass without imposing further structural assumptions on the type proportions; ii) the consistency of the Good-Turing estimator for the missing mass under the assumption that the tail of the type proportions decays to zero as a regularly varying function with parameter $\alpha\in(0,1)$. In this paper we rely on tools from Bayesian nonparametrics to provide an alternative, and simpler, proof of the impossibility of a distribution-free estimation of the missing mass. Up to our knowledge, the use of Bayesian ideas to study large sample asymptotics for the missing mass is new, and it could be of independent interest. Still relying on Bayesian nonparametric tools, we then show that under regularly varying type proportions the convergence rate of the Good-Turing estimator is the best rate that any estimator can achieve, up to a slowly varying function, and that minimax rate must be at least $n^{-\alpha/2}$. We conclude with a discussion of our results, and by conjecturing that the Good-Turing estimator is an rate optimal minimax estimator under regularly varying type proportions.

Discrete random structures are important tools in Bayesian nonparametrics and the resulting models have proven effective in density estimation, clustering, topic modeling and prediction, among others. In this paper, we consider nested processes and study the dependence structures they induce. Dependence ranges between homogeneity, corresponding to full exchangeability, and maximum heterogeneity, corresponding to (unconditional) independence across samples. The popular nested Dirichlet process is shown to degenerate to the fully exchangeable case when there are ties across samples at the observed or latent level. To overcome this drawback, inherent to nesting general discrete random measures, we introduce a novel class of latent nested processes. These are obtained by adding common and group-specific completely random measures and, then, normalising to yield dependent random probability measures. We provide results on the partition distributions induced by latent nested processes, and develop an Markov Chain Monte Carlo sampler for Bayesian inferences. A test for distributional homogeneity across groups is obtained as a by product. The results and their inferential implications are showcased on synthetic and real data.