Gibbs-type priors are combinatorial processes 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 and mixture modeling. We introduce a new family of processes which extends the Gibbs-type one, by including a contaminant component in the model to account for an excess of observations with frequency one. We first investigate the induced random partition, the associated predictive distribution, the asymptotic behavior of the total number of blocks and the number of blocks with a given frequency: all the results we obtain are in closed form and easily interpretable. A remarkable aspect of contaminated Gibbs-type priors relies on their predictive structure, compared to the one of the standard Gibbs-type family: it depends on the additional sampling information on the number of observations with frequency one out of the observed sample. As a noteworthy example we focus on the contaminated version of the Pitman-Yor process, which turns out to be analytically tractable and computationally feasible. Finally we pinpoint the advantage of our construction in different applications: we show how it helps to improve predictive inference in a species-related dataset exhibiting a high number of species with frequency one; we also discuss the use of the proposed construction in mixture models to perform density estimation and outlier detection.

Compositional data are vectors typically representing proportions of a whole, that is, those whose elements are strictly positive and subject to a unit-sum constraint. The increasing number of fields where this type of data arises makes the development of proper statistical tools an important issue. From a regression perspective, whenever the multivariate response is a compositional vector, a proper model that accounts for the unit-sum constraint is the well-established Dirichlet regression model. However, there are significant drawbacks mainly due to the limited flexibility of the Dirichlet distribution. The aim of this contribution is to introduce a new multivariate regression model for constrained responses, that is based on the extended flexible Dirichlet distribution (which is a structured mixture with Dirichlet distributed components). The new model is obtained by adopting a novel reparameterization which allows for, among other things, the presence of suitably designed cluster-specific regression patterns. It is shown to provide considerably greater flexibility and better performance than the standard Dirichlet regression model. In particular, from theoretical analysis, intensive simulation studies in many challenging scenarios, as well as from a real data application, it emerges that the new regression model can handle several issues affecting the Dirichlet regression, such as the presence of outliers, latent groups, multi-modality, and positive correlations.

Functional generalized linear models (FGLM) have been widely used to study the relations between non-Gaussian response and functional covariates. However, most existing works for FGLM assume independence among observations and therefore they are of limited applicability for correlated data. A particularly important example is spatial functional data, where we observe functions over spatial domains, such as the age population curve or temperature curve at each areal unit. In this paper, we extend FGLM by incorporating spatial random effects. Especially, we study the relationship between the non-Gaussian response variable and functional covariates that are spatially observed. However, such model has computational and inferential challenges. The high-dimensional spatial random effects cause the slow mixing of Markov chain Monte Carlo (MCMC) algorithms. Furthermore, spatial confounding can lead to bias in parameter estimates and inflate their variances. To address these issues, we propose an efficient Bayesian method using a sparse reparameterization of high-dimensional random effects. We also study the average coverage probabilities of the credible intervals of functional parameters. We apply our methods to simulated and real data examples, including malaria incidence data and US COVID-19 data. The proposed method is fast while providing accurate functional estimates.

Cytometry is the standard multi-parameter assay for measuring single cell phenotype and functionality. It is commonly used for quantifying the relative frequencies of cell subsets in blood and disaggregated tissues. A typical analysis of cytometry data involves cell classification—that is, the identification of cell subgroups in the sample—and comparisons of the cell subgroups across samples or conditions. While modern experiments often necessitate the collection and processing of samples in multiple batches, analysis of cytometry data across batches is challenging because differences across samples may occur due to either true biological variation or technical reasons such as antibody lot effects or instrument optics across batches. Thus a critical step in comparative analyses of multi-sample cytometry data—yet missing in existing automated methods for analyzing such data—is cross-sample calibration, whose goal is to align corresponding cell subsets across multiple samples in the presence of technical variations, so that biological variations can be meaningfully compared. We introduce a Bayesian nonparametric hierarchical modeling approach for accomplishing both calibration and cell classification simultaneously in a unified probabilistic manner. Three important features of our method make it particularly effective for analyzing multi-sample cytometry data: a nonparametric mixture avoids prespecifying the number of cell clusters; a hierarchical skew normal kernel that allows flexibility in the shapes of the cell subsets and cross-sample variation in their locations; and finally the “coarsening” strategy makes inference robust to departures from the model not captured by the skew normal kernels. We demonstrate the merits of our approach in simulated examples and carry out a case study in the analysis of a multi-sample cytometry data set. We provide an R package for our method.

Geographically weighted regression (GWR) models handle geographical dependence through a spatially varying coefficient model and have been widely used in applied science, but its general Bayesian extension is unclear because it involves a weighted log-likelihood which does not imply a probability distribution on data. We present a Bayesian GWR model and show that its essence is dealing with partial misspecification of the model. Current modularized Bayesian inference models accommodate partial misspecification from a single component of the model. We extend these models to handle partial misspecification in more than one component of the model, as required for our Bayesian GWR model. Information from the various spatial locations is manipulated via a geographically weighted kernel and the optimal manipulation is chosen according to a Kullback–Leibler (KL) divergence. We justify the model via an information risk minimization approach and show the consistency of the proposed estimator in terms of a geographically weighted KL divergence.

We revisit the Bayesian Context Trees (BCT) modelling framework for discrete time series, which was recently found to be very effective in numerous tasks including model selection, estimation and prediction. A novel representation of the induced posterior distribution on model space is derived in terms of a simple branching process, and several consequences of this are explored in theory and in practice. First, it is shown that the branching process representation leads to a simple variable-dimensional Monte Carlo sampler for the joint posterior distribution on models and parameters, which can efficiently produce independent samples. This sampler is found to be more efficient than earlier MCMC samplers for the same tasks. Then, the branching process representation is used to establish the asymptotic consistency of the BCT posterior, including the derivation of an almost-sure convergence rate. Finally, an extensive study is carried out on the performance of the induced Bayesian entropy estimator. Its utility is illustrated through both simulation experiments and real-world applications, where it is found to outperform several state-of-the-art methods.

Objective Bayesian inference procedures are derived for the parameters of the multivariate random effects model generalized to elliptically contoured distributions. The posterior for the overall mean vector and the between-study covariance matrix is deduced by assigning two noninformative priors to the model parameter, namely the Berger and Bernardo reference prior and the Jeffreys prior, whose analytical expressions are obtained under weak distributional assumptions. It is shown that the only condition needed for the posterior to be proper is that the sample size is larger than the dimension of the data-generating model, independently of the class of elliptically contoured distributions used in the definition of the generalized multivariate random effects model. The theoretical findings of the paper are applied to real data consisting of ten studies about the effectiveness of hypertension treatment for reducing blood pressure where the treatment effects on both the systolic blood pressure and diastolic blood pressure are investigated.

Bayesian inference is a popular and widely-used approach to infer phylogenies (evolutionary trees). However, despite decades of widespread application, it remains difficult to judge how well a given Bayesian Markov chain Monte Carlo (MCMC) run explores the space of phylogenetic trees. In this paper, we investigate the Monte Carlo error of phylogenies, focusing on high-dimensional summaries of the posterior distribution, including variability in estimated edge/branch (known in phylogenetics as “split”) probabilities and tree probabilities, and variability in the estimated summary tree. Specifically, we ask if there is any measure of effective sample size (ESS) applicable to phylogenetic trees which is capable of capturing the Monte Carlo error of these three summary measures. We find that there are some ESS measures capable of capturing the error inherent in using MCMC samples to approximate the posterior distributions on phylogenies. We term these tree ESS measures, and identify a set of three which are useful in practice for assessing the Monte Carlo error. Lastly, we present visualization tools that can improve comparisons between multiple independent MCMC runs by accounting for the Monte Carlo error present in each chain. Our results indicate that common post-MCMC workflows are insufficient to capture the inherent Monte Carlo error of the tree, and highlight the need for both within-chain mixing and between-chain convergence assessments.

The exponential random graph model (ERGM) is a popular model for social networks, which is known to have an intractable likelihood function. Sampling from the posterior for such a model is a long-standing problem in statistical research. We analyze the performance of the stochastic gradient Langevin dynamics (SGLD) algorithm (also known as noisy Longevin Monte Carlo) in tackling this problem, where the stochastic gradient is calculated via running a short Markov chain (the so-called inner Markov chain in this paper) at each iteration. We show that if the model size grows with the network size slowly enough, then SGLD converges to the true posterior in 2-Wasserstein distance as the network size and iteration number become large regardless of the length of the inner Markov chain performed at each iteration. Our study provides a scalable algorithm for analyzing large-scale social networks with possibly high-dimensional ERGMs.

Current protocols to estimate the number, size, and location of cancerous lesions in the prostate using multiparametric magnetic resonance imaging (mpMRI) are highly dependent on reader experience and expertise. Automatic voxel-wise cancer classifiers do not directly provide estimates of number, location, and size of cancerous lesions that are clinically important. Existing spatial partitioning methods estimate linear or piecewise-linear boundaries separating regions of local stationarity in spatially registered data and are inadequate for the application of lesion detection. Frequentist segmentation and clustering methods often require pre-specification of the number of clusters and do not quantify uncertainty. Previously, we developed a novel Bayesian functional spatial partitioning method to estimate the boundary surrounding a single cancerous lesion using data derived from mpMRI. We propose a Bayesian functional spatial partitioning method for multiple lesion detection with an unknown number of lesions. Our method utilizes functional estimation to model the smooth boundary curves surrounding each cancerous lesion. In a Reversible Jump Markov Chain Monte Carlo (RJ-MCMC) framework, we develop novel jump steps to jointly estimate and quantify uncertainty in the number of lesions, their boundaries, and the spatial parameters in each lesion. Through simulation we show that our method is robust to the shape of the lesions, number of lesions, and region-specific spatial processes. We illustrate our method through the detection of prostate cancer lesions using MRI.

When analysing multiple time series that may be subject to changepoints, it is sometimes possible to specify a priori, by means of a graph, which pairs of time series are likely to be impacted by simultaneous changepoints. This article proposes an informative prior for changepoints which encodes the information contained in the graph, inducing a changepoint model for multiple time series that borrows strength across clusters of connected time series to detect weak signals for synchronous changepoints. The graphical model for changepoints is further extended to allow dependence between nearby but not necessarily synchronous changepoints across neighbouring time series in the graph. A novel reversible jump Markov chain Monte Carlo (MCMC) algorithm making use of auxiliary variables is proposed to sample from the graphical changepoint model. The merit of the proposed approach is demonstrated through a changepoint analysis of computer network authentication logs from Los Alamos National Laboratory (LANL), demonstrating an improvement at detecting weak signals for network intrusions across users linked by network connectivity, whilst limiting the number of false alerts.