We develop a new class of dynamic multivariate Poisson count models that allow for fast online updating and we refer to these models as multivariate Poisson-scaled beta (MPSB). The MPSB model allows for serial dependence in the counts as well as dependence across multiple series with a random common environment. Other notable features include analytic forms for state propagation and predictive likelihood densities. Sequential updating occurs through the updating of the sufficient statistics for static model parameters, leading to a fully adapted particle learning algorithm and a new class of predictive likelihoods and marginal distributions which we refer to as the (dynamic) multivariate confluent hyper-geometric negative binomial distribution (MCHG-NB) and the the dynamic multivariate negative binomial (DMNB) distribution. To illustrate our methodology, we use various simulation studies and count data on weekly non-durable goods consumer demand.
An important feature of Bayesian statistics is the opportunity to do sequential inference: the posterior distribution obtained after seeing a dataset can be used as prior for a second inference. However, when Monte Carlo sampling methods are used for inference, we only have a set of samples from the posterior distribution. To do sequential inference, we then either have to evaluate the second posterior at only these locations and reweight the samples accordingly, or we can estimate a functional description of the posterior probability distribution from the samples and use that as prior for the…
In this paper we develop a Bayesian procedure for estimating multivariate stochastic volatility (MSV) using state space models. A multiplicative model based on inverted Wishart and multivariate singular beta distributions is proposed for the evolution of the volatility, and a flexible sequential volatility updating is employed. Being computationally fast, the resulting estimation procedure is particularly suitable for on-line forecasting. Three performance measures are discussed in the context of model selection: the log-likelihood criterion, the mean of standardized one-step forecast errors, …
We develop the methodology and a detailed case study in use of a class of Bayesian predictive synthesis (BPS) models for multivariate time series forecasting. This extends the recently introduced foundational framework of BPS to the multivariate setting, with detailed application in the topical and challenging context of multi-step macroeconomic forecasting in a monetary policy setting. BPS evaluates-- sequentially and adaptively over time-- varying forecast biases and facets of miscalibration of individual forecast densities, and-- critically-- of time-varying inter-dependencies among them ov…
The Dirichlet-multinomial (DM) distribution plays a fundamental role in modern statistical methodology development and application. Recently, the DM distribution and its variants have been used extensively to model multivariate count data generated by high-throughput sequencing technology in omics research due to its ability to accommodate the compositional structure of the data as well as overdispersion. A major limitation of the DM distribution is that it is unable to handle excess zeros typically found in practice which may bias inference. To fill this gap, we propose a novel Bayesian zero-…
The stochastic volatility model is a popular tool for modeling the volatility of assets. The model is a nonlinear and non-Gaussian state space model, and consequently is difficult to fit. Many approaches, both classical and Bayesian, have been developed that rely on numerically intensive techniques such as quasi-maximum likelihood estimation and Markov chain Monte Carlo (MCMC). Convergence and mixing problems still plague MCMC algorithms when drawing samples sequentially from the posterior distributions. While particle Gibbs methods have been successful when applied to nonlinear or non-Gaussia…
We consider multivariate copula-based stationary time-series under Gaussian subordination. Observed time series are subordinated to long-range dependent Gaussian processes and characterized by arbitrary marginal copula distributions. First of all, we establish limit theorems for the marginal and quantile marginal empirical processes of multivariate stationary long-range dependent sequences under Gaussian subordination. Furthermore, we establish the asymptotic behavior of sequential empirical copula processes under non-restrictive smoothness assumptions. The limiting processes in the case of lo…
Bayesian computation for filtering and forecasting analysis is developed for a broad class of dynamic models. The ability to scale-up such analyses in non-Gaussian, nonlinear multivariate time series models is advanced through the introduction of a novel copula construction in sequential filtering of coupled sets of dynamic generalized linear models. The new copula approach is integrated into recently introduced multiscale models in which univariate time series are coupled via nonlinear forms involving dynamic latent factors representing cross-series relationships. The resulting methodology of…
Motivated by the need, in some Bayesian likelihood free inference problems, of imputing a multivariate counting distribution based on its vector of means and variance-covariance matrix, we define a generic multivariate discrete distribution. Based on blending the Binomial, Poisson and Negative-Binomial distributions, and using a normal multivariate copula, the required distribution is defined. This distribution tends to the Multivariate Normal for large counts and has an approximate pmf version that is quite simple to evaluate.
Flow cytometry is a high-throughput technology used to quantify multiple surface and intracellular markers at the level of a single cell. This enables to identify cell sub-types, and to determine their relative proportions. Improvements of this technology allow to describe millions of individual cells from a blood sample using multiple markers. This results in high-dimensional datasets, whose manual analysis is highly time-consuming and poorly reproducible. While several methods have been developed to perform automatic recognition of cell populations, most of them treat and analyze each sample…
CIRAD（法国农业研究与国际合作组织）；Inria（法国国家信息与自动化研究所）；Univ. Grenoble Alpes（格勒诺布尔阿尔卑斯大学）；Laboratoire Jean Kuntzmann（让·库茨曼实验室）
Multivariate count data are defined as the number of items of different categories issued from sampling within a population, which individuals are grouped into categories. The analysis of multivariate count data is a recurrent and crucial issue in numerous modelling problems, particularly in the fields of biology and ecology (where the data can represent, for example, children counts associated with multitype branching processes), sociology and econometrics. We focus on I) Identifying categories that appear simultaneously, or on the contrary that are mutually exclusive. This is achieved by ide…
Tracking and estimating Daily Fine Particulate Matter (PM2.5) is very important as it has been shown that PM2.5 is directly related to mortality related to lungs, cardiovascular system, and stroke. That is, high values of PM2.5 constitute a public health problem in the US, and it is important that we precisely estimate PM2.5 to aid in public policy decisions. Thus, we propose a Bayesian hierarchical model for high-dimensional "multi-type" responses. By "multi-type" responses we mean a collection of correlated responses that have different distributional assumptions (e.g., continuous skewed obs…
Randomized experiments play a major role in data-driven decision making across many different fields and disciplines. In medicine, for example, randomized controlled trials (RCTs) are the backbone of clinical trial methodology for testing the efficacy of new drugs and therapies versus existing treatments or placebo. In business and marketing, randomized experiments are typically referred to as A/B tests when there are only two arms, or variants, in the experiment, and as multivariate A/B tests when there are more than two arms. Typical applications of A/B tests include comparing the effectiven…
Research on Poisson regression analysis for dependent data has been developed rapidly in the last decade. One of difficult problems in a multivariate case is how to construct a cross-correlation structure and at the meantime make sure that the covariance matrix is positive definite. To address the issue, we propose to use convolved Gaussian process (CGP) in this paper. The approach provides a semi-parametric model and offers a natural framework for modeling common mean structure and covariance structure simultaneously. The CGP enables the model to define different covariance structure for each…
While death rates due to diseases of the heart have experienced a sharp decline over the past 50 years, these diseases continue to be the leading cause of death in the United States, and the rate of decline varies by geographic location, race, and gender. We look to harness the power of hierarchical Bayesian methods to obtain a clearer picture of the declines from county-level, temporally varying heart disease death rates for men and women of different races in the US. Specifically, we propose a nonseparable multivariate spatio-temporal Bayesian model which allows for group-specific temporal c…
The multivariate extended skew-normal distribution allows for accommodating raw data which are skewed and heavy tailed, and has at least three appealing statistical properties, namely closure under conditioning, affine transformations, and marginalization. In this paper we propose a Bayesian computational approach based on a sequential Monte Carlo (SMC) sampler to estimate such distributions. The practical implementation of each step of the algorithm is discussed and the elicitation of prior distributions takes into consideration some unusual behaviour of the likelihood function and the corres…
Regular vine copulas can describe a wider array of dependency patterns than the multivariate Gaussian copula or the multivariate Student's t copula. This paper presents two contributions related to model selection of regular vine copulas. First, our pair copula family selection procedure extends existing Bayesian family selection methods by allowing pair families to be chosen from an arbitrary set of candidate families. Second, our method represents the first Bayesian model selection approach to include the regular vine density construction in its scope of inference. The merits of our approach…
We introduce a Bayesian approach for multivariate spatio-temporal prediction for high-dimensional count-valued data. Our primary interest is when there are possibly millions of data points referenced over different variables, geographic regions, and times. This problem requires extensive methodological advancements, as jointly modeling correlated data of this size leads to the so-called "big n problem." The computational complexity of prediction in this setting is further exacerbated by acknowledging that count-valued data are naturally non-Gaussian. Thus, we develop a new computationally effi…
Multivariate compositional count data arise in many applications including ecology, microbiology, genetics, and paleoclimate. A frequent question in the analysis of multivariate compositional count data is what values of a covariate(s) give rise to the observed composition. Learning the relationship between covariates and the compositional count allows for inverse prediction of unobserved covariates given compositional count observations. Gaussian processes provide a flexible framework for modeling functional responses with respect to a covariate without assuming a functional form. Many scient…
This paper develops a Bayesian procedure for estimation and forecasting of the volatility of multivariate time series. The foundation of this work is the matrix-variate dynamic linear model, for the volatility of which we adopt a multiplicative stochastic evolution, using Wishart and singular multivariate beta distributions. A diagonal matrix of discount factors is employed in order to discount the variances element by element and therefore allowing a flexible and pragmatic variance modelling approach. Diagnostic tests and sequential model monitoring are discussed in some detail. The proposed …
In many applications, such as economics, operations research and reinforcement learning, one often needs to estimate a multivariate regression function f subject to a convexity constraint. For example, in sequential decision processes the value of a state under optimal subsequent decisions may be known to be convex or concave. We propose a new Bayesian nonparametric multivariate approach based on characterizing the unknown regression function as the max of a random collection of unknown hyperplanes. This specification induces a prior with large support in a Kullback-Leibler sense on the space …
Change detection involves segmenting sequential data such that observations in the same segment share some desired properties. Multivariate change detection continues to be a challenging problem due to the variety of ways change points can be correlated across channels and the potentially poor signal-to-noise ratio on individual channels. In this paper, we are interested in locating additive outliers (AO) and level shifts (LS) in the unsupervised setting. We propose ABACUS, Automatic BAyesian Changepoints Under Sparsity, a Bayesian source separation technique to recover latent signals while al…
Multivariate probit models (MPM) have the appealing feature of capturing some of the dependence structure between the components of multidimensional binary responses. The key for the dependence modelling is the covariance matrix of an underlying latent multivariate Gaussian. Most approaches to MLE in multivariate probit regression rely on MCEM algorithms to avoid computationally intensive evaluations of multivariate normal orthant probabilities. As an alternative to the much used Gibbs sampler a new SMC sampler for truncated multivariate normals is proposed. The algorithm proceeds in two stage…
High throughput technologies have become the practice of choice for comparative studies in biomedical applications. Limited number of sample points due to sequencing cost or access to organisms of interest necessitates the development of efficient sample collections to maximize the power of downstream statistical analyses. We propose a method for sequentially choosing training samples under the Optimal Bayesian Classification framework. Specifically designed for RNA sequencing count data, the proposed method takes advantage of efficient Gibbs sampling procedure with closed-form updates. Our re…
The assessment of diversity and similarity is relevant in monitoring the status of ecosystems. The respective indicators are based on the taxonomic composition of biological communities of interest, currently estimated through the proportions computed from sampling multivariate counts. In this work we present a novel method able to work with only one sample to estimate the taxonomic composition when the data are affected by overdispersion. The presence of overdispersion in taxonomic counts may be the result of significant environmental factors which are often unobservable but influence communi…
We develop a Bayesian approach to learning from sequential data by using Gaussian processes (GPs) with so-called signature kernels as covariance functions. This allows to make sequences of different length comparable and to rely on strong theoretical results from stochastic analysis. Signatures capture sequential structure with tensors that can scale unfavourably in sequence length and state space dimension. To deal with this, we introduce a sparse variational approach with inducing tensors. We then combine the resulting GP with LSTMs and GRUs to build larger models that leverage the strengths…
We discuss Bayesian model uncertainty analysis and forecasting in sequential dynamic modeling of multivariate time series. The perspective is that of a decision-maker with a specific forecasting objective that guides thinking about relevant models. Based on formal Bayesian decision-theoretic reasoning, we develop a time-adaptive approach to exploring, weighting, combining and selecting models that differ in terms of predictive variables included. The adaptivity allows for changes in the sets of favored models over time, and is guided by the specific forecasting goals. A synthetic example illus…
The aim of sequential change-point detection is to issue an alarm when it is thought that certain probabilistic properties of the monitored observations have changed. This work is concerned with nonparametric, closed-end testing procedures based on differences of empirical distribution functions that are designed to be particularly sensitive to changes in the comtemporary distribution of multivariate time series. The proposed detectors are adaptations of statistics used in a posteriori (offline) change-point testing and involve a weighting allowing to give more importance to recent observation…
Nonparametric tests for equality of multivariate distributions are frequently desired in research. It is commonly required that test-procedures based on relatively small samples of vectors accurately control the corresponding Type I Error (TIE) rates. Often, in the multivariate testing, extensions of null-distribution-free univariate methods, e.g., Kolmogorov-Smirnov and Cramer-von Mises type schemes, are not exact, since their null distributions depend on underlying data distributions. The present paper extends the density-based empirical likelihood technique in order to nonparametrically app…
We propose a new framework for the detection of change-points in online, sequential data analysis. The approach utilizes nearest neighbor information and can be applied to sequences of multivariate observations or non-Euclidean data objects, such as network data. Different stopping rules are explored, and one specific rule is recommended due to its desirable properties. An accurate analytic approximation of the average run length is derived for the recommended rule, making it an easy off-the-shelf approach for real multivariate/object sequential data monitoring applications. Simulations reveal…
We review autoregressive models for the analysis of multivariate count time series. In doing so, we discuss the choice of a suitable distribution for a vectors of count random variables. This review focus on three main approaches taken for multivariate count time series analysis: (a) integer autoregressive processes, (b) parameter-driven models and (c) observation-driven models. The aim of this work is to highlight some recent methodological developments and propose some potentially useful research topics.
We study a class of missingness mechanisms, called sequentially additive nonignorable, for modeling multivariate data with item nonresponse. These mechanisms explicitly allow the probability of nonresponse for each variable to depend on the value of that variable, thereby representing nonignorable missingness mechanisms. These missing data models are identified by making use of auxiliary information on marginal distributions, such as marginal probabilities for multivariate categorical variables or moments for numeric variables. We present theory proving identification results, and illustrate t…
This paper introduces multivariate Poisson autoregressive models with exogenous covariates (PoARX) for modelling multivariate time series of counts. We obtain conditions for the PoARX process to be stationary and ergodic before proposing a computationally efficient procedure for estimation of parameters by the method of inference functions (IFM) and obtaining asymptotic normality of these estimators. Lastly, we demonstrate an application to count data for the number of people entering and exiting a building, and show how the different aspects of the model combine to produce a strong predictive…
I begin my discussion by summarizing the methodology proposed and new distributional results on multivariate log-Gamma derived in the paper. Then, I draw an interesting connection between their work with mean field variational Bayes. Lastly, I make some comments on the simulation results and the performance of the proposed Poisson multivariate spatio-temporal mixed effects model (P-MSTM).
Responding appropriately to the detections of a sequential change detector requires knowledge of the rate at which false positives occur in the absence of change. Setting detection thresholds to achieve a desired false positive rate is challenging. Existing works resort to setting time-invariant thresholds that focus on the expected runtime of the detector in the absence of change, either bounding it loosely from below or targeting it directly but with asymptotic arguments that we show cause significant miscalibration in practice. We present a simulation-based approach to setting time-varying …
There are many different ways in which change point analysis can be performed, from purely parametric methods to those that are distribution free. The ecp package is designed to perform multiple change point analysis while making as few assumptions as possible. While many other change point methods are applicable only for univariate data, this R package is suitable for both univariate and multivariate observations. Estimation can be based upon either a hierarchical divisive or agglomerative algorithm. Divisive estimation sequentially identifies change points via a bisection algorithm. The aggl…
We propose nonparametric open-end sequential testing procedures that can detect all types of changes in the contemporary distribution function of possibly multivariate observations. Their asymptotic properties are theoretically investigated under stationarity and under alternatives to stationarity. Monte Carlo experiments reveal their good finite-sample behavior in the case of continuous univariate, bivariate and trivariate observations. A short data example concludes the work.
Modeling data with multivariate count responses is a challenging problem due to the discrete nature of the responses. Existing methods for univariate count responses cannot be easily extended to the multivariate case since the dependency among multiple responses needs to be properly accommodated. In this paper, we propose a multivariate Poisson log-normal regression model for multivariate data with count responses. By simultaneously estimating the regression coefficients and inverse covariance matrix over the latent variables with an efficient Monte Carlo EM algorithm, the proposed regression …
This article presents a new continuous-time modelling framework for multivariate time series of counts which have an infinitely divisible marginal distribution. The model is based on a mixed moving average process driven by Lévy noise - called a trawl process - where the serial correlation and the cross-sectional dependence are modelled independently of each other. Such processes can exhibit short or long memory. We derive a stochastic simulation algorithm and a statistical inference method for such processes. The new methodology is then applied to high frequency financial data, where we inves…
The Poisson distribution has been widely studied and used for modeling univariate count-valued data. Multivariate generalizations of the Poisson distribution that permit dependencies, however, have been far less popular. Yet, real-world high-dimensional count-valued data found in word counts, genomics, and crime statistics, for example, exhibit rich dependencies, and motivate the need for multivariate distributions that can appropriately model this data. We review multivariate distributions derived from the univariate Poisson, categorizing these models into three main classes: 1) where the mar…
Univariate regression models have rich literature for counting data. However, this is not the case for multivariate count data. Therefore, we present the Multivariate Generalized Linear Mixed Models framework that deals with a multivariate set of responses, measuring the correlation between them through random effects that follows a multivariate normal distribution. This model is based on a GLMM with a random intercept and the estimation process remains the same as a standard GLMM with random effects integrated out via Laplace approximation. We efficiently implemented this model through the TM…
We are studying the problems of modeling and inference for multivariate count time series data with Poisson marginals. The focus is on linear and log-linear models. For studying the properties of such processes we develop a novel conceptual framework which is based on copulas. However, our approach does not impose the copula on a vector of counts; instead the joint distribution is determined by imposing a copula function on a vector of associated continuous random variables. This specific construction avoids conceptual difficulties resulting from the joint distribution of discrete random varia…
In various situations in the insurance industry, in finance, in epidemiology, etc., one needs to represent the joint evolution of the number of occurrences of an event. In this paper, we present a multivariate integer-valued autoregressive (MINAR) model, derive its properties and apply the model to earthquake occurrences across various pairs of tectonic plates. The model is an extension of Pedelis & Karlis (2011) where cross autocorrelation (spatial contagion in a seismic context) is considered. We fit various bivariate count models and find that for many contiguous tectonic plates, spatial co…
In many fields and applications count data can be subject to delayed reporting. This is where the total count, such as the number of disease cases contracted in a given week, may not be immediately available, instead arriving in parts over time. For short term decision making, the statistical challenge lies in predicting the total count based on any observed partial counts, along with a robust quantification of uncertainty. In this article we discuss previous approaches to modelling delayed reporting and present a multivariate hierarchical framework where the count generating process and delay…
Two-sample tests for multivariate data and non-Euclidean data are widely used in many fields. Parametric tests are mostly restrained to certain types of data that meets the assumptions of the parametric models. In this paper, we study a nonparametric testing procedure that utilizes graphs representing the similarity among observations. It can be applied to any data types as long as an informative similarity measure on the sample space can be defined. The classic test based on a similarity graph has a problem when the two sample sizes are different. We solve the problem by applying appropriate …
Researchers are often interested in understanding the relationship between a set of covariates and a set of response variables. To achieve this goal, the use of regression analysis, either linear or generalized linear models, is largely applied. However, such models only allow users to model one response variable at a time. Moreover, it is not possible to directly calculate from the regression model a correlation measure between the response variables. In this article, we employed the Multivariate Generalized Linear Mixed Models framework, which allows the specification of a set of response va…
