Multivariate Count Data Research Articles

Automatic cross-validation in structured models: Is it time to leave out leave-one-out?

Standard techniques such as leave-one-out cross-validation (LOOCV) might not be suitable for evaluating the predictive performance of models incorporating structured random effects. In such cases, the correlation between the training and test sets could have a notable impact on the model’s prediction error. To overcome this issue, an automatic group construction procedure for leave-group-out cross validation (LGOCV) has recently emerged as a valuable tool for enhancing predictive performance measurement in structured models. The purpose of this paper is (i) to compare LOOCV and LGOCV within structured models, emphasizing model selection and predictive performance, and (ii) to provide real data applications in spatial statistics using complex structured models fitted with INLA, showcasing the utility of the automatic LGOCV method. First, we briefly review the key aspects of the recently proposed LGOCV method for automatic group construction in latent Gaussian models. We also demonstrate the effectiveness of this method for selecting the model with the highest predictive performance by simulating extrapolation tasks in both temporal and spatial data analyses. Finally, we provide insights into the effectiveness of the LGOCV method in modeling complex structured data, encompassing spatio-temporal multivariate count data, spatial compositional data, and spatio-temporal geospatial data.

Predicting the multivariate zero-inflated counts: A novel model averaging method under Pearson loss.

Excessive zeros in multivariate count data are often observed in scenarios of biomedicine and public health. To provide a better analysis on this type of data, we first develop a marginalized multivariate zero-inflated Poisson (MZIP) regression model to directly interpret the overall exposure effects on marginal means. Then, we define a multiple Pearson residual for our newly developed MZIP regression model by simultaneously taking heterogeneity and correlation into consideration. Furthermore, a new model averaging prediction method is introduced based on the multiple Pearson residual, and the asymptotical optimality of this model averaging prediction is proved. Simulations and two empirical applications in medicine are used to illustrate the effectiveness of the proposed method.

Determination of correlations in multivariate count data with informative observation times.

We consider there are various types of recurrent events and the total number of occurrences are collected at the random observation times. It has concerned that the observation process may not be independent to the multivariate event processes, hence the total counts and observation times may be correlated and the dependence may exist among different types of the event processes as well. Many methods have developed nonparametric models to accommodate such unknown structures; however, it is difficult to assess and directly quantify their correlation relationships. A multivariate frailty model is proposed to this study, in which the event and observation processes are linked by frailty variables whose joint distribution can be implicitly specified through the multivariate normal distribution with some unknown covariance matrix. The Bayesian inference method is conducted to obtain the estimates of the regression coefficients and correlation parameters. We use a form of trigonometric functions to represent the covariance matrix, so that it meets the positive-definiteness condition efficiently during the estimation schemes. The simulation studies demonstrate the utility of the proposed models. We apply the model to a skin cancer prevention study, and aim to determine the covariate and association effects. We found treatment is significant in determining the duration of examination times; prior-counts, age and gender are significant variables on the occurrence rates of tumor counts. Using the covariance matrix to access the underlying dependent structure, the mutual correlations among them are all positive, and the basal cell counts are more related to the examination times.

Multivariate Generalized Linear Mixed Models for Count Data

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 TMB package available in R. We used Poisson, negative binomial (NB), and COM-Poisson distributions. To assess the estimator properties, we conducted a simulation study considering four different sample sizes and three different correlation values for each distribution. We achieved unbiased and consistent estimators for Poisson and NB distributions; for COM-Poisson estimators were consistent, but biased, especially for dispersion, variance, and correlation parameter estimators. These models were applied to two datasets. The first concerns a sample from 30 different sites collected in Australia where the number of times each one of the 41 different ant species was registered; which results in an impressive 820 variance-covariance and 41 dispersion parameters are estimated simultaneously, let alone the regression parameters. The second is from the Australia Health Survey with 5 response variables and 5190 respondents. These datasets can be considered overdispersed by the generalized dispersion index. The COM-Poisson model overcame the other two competitors considering three goodness-of-fit indexes, AIC, BIC, and maximized log-likelihood values. As a result, it estimated parameters with smaller standard errors and a greater number of significant correlation coefficients. Therefore, the proposed model is capable of dealing with multivariate count data, either under- equi- or overdispersed responses, and measuring any kind of correlation between them taking into account the effects of the covariates.

Bayesian modeling of interaction between features in sparse multivariate count data with application to microbiome study

Bayesian modeling of interaction between features in sparse multivariate count data with application to microbiome study

A Bayesian joint model for compositional mediation effect selection in microbiome data.

Analyzing multivariate count data generated by high-throughput sequencing technology in microbiome research studies is challenging due to the high-dimensional and compositional structure of the data and overdispersion. In practice, researchers are often interested in investigating how the microbiome may mediate the relation between an assigned treatment and an observed phenotypic response. Existing approaches designed for compositional mediation analysis are unable to simultaneously determine the presence of direct effects, relative indirect effects, and overall indirect effects, while quantifying their uncertainty. We propose a formulation of a Bayesian joint model for compositional data that allows for the identification, estimation, and uncertainty quantification of various causal estimands in high-dimensional mediation analysis. We conduct simulation studies and compare our method's mediation effects selection performance with existing methods. Finally, we apply our method to a benchmark data set investigating the sub-therapeutic antibiotic treatment effect on body weight in early-life mice.

A Bayesian zero-inflated Dirichlet-multinomial regression model for multivariate compositional count data.

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-inflated DM model for multivariate compositional count data with excess zeros. We then extend our approach to regression settings and embed sparsity-inducing priors to perform variable selection for high-dimensional covariate spaces. Throughout, modeling decisions are made to boost scalability without sacrificing interpretability or imposing limiting assumptions. Extensive simulations and an application to a human gut microbiome dataset are presented to compare the performance of the proposed method to existing approaches. We provide an accompanying R package with a user-friendly vignette to apply our method to otherdatasets.

Multiple inflated negative binomial regression for correlated multivariate count data

Abstract This article aims to provide a method of regression for multivariate multiple inflated count responses assuming the responses follow a negative binomial distribution. Negative binomial regression models are common in the literature for modeling univariate and multivariate count data. However, two problems commonly arise in modeling such data: choice of the multivariate form of the underlying distribution and modeling the zero-inflated structure of the data. Copula functions have become a popular solution to the former problem because they can model the response variables’ dependence structure. The latter problem is often solved by modeling an assumed latent variable Z Z generating excess zero-valued counts in addition to the underlying distribution. However, despite their flexibility, zero-inflation models do not account for the case of m m additional inflated values at k 1 , k 2 , … , k m {{\bf{k}}}_{1},{{\bf{k}}}_{2},\ldots ,{{\bf{k}}}_{m} . We propose a multivariate multiple-inflated negative binomial regression model for modeling such cases. Furthermore, we present an iterative procedure for estimating model parameters using maximum likelihood estimation. The multivariate distribution functions considering the dependence structure of the response vectors are found using copula methods. The proposed method is illustrated using simulated data and applied to real data.

Clustering multivariate count data via Dirichlet-multinomial network fusion

Clustering of multivariate count data has widespread applications in areas such as text analysis and microbiome studies. The need to account for overdispersion generally results in a nonconvex loss function, which does not fit into the existing convex clustering framework. Moreover, prior knowledge of a network over the samples, often available from citation or similarity relationships, is not taken into account. We introduce Dirichlet-multinomial network fusion (DMNet) for clustering multivariate count data, which models the samples via Dirichlet-multinomial distributions with individual parameters and employs a weighted group L1 fusion penalty to pursue homogeneity over a prespecified network. To circumvent the nonconvexity issue, we present two exponential family approximations to the Dirichlet-multinomial distribution, which are amenable to efficient optimization and theoretical analysis. We derive an ADMM algorithm and establish nonasymptotic error bounds for the proposed methods. Our bounds involve a trade-off between the connectivity of the network and its fidelity to the true parameter. The usefulness of our methods is illustrated through simulation studies and two text clustering applications.

Change-Point detection for autocorrelated multivariate Poisson processes

ABSTRACT Statistical process control for count data has attracted increasing attention in recent years. The need for efficient control charts suitable for autocorrelated multivariate count processes is well recognized. However, there is a scarcity of research aiming to take into account the autocorrelation among the multivariate count data. We are motivated to study the Phase I analysis of autocorrelated multivariate Poisson processes to detect and estimate change points in reference datasets. A change-point method is proposed based on the multivariate Poisson INAR(1) model by integrating generalized likelihood ratio tests with the binary segmentation procedure. A diagnostic procedure for pinpointing the location of the change point is also discussed. Our simulation results show that the proposed method has a better performance than the benchmark method, across a range of possible shifts, in the detection effectiveness and diagnostic accuracy. Furthermore, a real example from the manufacturing industry is used to illustrate the implementation steps of the proposed method.

Bayesian Semiparametric Regression Analysis of Multivariate Panel Count Data

Panel count data often occur in a long-term recurrent event study, where the exact occurrence time of the recurrent events is unknown, but only the occurrence count between any two adjacent observation time points is recorded. Most traditional methods only handle panel count data for a single type of event. In this paper, we propose a Bayesian semiparameteric approach to analyze panel count data for multiple types of events. For each type of recurrent event, the proportional mean model is adopted to model the mean count of the event, where its baseline mean function is approximated by monotone I-splines. The correlation between multiple types of events is modeled by common frailty terms and scale parameters. Unlike many frequentist estimating equation methods, our approach is based on the observed likelihood and makes no assumption on the relationship between the recurrent process and the observation process. Under the Poisson counting process assumption, we develop an efficient Gibbs sampler based on novel data augmentation for the Markov chain Monte Carlo sampling. Simulation studies show good estimation performance of the baseline mean functions and the regression coefficients; meanwhile, the importance of including the scale parameter to flexibly accommodate the correlation between events is also demonstrated. Finally, a skin cancer data example is fully analyzed to illustrate the proposed methods.

Dealing with overdispersion in multivariate count data

The problem of overdispersion in multivariate count data is a challenging issue. It covers a central role mainly due to the relevance of modern technology-based data, such as Next Generation Sequencing and textual data from the web or digital collections. A comprehensive analysis of the likelihood-based models for extra-variation data is presented. Particular attention is paid to the models feasible for high-dimensional data. A new approach together with its parametric-estimation procedure is proposed. It can be viewed as a deeper version of the Dirichlet-Multinomial distribution and it leads to important results allowing to get a better approximation of the observed variability. A significative comparison of the proposed model and existing strategies is made through two different simulation studies and an empirical data set, that confirm a better capability to describe overdispersion.

A NEW MULTIVARIATE ZERO-INFLATED HURDLE MODEL WITH APPLICATIONS IN AUTOMOBILE INSURANCE

AbstractThe fact that a large proportion of insurance policyholders make no claims during a one-year period highlights the importance of zero-inflated count models when analyzing the frequency of insurance claims. There is a vast literature focused on the univariate case of zero-inflated count models, while work in the area of multivariate models is considerably less advanced. Given that insurance companies write multiple lines of insurance business, where the claim counts on these lines of business are often correlated, there is a strong incentive to analyze multivariate claim count models. Motivated by the idea of Liu and Tian (Computational Statistics and Data Analysis, 83, 200–222; 2015), we develop a multivariate zero-inflated hurdle model to describe multivariate count data with extra zeros. This generalization offers more flexibility in modeling the behavior of individual claim counts while also incorporating a correlation structure between claim counts for different lines of insurance business. We develop an application of the expectation–maximization (EM) algorithm to enable the statistical inference necessary to estimate the parameters associated with our model. Our model is then applied to an automobile insurance portfolio from a major insurance company in Spain. We demonstrate that the model performance for the multivariate zero-inflated hurdle model is superior when compared to several alternatives.

Multivariate zero-inflated Bell distribution and its inference and applications

In this paper we introduce a multivariate family of distributions for multivariate count data with excess zeros, which is a multivariate extension of the univariate zero-inflated Bell distribution. We derive various general properties of this multivariate distribution. In particular, the marginal distributions are univariate zero-inflated Bell distributions. The model parameters are estimated using the traditional maximum likelihood estimation method. In addition, we develop a simple EM algorithm to compute the maximum likelihood estimates of the parameters of the new multivariate distribution with closed-form expressions for the maximum likelihood estimators. Empirical applications that employ real multivariate count data are considered to illustrate the usefulness of the new class of multivariate distributions, and comparisons with the multivariate zero-inflated Poisson distribution, multivariate zero-adjusted Poisson distributions, and multivariate zero-inflated generalized Poisson distribution are made.

Type I multivariate zero-inflated COM-Poisson regression model.

In this paper, we present the Type I multivariate zero-inflated Conway-Maxwell-Poisson distribution, whose development is based on the extension of the Type I multivariate zero-inflated Poisson distribution. We developed important properties of the distribution and present a regression model. The AIC and BIC criteria are used to select the best fitted model. Two real data sets have been used to illustrate the proposed model. Moreover, we conclude by stating that the Type I multivariate zero-inflated Conway-Maxwell-Poisson distribution produces a better fitted model for multivariate count data with excess of zeros.

Modelling Excess Zeros in Count Data: A New Perspective on Modelling Approaches

SummaryWe consider the analysis of count data in which the observed frequency of zero counts is unusually large, typically with respect to the Poisson distribution. We focus on two alternative modelling approaches: over‐dispersion (OD) models and zero‐inflation (ZI) models, both of which can be seen as generalisations of the Poisson distribution; we refer to these as implicit and explicit ZI models, respectively. Although sometimes seen as competing approaches, they can be complementary; OD is a consequence of ZI modelling, and ZI is a by‐product of OD modelling. The central objective in such analyses is often concerned with inference on the effect of covariates on the mean, in light of the apparent excess of zeros in the counts. Typically, the modelling of the excess zerosper seis a secondary objective, and there are choices to be made between, and within, the OD and ZI approaches. The contribution of this paper is primarily conceptual. We contrast, descriptively, the impact on zeros of the two approaches. We further offer a novel descriptive characterisation of alternative ZI models, including the classic hurdle and mixture models, by providing a unifying theoretical framework for their comparison. This in turn leads to a novel and technically simpler ZI model. We develop the underlying theory for univariate counts and touch on its implication for multivariate count data.

Semiparametric analysis of multivariate panel count data with nonlinear interactions.

Multivariate panel count data frequently arise in follow up studies involving several related types of recurrent events. For univariate panel count data, several varying coefficient models have been developed. However, varying coefficient models for multivariate panel count data remain to be studied. In this paper, we propose a varying coefficient mean model for multivariate panel count data to describe the possible nonlinear interact effects between the covariates and the local logarithm partial likelihood procedure is considered to estimate the unknown covariate effects. Furthermore, a Breslow-type estimator is constructed for the baseline mean functions. The consistency and asymptotic normality of the proposed estimators are established under some mild conditions. The utility of the proposed approach is evaluated by some numerical simulations and an application to a dataset of skin cancer study.

Filtering the Intensity of Public Concern from Social Media Count Data with Jumps

Abstract Count time series obtained from online social media data, such as Twitter, have drawn increasing interest among academics and market analysts over the past decade. Transforming Web activity records into counts yields time series with peculiar features, including the coexistence of smooth paths and sudden jumps, as well as cross-sectional and temporal dependence. Using Twitter posts about country risks for the United Kingdom and the United States, this paper proposes an innovative state space model for multivariate count data with jumps. We use the proposed model to assess the impact of public concerns in these countries on market systems. To do so, public concerns inferred from Twitter data are unpacked into country-specific persistent terms, risk social amplification events and co-movements of the country series. The identified components are then used to investigate the existence and magnitude of country-risk spillovers and social amplification effects on the volatility of financial markets.

A Bayesian nonparametric analysis for zero-inflated multivariate count data with application to microbiome study.

High-throughput sequencing technology has enabled researchers to profile microbial communities from a variety of environments, but analysis of multivariate taxon count data remains challenging. We develop a Bayesian nonparametric (BNP) regression model with zero inflation to analyse multivariate count data from microbiome studies. A BNP approach flexibly models microbial associations with covariates, such as environmental factors and clinical characteristics. The model produces estimates for probability distributions which relate microbial diversity and differential abundance to covariates, and facilitates community comparisons beyond those provided by simple statistical tests. We compare the model to simpler models and popular alternatives in simulation studies, showing, in addition to these additional community-level insights, it yields superior parameter estimates and model fit in various settings. The model's utility is demonstrated by applying it to a chronic wound microbiome data set and a Human Microbiome Project data set, where it is used to compare microbial communities present in different environments.

Multivariate Count Data Models for Time Series Forecasting.

Count data appears in many research fields and exhibits certain features that make modeling difficult. Most popular approaches to modeling count data can be classified into observation and parameter-driven models. In this paper, we review two models from these classes: the log-linear multivariate conditional intensity model (also referred to as an integer-valued generalized autoregressive conditional heteroskedastic model) and the non-linear state-space model for count data. We compare these models in terms of forecasting performance on simulated data and two real datasets. In simulations, we consider the case of model misspecification. We find that both models have advantages in different situations, and we discuss the pros and cons of inference for both models in detail.