Negative binomial regression is commonly employed to analyze overdispersed count data. With small to moderate sample sizes, the maximum likelihood estimator of the dispersion parameter may be subject to a significant bias, that in turn affects inference on mean parameters. This paper proposes inference for negative binomial regression based on adjustments of the score function aimed at mean and median bias reduction. The resulting estimating equations are similar to those available for improved inference in generalized linear models and, in particular, can be solved using a suitable extension of iterative weighted least squares. Simulation studies show a remarkable performance of the new methods, which are also found to solve in many cases numerical problems of maximum likelihood estimates. The methods are illustrated and evaluated using two case studies: an Ames salmonella assay data set and data on epileptic seizures. Inference based on adjusted scores turns out to be generally preferable to explicit bias correction.
This paper introduces a new biased estimator for the negative binomial regression model that is a generalization of Liu-type estimator proposed for the linear model in [12]. Since the variance of the maximum likelihood estimator (MLE) is inflated when there is multicollinearity between the explanatory variables, a new biased estimator is proposed to solve the problem and decrease the variance of MLE in order to make stable inferences. Moreover, we obtain some theoretical comparisons between the new estimator and some others via matrix mean squared error (MMSE) criterion. Furthermore, a Monte C…
Two-sample inference for the difference of population means typically relies upon a Central Limit Theorem approximation. When data are drawn from a Negative Binomial distribution, previous work of Shilane et al. (2010) showed that a Normal approximation is often unreliable in one-sample inference and proposed alternative techniques. We seek to extend these methods to the problem of two-sample inference on the difference of sample means in highly dispersed Negative Binomial models. We demonstrate that the Normal approximation is considerably more robust in the two-sample setting and may often b…
The Negative Binomial distribution becomes highly skewed under extreme dispersion. Even at moderately large sample sizes, the sample mean exhibits a heavy right tail. The standard Normal approximation often does not provide adequate inferences about the data's mean in this setting. In previous work, we have examined alternative methods of generating confidence intervals for the expected value. These methods were based upon Gamma and Chi Square approximations or tail probability bounds such as Bernstein's Inequality. We now propose growth estimators of the Negative Binomial mean. Under high dis…
Quantile regression relates the quantile of the response to a linear predictor. For a discrete response distributions, like the Poission, Binomial and the negative Binomial, this approach is not feasible as the quantile function is not bijective. We argue to use a continuous model-aware interpolation of the quantile function, allowing for proper quantile inference while retaining model interpretation. This approach allows for proper uncertainty quantification and mitigates the issue of quantile crossing. Our reanalysis of hospitalisation data considered in Congdon (2017) shows the advantages o…
In this article, we propose a new three parameter distribution by compounding negative binomial with reciprocal inverse Gaussian model called negative binomial-reciprocal inverse Gaussian distribution. This model is tractable with some important properties not only in actuarial science but in other fields as well where overdispersion pattern is seen. Some basic properties including recurrence relation of probabilities for computation of successive probabilities have been discussed. In its compound version, when the claims are absolutely continuous, an integral equation for the probability dens…
The logistic regression model is known to converge to a Poisson point process model if the binary response tends to infinitely imbalanced. In this paper, it is shown that this phenomenon is universal in a wide class of link functions on binomial regression. The proof relies on the extreme value theory. For the logit, probit and complementary log-log link functions, the intensity measure of the point process becomes an exponential family. For some other link functions, deformed exponential families appear. A penalized maximum likelihood estimator for the Poisson point process model is suggested…
Zero-inflated regression models have had wide application recently and have provenuseful in modeling data with many zeros. Zero-inflated Binomial (ZIB) regression model is an extension of the ordinary binomial distribution that takes into account the excess of zeros. In comparing the probit model to the logistic model, many authors believe that there is little theoretical justification in choosing one formulation over the other in most circumstances involving binary responses. The logit model is considered to be computationally simpler but it is based on a more restrictive assumption of error …
We describe a general method for the construction of a confidence region for the two parameters of the Negative Binomial Distribution. This is achieved by expanding the sampling distribution of Method-of-Moments estimators, using the Central Limit Theorem.
In behavioral and psychiatric research, data consisting of a per-subject proportion of "successes" and "failures" over a finite number of trials often arise. This kind of clustered binary data are usually non-normally distributed, which can cause issues with parameter estimation and predictions if the usual general linear model is applied and sample size is small. Here we studied the performances of some of the available analytic methods applicable to the analysis of proportion data; namely linear regression, Poisson regression, beta-binomial regression and Generalized Linear Mixed Models (GLM…
The generalized negative binomial distribution (GNB) is a new flexible family of discrete distributions that are mixed Poisson laws with the mixing generalized gamma (GG) distributions. This family of discrete distributions is very wide and embraces Poisson distributions, negative binomial distributions, Sichel distributions, Weibull--Poisson distributions and many other types of distributions supplying descriptive statistics with many flexible models. These distributions seem to be very promising for the statistical description of many real phenomena. GG distributions are widely applied in si…
Penalization of the likelihood by Jeffreys' invariant prior, or by a positive power thereof, is shown to produce finite-valued maximum penalized likelihood estimates in a broad class of binomial generalized linear models. The class of models includes logistic regression, where the Jeffreys-prior penalty is known additionally to reduce the asymptotic bias of the maximum likelihood estimator; and also models with other commonly used link functions such as probit and log-log. Shrinkage towards equiprobability across observations, relative to the maximum likelihood estimator, is established theore…
Count data and recurrent events in clinical trials, such as the number of lesions in magnetic resonance imaging in multiple sclerosis, the number of relapses in multiple sclerosis, the number of hospitalizations in heart failure, and the number of exacerbations in asthma or in chronic obstructive pulmonary disease (COPD) are often modeled by negative binomial distributions. In this manuscript we study planning and analyzing clinical trials with group sequential designs for negative binomial outcomes. We propose a group sequential testing procedure for negative binomial outcomes based on Wald s…
This paper proposes new linear regression models to deal with overdispersed binomial datasets. These new models, called tilted beta binomial regression models, are defined from the tilted beta binomial distribution, proposed assuming that the parameter of the binomial distribution follows a tilted beta distribution. As a particular case of this regression models, we propose the beta rectangular binomial regression models, defined from the binomial distribution assuming that their parameters follow a beta rectangular distribution. These new linear regression models, defined assuming that the pa…
The negative-binomial distribution is adopted for analyzing asbestos-fiber counts so as to account for both the sampling errors in capturing only a finite number of fibers as well as the inevitable human variation in identifying and counting sampled fibers. A simple approximation to this distribution is developed for the derivation of quantiles and approximate confidence limits. The success of the approximation depends critically on the use of the Stirling expansion to sufficient order, on exact normalization of the approximating distribution, on reasonable perturbation of quantities from the …
This article introduces a k-Inflated Negative Binomial mixture distribution/regression model as a more flexible alternative to zero-inflated Poisson distribution/regression model. An EM algorithm has been employed to estimate the model's parameters. Then, such new model along with a Pareto mixture model have been employed to design an optimal rate--making system. Namely, this article employs number/size of reported claims of Iranian third party insurance dataset. Then, it employs the k-Inflated Negative Binomial mixture distribution/regression model as well as other well developed counting mod…
We introduce a semi-parametric approach to ecological regression for disease mapping, based on modelling the regression M-quantiles of a Negative Binomial variable. The proposed method is robust to outliers in the model covariates, including those due to measurement error, and can account for both spatial heterogeneity and spatial clustering. A simulation experiment based on the well-known Scottish lip cancer data set is used to compare the M-quantile modelling approach and a random effects modelling approach for disease mapping. This suggests that the M-quantile approach leads to predicted re…
This paper introduces a cure rate survival model by assuming that the time to the event of interest follows a beta prime distribution and that the number of competing causes of the event of interest follows a negative binomial distribution. This model provides a novel alternative to the existing cure rate regression models due to its flexibility, as the beta prime model can exhibit greater levels of skewness and kurtosis than those of the gamma and inverse Gaussian distributions. Moreover, the hazard rate of this model can have an upside-down bathtub or an increasing shape. We approach both pa…
In this article, we discuss a bivariate distribution whose conditionals are univariate binomial distributions and the marginals are not binomial that exhibits negative correlation. Some useful structural properties of this distribution namely marginals, moments, generating functions, stochastic ordering are investigated. Simple proofs of negative correlation, marginal over-dispersion, distribution of sum and conditional given the sum are also derived. The distribution is shown to be a member of the multi-parameter exponential family and some natural but useful consequences are also outlined. T…
Beta-binomial/Poisson models have been used by many authors to model multivariate count data. Lora and Singer (Statistics in Medicine, 2008) extended such models to accommodate repeated multivariate count data with overdipersion in the binomial component. To overcome some of the limitations of that model, we consider a beta-binomial/gamma-Poisson alternative that also allows for both overdispersion and different covariances between the Poisson counts. We obtain maximum likelihood estimates for the parameters using a Newton-Raphson algorithm and compare both models in a practical example.
Bayesian variable selection is a powerful tool for data analysis, as it offers a principled method for variable selection that accounts for prior information and uncertainty. However, wider adoption of Bayesian variable selection has been hampered by computational challenges, especially in difficult regimes with a large number of covariates or non-conjugate likelihoods. Generalized linear models for count data, which are prevalent in biology, ecology, economics, and beyond, represent an important special case. Here we introduce an efficient MCMC scheme for variable selection in binomial and ne…
RNA-Seq data characteristically exhibits large variances, which need to be appropriately accounted for in the model. We first explore the effects of this variability on the maximum likelihood estimator (MLE) of the overdispersion parameter of the negative binomial distribution, and propose instead the use an estimator obtained via maximization of the marginal likelihood in a conjugate Bayesian framework. We show, via simulation studies, that the marginal MLE can better control this variation and produce a more stable and reliable estimator. We then formulate a conjugate Bayesian hierarchical m…
In this work we apply the methodology of integral priors to handle Bayesian model selection in binomial regression models with a general link function. These models are very often used to investigate associations and risks in epidemiological studies where one goal is to exhibit whether or not an exposure is a risk factor for developing a certain disease; the purpose of the current paper is to test the effect of specific exposure factors. We formulate the problem as a Bayesian model selection case and solve it using objective Bayes factors. To construct the reference prior distributions on the …
We derive the sample size formulae for comparing two negative binomial rates based on both the relative and absolute rate difference metrics in noninferiority and equivalence trials with unequal follow-up times, and establish an approximate relationship between the sample sizes required for the treatment comparison based on the two treatment effect metrics. The proposed method allows the dispersion parameter to vary by treatment groups. The accuracy of these methods is assessed by simulations. It is demonstrated that ignoring the between-subject variation in the follow-up time by setting the f…
Using a sample from a population to estimate the proportion of the population with a certain category label is a broadly important problem. In the context of microbiome studies, this problem arises when researchers wish to use a sample from a population of microbes to estimate the population proportion of a particular taxon, known as the taxon's relative abundance. In this paper, we propose a beta-binomial model for this task. Like existing models, our model allows for a taxon's relative abundance to be associated with covariates of interest. However, unlike existing models, our proposal also …
The study of sums of possibly associated Bernoulli random variables has been hampered by an asymmetry between positive correlation and negative correlation. The Conway-Maxwell Binomial (COMB) distribution and its multivariate extension, the Conway-Maxwell Multinomial (COMM) distribution, gracefully model both positive and negative association. Sufficient statistics and a family of proper conjugate distributions are found. The relationship of this distribution to the exchangeable special case is explored, and two applications are discussed.
This work presents a construction of stationary Markov models with negative-binomial marginal distributions. A simple closed form expression for the corresponding transition probabilities is given, linking the proposal to well-known classes of birth and death processes and thus revealing interesting characterizations. The advantage of having such closed form expressions is tested on simulated and real data.
In this paper, we present a Weibull link (skewed) model for categorical response data arising from binomial as well as multinomial model. We show that, for such types of categorical data, the most commonly used models (logit, probit and complementary log-log) can be obtained as limiting cases. We further compare the proposed model with some other asymmetrical models. The Bayesian as well as frequentist estimation procedures for binomial and multinomial data responses are presented in details. The analysis of two data sets to show the efficiency of the proposed model is performed.
Count data, for example the number of observed cases of a disease in a city, often arise in the fields of healthcare analytics and epidemiology. In this paper, we consider performing regression on multivariate data in which our outcome is a count. Specifically, we derive log-likelihood functions for finite mixtures of regression models involving counts that come from a Poisson distribution, as well as a negative binomial distribution when the counts are significantly overdispersed. Within our proposed modeling framework, we carry out optimal component selection using the information criteria s…
By developing data augmentation methods unique to the negative binomial (NB) distribution, we unite seemingly disjoint count and mixture models under the NB process framework. We develop fundamental properties of the models and derive efficient Gibbs sampling inference. We show that the gamma-NB process can be reduced to the hierarchical Dirichlet process with normalization, highlighting its unique theoretical, structural and computational advantages. A variety of NB processes with distinct sharing mechanisms are constructed and applied to topic modeling, with connections to existing algorithm…
A beta-negative binomial (BNB) process is proposed, leading to a beta-gamma-Poisson process, which may be viewed as a "multi-scoop" generalization of the beta-Bernoulli process. The BNB process is augmented into a beta-gamma-gamma-Poisson hierarchical structure, and applied as a nonparametric Bayesian prior for an infinite Poisson factor analysis model. A finite approximation for the beta process Levy random measure is constructed for convenient implementation. Efficient MCMC computations are performed with data augmentation and marginalization techniques. Encouraging results are shown on docu…
In this article, a generalized version of Negative binomial-beta exponential distribution with five parameters have been introduced. Some interesting submodels have been derived from it. A comprehensive mathematical treatment of proposed distribution is being provided. Various expressions like that of moment generating function, moments are derived. The model parameters are estimated by the maximum likelihood method. Finally, the application of proposed distribution is carried out on one sample of automobile insurance data.
In regression analysis of counts, a lack of simple and efficient algorithms for posterior computation has made Bayesian approaches appear unattractive and thus underdeveloped. We propose a lognormal and gamma mixed negative binomial (NB) regression model for counts, and present efficient closed-form Bayesian inference; unlike conventional Poisson models, the proposed approach has two free parameters to include two different kinds of random effects, and allows the incorporation of prior information, such as sparsity in the regression coefficients. By placing a gamma distribution prior on the NB…
We develop a Bayesian nonparametric approach to a general family of latent class problems in which individuals can belong simultaneously to multiple classes and where each class can be exhibited multiple times by an individual. We introduce a combinatorial stochastic process known as the negative binomial process (NBP) as an infinite-dimensional prior appropriate for such problems. We show that the NBP is conjugate to the beta process, and we characterize the posterior distribution under the beta-negative binomial process (BNBP) and hierarchical models based on the BNBP (the HBNBP). We study t…
A common approach to analyze a covariate-sample count matrix, an element of which represents how many times a covariate appears in a sample, is to factorize it under the Poisson likelihood. We show its limitation in capturing the tendency for a covariate present in a sample to both repeat itself and excite related ones. To address this limitation, we construct negative binomial factor analysis (NBFA) to factorize the matrix under the negative binomial likelihood, and relate it to a Dirichlet-multinomial distribution based mixed-membership model. To support countably infinite factors, we propos…
We consider the segmentation problem of Poisson and negative binomial (i.e. overdispersed Poisson) rate distributions. In segmentation, an important issue remains the choice of the number of segments. To this end, we propose a penalized log-likelihood estimator where the penalty function is constructed in a non-asymptotic context following the works of L. Birgé and P. Massart. The resulting estimator is proved to satisfy an oracle inequality. The performances of our criterion is assessed using simulated and real datasets in the RNA-seq data analysis context.
In this paper, two-state Markov switching models are proposed to study accident frequencies. These models assume that there are two unobserved states of roadway safety, and that roadway entities (roadway segments) can switch between these states over time. The states are distinct, in the sense that in the different states accident frequencies are generated by separate counting processes (by separate Poisson or negative binomial processes). To demonstrate the applicability of the approach presented herein, two-state Markov switching negative binomial models are estimated using five-year acciden…
We analyse tourism behaviour of Italian residents in the period covering the 2008 Great Recession. Using the Trips of Italian Residents in Italy and Abroad quarterly survey, carried out by the Italian National Institute of Statistics, we investigate whether and how the economic recession has affected the total number of overnight stays. The response variable is the result of a two-stage decision process: first we choose to take a holiday, then for how long. Moreover, since the number of overnight stays is typically concentrated on specific lengths (week-end, week, fortnight) we observe multipl…
The spectrum of mutations in a collection of cancer genomes can be described by a mixture of a few mutational signatures. The mutational signatures can be found using non-negative matrix factorization (NMF). To extract the mutational signatures we have to assume a distribution for the observed mutational counts and a number of mutational signatures. In most applications, the mutational counts are assumed to be Poisson distributed, and the rank is chosen by comparing the fit of several models with the same underlying distribution and different values for the rank using classical model selection…
Epigenetic observations are represented by the total number of reads from a given pool of cells and the number of methylated reads, making it reasonable to model this data by a binomial distribution. There are numerous factors that can influence the probability of success in a particular region. Moreover, there is a strong spatial (alongside the genome) dependence of these probabilities. We incorporate dependence on the covariates and the spatial dependence of the methylation probability for observations from a pool of cells by means of a binomial regression model with a latent Gaussian field …
In this paper, we propose a closed form approximation to the mean and variance of a new generalization of negative binomial (NGNB) distribution arising from the Extended COM-Poisson (ECOMP) distribution developed by Chakraborty and Imoto (2016)(see [4]). The NGNB is a special case of the ECOMP distribution and was named so by these authors. This distribution is more flexible in terms of the dispersion index as compared to its ordinary counterparts. It approaches the COM-Poisson distribution (Shmueli et al. 2005) [11] under suitable limiting conditions. The NGNB can also be obtained from the CO…
The beta-negative binomial process (BNBP), an integer-valued stochastic process, is employed to partition a count vector into a latent random count matrix. As the marginal probability distribution of the BNBP that governs the exchangeable random partitions of grouped data has not yet been developed, current inference for the BNBP has to truncate the number of atoms of the beta process. This paper introduces an exchangeable partition probability function to explicitly describe how the BNBP clusters the data points of each group into a random number of exchangeable partitions, which are shared a…
