A new approach for Bayesian model averaging (BMA) and selection is proposed, based on the mixture model approach for hypothesis testing in Kaniav et al., 2014. Inheriting from the good properties of this approach, it extends BMA to cases where improper priors are chosen for parameters that are common to all candidate models.
From an algorithmic point of view, our approach consists in sampling from the posterior distribution of the single-datum mixture of all candidate models, weighted by their prior probabilities. We show that this posterior distribution is equal to the 'Bayesian-model averaged' posterior distribution over all candidate models, weighted by their posterior probability. From this BMA posterior sample, a simple Monte-Carlo estimate of each model's posterior probability is derived, as well as importance sampling estimates for expectations under each model's posterior distribution.
Chain Event Graphs (CEGs) are a widely applicable class of probabilistic graphical model that can represent context-specific independence statements and asymmetric unfoldings of events in an easily interpretable way. Existing model selection literature on CEGs has largely focused on obtaining the maximum a posteriori (MAP) CEG. However, MAP selection is well-known to ignore model uncertainty. Here, we explore the use of Bayesian model averaging over this class. We demonstrate how this approach can quantify model uncertainty and leads to more robust inference by identifying shared features acro…
In mixture model-based clustering applications, it is common to fit several models from a family and report clustering results from only the `best' one. In such circumstances, selection of this best model is achieved using a model selection criterion, most often the Bayesian information criterion. Rather than throw away all but the best model, we average multiple models that are in some sense close to the best one, thereby producing a weighted average of clustering results. Two (weighted) averaging approaches are considered: averaging the component membership probabilities and averaging models…
In this paper we construct optimal designs for frequentist model averaging estimation. We derive the asymptotic distribution of the model averaging estimate with fixed weights in the case where the competing models are non-nested and none of these models is correctly specified. A Bayesian optimal design minimizes an expectation of the asymptotic mean squared error of the model averaging estimate calculated with respect to a suitable prior distribution. We demonstrate that Bayesian optimal designs can improve the accuracy of model averaging substantially. Moreover, the derived designs also impr…
Bayesian model averaging (BMA) is a statistical method for post-processing forecast ensembles of atmospheric variables, obtained from multiple runs of numerical weather prediction models, in order to create calibrated predictive probability density functions (PDFs). The BMA predictive PDF of the future weather quantity is the mixture of the individual PDFs corresponding to the ensemble members and the weights and model parameters are estimated using ensemble members and validating observation from a given training period. In the present paper we introduce a BMA model for calibrating wind speed…
Determining the extent to which a patient is benefiting from cancer therapy is challenging. Criteria for quantifying the extent of "tumor response" observed within a few cycles of treatment have been established for various types of solid as well as hematologic malignancies. These measures comprise the primary endpoints of phase II trials. Regulatory approvals of new cancer therapies, however, are usually contingent upon the demonstration of superior overall survival with randomized evidence acquired with a phase III trial comparing the novel therapy to an appropriate standard of care treatmen…
This paper deals with Bayesian inference of a mixture of Gaussian distributions. A novel formulation of the mixture model is introduced, which includes the prior constraint that each Gaussian component is always assigned a minimal number of data points. This enables noninformative improper priors such as the Jeffreys prior to be placed on the component parameters. We demonstrate difficulties involved in specifying a prior for the standard Gaussian mixture model, and show how the new model can be used to overcome these. MCMC methods are given for efficient sampling from the posterior of this mo…
The integrated nested Laplace approximation (INLA) for Bayesian inference is an efficient approach to estimate the posterior marginal distributions of the parameters and latent effects of Bayesian hierarchical models that can be expressed as latent Gaussian Markov random fields (GMRF). The representation as a GMRF allows the associated software R-INLA to estimate the posterior marginals in a fraction of the time as typical Markov chain Monte Carlo algorithms. INLA can be extended by means of Bayesian model averaging (BMA) to increase the number of models that it can fit to conditional latent G…
Rankings and ratings are commonly used to express preferences but provide distinct and complementary information. Rankings give ordinal and scale-free comparisons but lack granularity; ratings provide cardinal and granular assessments but may be highly subjective or inconsistent. Collecting and analyzing rankings and ratings jointly has not been performed until recently due to a lack of principled methods. In this work, we propose a flexible, joint statistical model for rankings and ratings under heterogeneous preferences: the Bradley-Terry-Luce-Binomial (BTL-Binomial). We employ a Bayesian mi…
Finite mixture models are used in statistics and other disciplines, but inference for mixture models is challenging due, in part, to the multimodality of the likelihood function and the so-called label switching problem. We propose extensions of the Approximate Bayesian Computation-Population Monte Carlo (ABC-PMC) algorithm as an alternative framework for inference on finite mixture models. There are several decisions to make when implementing an ABC-PMC algorithm for finite mixture models, including the selection of the kernels used for moving the particles through the iterations, how to addr…
We exploit a suitable moment-based characterization of the mixture of Poisson distribution for developing Bayesian inference for the unknown size of a finite population whose units are subject to multiple occurrences during an enumeration sampling stage. This is a particularly challenging setting for which many other attempts have been made for inferring the unknown characteristics of the population. Here we put particular emphasis on the construction of a default prior elicitation of the characteristics of the mixing distribution. We assess the comparative performance of our approach in real …
The exponential and the Lomax distributions are widely used in life testing experiments in mixture models. A mixture model of exponential distribution and Lomax distribution is proposed. Parameters of the proposed model are estimated using classical and Bayesian procedures under type-I right censoring. Expressions for Bayes estimators are derived assuming noninformative (uniform and Jeffreys) priors under symmetric and asymmetric loss functions. Posterior predictive distributions of a future observation are derived and predictive estimates are obtained. Extensive Monte Carlo simulations are ca…
The use of a finite mixture of normal distributions in model-based clustering allows to capture non-Gaussian data clusters. However, identifying the clusters from the normal components is challenging and in general either achieved by imposing constraints on the model or by using post-processing procedures. Within the Bayesian framework we propose a different approach based on sparse finite mixtures to achieve identifiability. We specify a hierarchical prior where the hyperparameters are carefully selected such that they are reflective of the cluster structure aimed at. In addition this prior a…
In this article we propose novel Bayesian nonparametric methods using Dirichlet Process Mixture (DPM) models for detecting pairwise dependence between random variables while accounting for uncertainty in the form of the underlying distributions. A key criteria is that the procedures should scale to large data sets. In this regard we find that the formal calculation of the Bayes factor for a dependent-vs.-independent DPM joint probability measure is not feasible computationally. To address this we present Bayesian diagnostic measures for characterising evidence against a "null model" of pairwis…
Discrete mixture models are one of the most successful approaches for density estimation. Under a Bayesian nonparametric framework, Dirichlet process location-scale mixture of Gaussian kernels is the golden standard, both having nice theoretical properties and computational tractability. In this paper we explore the use of the skew-normal kernel, which can naturally accommodate several degrees of skewness by the use of a third parameter. The choice of this kernel function allows us to formulate nonparametric location-scale-shape mixture prior with large support and good performance in differen…
The elicitation of an ordinal judgment on multiple alternatives is often required in many psychological and behavioral experiments to investigate preference/choice orientation of a specific population. The Plackett-Luce model is one of the most popular and frequently applied parametric distributions to analyze rankings of a finite set of items. The present work introduces a Bayesian finite mixture of Plackett-Luce models to account for unobserved sample heterogeneity of partially ranked data. We describe an efficient way to incorporate the latent group structure in the data augmentation approa…
We present a Bayesian mixture model for estimating the joint distribution of mixed ordinal, nominal, and continuous data conditional on a set of fixed variables. The model uses multivariate normal and categorical mixture kernels for the random variables. It induces dependence between the random and fixed variables through the means of the multivariate normal mixture kernels and via a truncated local Dirichlet process. The latter encourages observations with similar values of the fixed variables to share mixture components. Using a simulation of data fusion, we illustrate that the model can est…
Analysis of a Bayesian mixture model for the Matrix Langevin distribution on the Stiefel manifold is presented. The model exploits a particular parametrization of the Matrix Langevin distribution, various aspects of which are elaborated on. A general, and novel, family of conjugate priors, and an efficient Markov chain Monte Carlo (MCMC) sampling scheme for the corresponding posteriors is then developed for the mixture model. Theoretical properties of the prior and posterior distributions, including posterior consistency, are explored in detail. Extensive simulation experiments are presented t…
For many decades now, Bayesian Model Averaging (BMA) has been a popular framework to systematically account for model uncertainty that arises in situations when multiple competing models are available to describe the same or similar physical process. The implementation of this framework, however, comes with a multitude of practical challenges including posterior approximation via Markov Chain Monte Carlo and numerical integration. We present a Variational Bayesian Inference approach to BMA as a viable alternative to the standard solutions which avoids many of the aforementioned pitfalls. The p…
Describing the complex dependence structure of extreme phenomena is particularly challenging. To tackle this issue we develop a novel statistical algorithm that describes extremal dependence taking advantage of the inherent hierarchical dependence structure of the max-stable nested logistic distribution and that identifies possible clusters of extreme variables using reversible jump Markov chain Monte Carlo techniques. Parsimonious representations are achieved when clusters of extreme variables are found to be completely independent. Moreover, we significantly decrease the computational comple…
Discrete choice experiments are frequently used to quantify consumer preferences by having respondents choose between different alternatives. Choice experiments involving mixtures of ingredients have been largely overlooked in the literature, even though many products and services can be described as mixtures of ingredients. As a consequence, little research has been done on the optimal design of choice experiments involving mixtures. The only existing research has focused on D-optimal designs, which means that an estimation-based approach was adopted. However, in experiments with mixtures, it…
We develop a flexible Erlang mixture model for survival analysis. The model for the survival density is built from a structured mixture of Erlang densities, mixing on the integer shape parameter with a common scale parameter. The mixture weights are constructed through increments of a distribution function on the positive real line, which is assigned a Dirichlet process prior. The model has a relatively simple structure, balancing flexibility with efficient posterior computation. Moreover, it implies a mixture representation for the hazard function that involves time-dependent mixture weights,…
In this paper, we propose a nonparametric Bayesian approach for Lindsey and penalized Gaussian mixtures methods. We compare these methods with the Dirichlet process mixture model. Our approach is a Bayesian nonparametric method not based solely on a parametric family of probability distributions. Thus, the fitted models are more robust to model misspecification. Also, with the Bayesian approach, we have the entire posterior distribution of our parameter of interest; it can be summarized through credible intervals, mean, median, standard deviation, quantiles, etc. The Lindsey, penalized Gaussia…
Financial studies require volatility based models which provides useful insights on risks related to investments. Stochastic volatility models are one of the most popular approaches to model volatility in such studies. The asset returns under study may come in multiple clusters which are not captured well assuming standard distributions. Mixture distributions are more appropriate in such situations. In this work, an algorithm is demonstrated which is capable of studying finite mixtures but with unknown number of components. This algorithm uses a Birth-Death process to adjust the number of comp…
When using mixture models it may be the case that the modeller has a-priori beliefs or desires about what the components of the mixture should represent. For example, if a mixture of normal densities is to be fitted to some data, it may be desirable for components to focus on capturing differences in location rather than scale. We introduce a framework called proximity penalty priors (PPPs) that allows this preference to be made explicit in the prior information. The approach is scale-free and imposes minimal restrictions on the posterior; in particular no arbitrary thresholds need to be set. …
We develop a method to perform model averaging in two-stage linear regression systems subject to endogeneity. Our method extends an existing Gibbs sampler for instrumental variables to incorporate a component of model uncertainty. Direct evaluation of model probabilities is intractable in this setting. We show that by nesting model moves inside the Gibbs sampler, model comparison can be performed via conditional Bayes factors, leading to straightforward calculations. This new Gibbs sampler is only slightly more involved than the original algorithm and exhibits no evidence of mixing difficultie…
Analysts often use data-driven approaches to supplement their substantive knowledge when selecting covariates for causal effect estimation. Multiple variable selection procedures tailored for causal effect estimation have been devised in recent years, but additional developments are still required to adequately address the needs of data analysts. In this paper, we propose a Generalized Bayesian Causal Effect Estimation (GBCEE) algorithm to perform variable selection and produce double robust estimates of causal effects for binary or continuous exposures and outcomes. GBCEE employs a prior dist…
Statistical modeling is a key component in the extraction of physical results from lattice field theory calculations. Although the general models used are often strongly motivated by physics, many model variations can frequently be considered for the same lattice data. Model averaging, which amounts to a probability-weighted average over all model variations, can incorporate systematic errors associated with model choice without being overly conservative. We discuss the framework of model averaging from the perspective of Bayesian statistics, and give useful formulae and approximations for the…
In this paper we present a novel methodology to perform Bayesian model selection in linear models with heavy-tailed distributions. We consider a finite mixture of distributions to model a latent variable where each component of the mixture corresponds to one possible model within the symmetrical class of normal independent distributions. Naturally, the Gaussian model is one of the possibilities. This allows for a simultaneous analysis based on the posterior probability of each model. Inference is performed via Markov chain Monte Carlo - a Gibbs sampler with Metropolis-Hastings steps for a clas…
A Bayesian approach is used to estimate the covariance matrix of Gaussian data. Ideas from Gaussian graphical models and model selection are used to construct a prior for the covariance matrix that is a mixture over all decomposable graphs. For this prior the probability of each graph size is specified by the user and graphs of equal size are assigned equal probability. Most previous approaches assume that all graphs are equally probable. We show empirically that the prior that assigns equal probability over graph sizes outperforms the prior that assigns equal probability over all graphs, both…
The distribution of single Stop Signal Reaction Times (SSRT) in the stop signal task (SST) as a measurement of the latency of the unobservable stopping process has been modeled with a nonparametric method by Hans Colonius (1990) and with a Bayesian parametric method by Eric-Jan Wagenmakers and colleagues (2012). These methods assume equal impact of the preceding trial type (go/stop) in the SST trials on the SSRT distributional estimation without addressing the case of the violated assumption. This study presents the required model by considering two-state mixture model for the SSRT distributio…
Recent advances on overfitting Bayesian mixture models provide a solid and straightforward approach for inferring the underlying number of clusters and model parameters in heterogeneous datasets. The applicability of such a framework in clustering correlated high dimensional data is demonstrated. For this purpose an overfitting mixture of factor analyzers is introduced, assuming that the number of factors is fixed. A Markov chain Monte Carlo (MCMC) sampler combined with a prior parallel tempering scheme is used to estimate the posterior distribution of model parameters. The optimal number of f…
We study the problem of learning Bayesian network structures from data. We develop an algorithm for finding the k-best Bayesian network structures. We propose to compute the posterior probabilities of hypotheses of interest by Bayesian model averaging over the k-best Bayesian networks. We present empirical results on structural discovery over several real and synthetic data sets and show that the method outperforms the model selection method and the state of-the-art MCMC methods.
Bayesian Model Averaging (BMA) is an application of Bayesian inference to the problems of model selection, combined estimation and prediction that produces a straightforward model choice criteria and less risky predictions. However, the application of BMA is not always straightforward, leading to diverse assumptions and situational choices on its different aspects. Despite the widespread application of BMA in the literature, there were not many accounts of these differences and trends besides a few landmark revisions in the late 1990s and early 2000s, therefore not taking into account any adva…
We assess the accuracy of Bayesian polynomial extrapolations from small parameter values, x, to large values of x. We consider a set of polynomials of fixed order, intended as a proxy for a fixed-order effective field theory (EFT) description of data. We employ Bayesian Model Averaging (BMA) to combine results from different order polynomials (EFT orders). Our study considers two "toy problems" where the underlying function used to generate data sets is known. We use Bayesian parameter estimation to extract the polynomial coefficients that describe these data at low x. A "naturalness" prior is…
We show that a probabilistic version of the classical forward-stepwise variable inclusion procedure can serve as a general data-augmentation scheme for model space distributions in (generalized) linear models. This latent variable representation takes the form of a Markov process, thereby allowing information propagation algorithms to be applied for sampling from model space posteriors. In particular, we propose a sequential Monte Carlo method for achieving effective unbiased Bayesian model averaging in high-dimensional problems, utilizing proposal distributions constructed using local informa…
Bayesian Additive Regression Trees (BART) is a statistical sum of trees model. It can be considered a Bayesian version of machine learning tree ensemble methods where the individual trees are the base learners. However for data sets where the number of variables $p$ is large (e.g. $p>5,000$) the algorithm can become prohibitively expensive, computationally. Another method which is popular for high dimensional data is random forests, a machine learning algorithm which grows trees using a greedy search for the best split points. However, as it is not a statistical model, it cannot produce probab…
Economic modeling in the presence of endogeneity is subject to model uncertainty at both the instrument and covariate level. We propose a Two-Stage Bayesian Model Averaging (2SBMA) methodology that extends the Two-Stage Least Squares (2SLS) estimator. By constructing a Two-Stage Unit Information Prior in the endogenous variable model, we are able to efficiently combine established methods for addressing model uncertainty in regression models with the classic technique of 2SLS. To assess the validity of instruments in the 2SBMA context, we develop Bayesian tests of the identification restrictio…
This article studies Bayesian model averaging (BMA) in the context of competing expensive computer models in a typical nuclear physics setup. While it is well known that BMA accounts for the additional uncertainty of the model itself, we show that it also decreases the posterior variance of the prediction errors via an explicit decomposition. We extend BMA to the situation where the competing models are defined on non-identical study regions. Any model's local forecasting difficulty is offset by predictions obtained from the average model, thus extending individual models to the full domain. W…
This survey covers state-of-the-art Bayesian techniques for the estimation of mixtures. It complements the earlier Marin, Mengersen and Robert (2005) by studying new types of distributions, the multinomial, latent class and t distributions. It also exhibits closed form solutions for Bayesian inference in some discrete setups. Lastly, it sheds a new light on the computation of Bayes factors via the approximation of Chib (1995).
We present a proposal to deal with the non-normality issue in the context of regression models with measurement errors when both the response and the explanatory variable are observed with error. We extend the normal model by jointly modeling the unobserved covariate and the random errors by a finite mixture of scale mixture of skew-normal distributions. This approach allows us to model data with great flexibility, accommodating skewness, heavy tails, and multi-modality.
The method of model averaging has become an important tool to deal with model uncertainty, for example in situations where a large amount of different theories exist, as are common in economics. Model averaging is a natural and formal response to model uncertainty in a Bayesian framework, and most of the paper deals with Bayesian model averaging. The important role of the prior assumptions in these Bayesian procedures is highlighted. In addition, frequentist model averaging methods are also discussed. Numerical methods to implement these methods are explained, and I point the reader to some fr…
Dirichlet process mixture model (DPMM) is a popular Bayesian nonparametric model. In this paper, we apply this model to weighted data and then estimate the un-weighted distribution from the corresponding weighted distribution using the metropolis-Hastings algorithm. We then apply the DPMM with different kernels to simulated and real data sets. In particular, we work with lifetime data in the presence of censored data and then calculate estimated density and survival values.
In economic applications, model averaging has found principal use examining the validity of various theories related to observed heterogeneity in outcomes such as growth, development, and trade.Though often easy to articulate, these theories are imperfectly captured quantitatively. A number of different proxies are often collected for a given theory and the uneven nature of this collection requires care when employing model averaging. Furthermore, if valid, these theories ought to be relevant outside of any single narrowly focused outcome equation. We propose a methodology which treats theorie…
A new method for the computation of the posterior distribution of the number k of components in a finite mixture is presented. Two aspects of prior specification are also studied: an argument is made for the use of a Poisson(1) distribution as the prior for k; and methods are given for the selection of hyperparameter values in the mixture of normals model, with natural conjugate priors on the components parameters.
