Composite likelihood estimation has an important role in the analysis of multivariate data for which the full likelihood function is intractable. An important issue in composite likelihood inference is the choice of the weights associated with lower-dimensional data sub-sets, since the presence of incompatible sub-models can deteriorate the accuracy of the resulting estimator. In this paper, we introduce a new approach for simultaneous parameter estimation by tilting, or re-weighting, each sub-likelihood component called discriminative composite likelihood estimation (D-McLE). The data-adaptive weights maximize the composite likelihood function, subject to moving a given distance from uniform weights; then, the resulting weights can be used to rank lower-dimensional likelihoods in terms of their influence in the composite likelihood function. Our analytical findings and numerical examples support the stability of the resulting estimator compared to estimators constructed using standard composition strategies based on uniform weights. The properties of the new method are illustrated through simulated data and real spatial data on multivariate precipitation extremes.
It is well-known that in some situations it is not easy to compute the likelihood function as the datasets might be large or the model is too complex. In that contexts composite likelihood, derived by multiplying the likelihoods of subjects of the variables, may be useful. The extension of the classical likelihood ratio test statistics to the framework of composite likelihoods is used as a procedure to solve the problem of testing in the context of composite likelihood. In this paper we introduce and study a new family of test statistics for composite likelihood: Composite ϕ-divergence test st…
A composite likelihood is a combination of low-dimensional likelihood objects useful in applications where the data have complex structure. Although composite likelihood construction is a crucial aspect influencing both computing and statistical properties of the resulting estimator, currently there does not seem to exist a universal rule to combine low-dimensional likelihood objects that is statistically justified and fast in execution. This paper develops a methodology to select and combine the most informative low-dimensional likelihoods from a large set of candidates while carrying out par…
Maximum composite likelihood estimation is a useful alternative to maximum likelihood estimation when data arise from data generating processes (DGPs) that do not admit tractable joint specification. We demonstrate that generic composite likelihoods consisting of marginal and conditional specifications permit the simple construction of composite likelihood ratio-like statistics from which finite-sample valid confidence sets and hypothesis tests can be constructed. These statistics are universal in the sense that they can be constructed from any estimator for the parameter of the underlying DGP…
Composite likelihood has shown promise in settings where the number of parameters $p$ is large due to its ability to break down complex models into simpler components, thus enabling inference even when the full likelihood is not tractable. Although there are a number of ways to formulate a valid composite likelihood in the finite-$p$ setting, there does not seem to exist agreement on how to construct composite likelihoods that are comp utationally efficient and statistically sound when $p$ is allowed to diverge. This article introduces a method to select sparse composite likelihoods by minimiz…
A composite likelihood is a non-genuine likelihood function that allows to make inference on limited aspects of a model, such as marginal or conditional distributions. Composite likelihoods are not proper likelihoods and need therefore calibration for their use in inference, from both a frequentist and a Bayesian perspective. The maximizer to the composite likelihood can serve as an estimator and its variance is assessed by means of a suitably defined sandwich matrix. In the Bayesian setting, the composite likelihood can be adjusted by means of magnitude and curvature methods. Magnitude method…
We present a vine copula based composite likelihood approach to model spatial dependencies, which allows to perform prediction at arbitrary locations. This approach combines established methods to model (spatial) dependencies. On the one hand the geostatistical concept utilizing spatial differences between the variable locations to model the extend of spatial dependencies is applied. On the other hand the flexible class of C-vine copulas is utilized to model the spatial dependency structure locally. These local C-vine copulas are parametrized jointly, exploiting an existing relationship betwee…
In the last years there has been a growing interest in proposing methods for estimating covariance functions for geostatistical data. Among these, maximum likelihood estimators have nice features when we deal with a Gaussian model. However maximum likelihood becomes impractical when the number of observations is very large. In this work we review some solutions and we contrast them in terms of loss of statistical efficiency and computational burden. Specifically we focus on three types of weighted composite likelihood functions based on pairs and we compare them with the method of covariance t…
This paper proposes a penalized composite likelihood method for model selection in colored graphical Gaussian models. The method provides a sparse and symmetry-constrained estimator of the precision matrix, and thus conducts model selection and precision matrix estimation simultaneously. In particular, the method uses penalty terms to constrain the elements of the precision matrix, which enables us to transform the model selection problem into a constrained optimization problem. Further, computer experiments are conducted to illustrate the performance of the proposed new methodology. It is sho…
Composite likelihoods are increasingly used in applications where the full likelihood is analytically unknown or computationally prohibitive. Although the maximum composite likelihood estimator has frequentist properties akin to those of the usual maximum likelihood estimator, Bayesian inference based on composite likelihoods has yet to be explored. In this paper we investigate the use of the Metropolis--Hastings algorithm to compute a pseudo-posterior distribution based on the composite likelihood. Two methodologies for adjusting the algorithm are presented and their performance on approximat…
The traditional maximum likelihood estimator (MLE) is often of limited use in complex high-dimensional data due to the intractability of the underlying likelihood function. Maximum composite likelihood estimation (McLE) avoids full likelihood specification by combining a number of partial likelihood objects depending on small data subsets, thus enabling inference for complex data. A fundamental difficulty in making the McLE approach practicable is the selection from numerous candidate likelihood objects for constructing the composite likelihood function. In this paper, we propose a flexible Gi…
Computer models are used to model complex processes in various disciplines. Often, a key source of uncertainty in the behavior of complex computer models is uncertainty due to unknown model input parameters. Statistical computer model calibration is the process of inferring model parameter values, along with associated uncertainties, from observations of the physical process and from model outputs at various parameter settings. Observations and model outputs are often in the form of high-dimensional spatial fields, especially in the environmental sciences. Sound statistical inference may be co…
Max-stable processes are a popular tool for the study of environmental extremes, and the extremal skew-$t$ process is a general model that allows for a flexible extremal dependence structure. For inference on max-stable processes with high-dimensional data, exact likelihood-based estimation is computationally intractable. Composite likelihoods, using lower dimensional components, and Stephenson-Tawn likelihoods, using occurrence times of maxima, are both attractive methods to circumvent this issue for moderate dimensions. In this article we establish the theoretical formulae for simulations of…
Positive-definite matrix-variate data is becoming popular in computer vision. The computer vision data descriptors in the form of Region Covariance Descriptors (RCD) are positive definite matrices, which extract the key features of the images. The RCDs are extensively used in image set classification. Some classification methods treating RCDs as Wishart distributed random matrices are being proposed. However, the majority of the current methods preclude the potential correlation among the RCDs caused by the so-called non-voxel information (e.g., subjects' ages and nose widths, etc). Modeling c…
The correct use and interpretation of models depends on several steps, two of which being the calibration by parameter estimation and the analysis of uncertainty. In the biological literature, these steps are seldom discussed together, but they can be seen as fitting pieces of the same puzzle. In particular, analytical procedures for uncertainty estimation may be masking a high degree of uncertainty coming from a model with a stable structure, but insufficient data. Under a likelihoodist approach, the problem of uncertainty estimation is closely related to the problem of composite hypothesis. …
The class of composite likelihood functions provides a flexible and powerful toolkit to carry out approximate inference for complex statistical models when the full likelihood is either impossible to specify or unfeasible to compute. However, the strenght of the composite likelihood approach is dimmed when considering hypothesis testing about a multidimensional parameter because the finite sample behavior of likelihood ratio, Wald, and score-type test statistics is tied to the Godambe information matrix. Consequently inaccurate estimates of the Godambe information translate in inaccurate p-val…
The multivariate probit is popular for modeling correlated binary data, with an attractive balance of flexibility and simplicity. However, considerable challenges remain in computation and in devising a clear statistical framework. Interest in the multivariate probit has increased in recent years. Current applications include genomics and precision medicine, where simultaneous modeling of multiple traits may be of interest, and computational efficiency is an important consideration. We propose a fast method for multivariate probit estimation via a two-stage composite likelihood. We explore com…
Testing the association between a phenotype and many genetic variants from case-control data is essential in genome-wide association study (GWAS). This is a challenging task as many such variants are correlated or non-informative. Similarities exist in testing the population difference between two groups of high dimensional data with intractable full likelihood function. Testing may be tackled by a maximum composite likelihood (MCL) not entailing the full likelihood, but current MCL tests are subject to power loss for involving non-informative or redundant sub-likelihoods. In this paper, we de…
We consider a discrete latent variable model for two-way data arrays, which allows one to simultaneously produce clusters along one of the data dimensions (e.g. exchangeable observational units or features) and contiguous groups, or segments, along the other (e.g. consecutively ordered times or locations). The model relies on a hidden Markov structure but, given its complexity, cannot be estimated by full maximum likelihood. We therefore introduce composite likelihood methodology based on considering different subsets of the data. The proposed approach is illustrated by simulation, and with an…
In almost any geostatistical analysis, one of the underlying, often implicit, modelling assump- tions is that the spatial locations, where measurements are taken, are recorded without error. In this study we develop geostatistical inference when this assumption is not valid. This is often the case when, for example, individual address information is randomly altered to provide pri- vacy protection or imprecisions are induced by geocoding processes and measurement devices. Our objective is to develop a method of inference based on the composite likelihood that over- comes the inherent computati…
The method of generalized estimating equations (GEE) is popular in the biostatistics literature for analyzing longitudinal binary and count data. It assumes a generalized linear model (GLM) for the outcome variable, and a working correlation among repeated measurements. In this paper, we introduce a viable competitor: the weighted scores method for GLM margins. We weight the univariate score equations using a working discretized multivariate normal model that is a proper multivariate model. Since the weighted scores method is a parametric method based on likelihood, we propose composite likeli…
Large-scale Gaussian process models are becoming increasingly important and widely used in many areas, such as, computer experiments, stochastic optimization via simulation, and machine learning using Gaussian processes. The standard methods, such as maximum likelihood estimation (MLE) for parameter estimation and the best linear unbiased predictor (BLUP) for prediction, are generally the primary choices in many applications. In spite of their merits, those methods are not feasible due to intractable computation when the sample size is huge. A novel method for the purposes of parameter estimat…
Max-stable processes are the most popular models for high-impact spatial extreme events, as they arise as the only possible limits of spatially-indexed block maxima. However, likelihood inference for such models suffers severely from the curse of dimensionality, since the likelihood function involves a combinatorially exploding number of terms. In this paper, we propose using the Vecchia approximation, which conveniently decomposes the full joint density into a linear number of low-dimensional conditional density terms based on well-chosen conditioning sets designed to improve and accelerate i…
The literature on clustering for continuous data is rich and wide; differently, that one developed for categorical data is still limited. In some cases, the problem is made more difficult by the presence of noise variables/dimensions that do not contain information about the clustering structure and could mask it. The aim of this paper is to propose a model for simultaneous clustering and dimensionality reduction of ordered categorical data able to detect the discriminative dimensions discarding the noise ones. Following the underlying response variable approach, the observed variables are con…
The role played by the composite analogue of the log likelihood ratio in hypothesis testing and in setting confidence regions is not as prominent as it is in the canonical likelihood setting, since its asymptotic distribution depends on the unknown parameter. Approximate pivots based on the composite log likelihood ratio can be derived by using asymptotic arguments. However, the actual distribution of such pivots may differ considerably from the asymptotic reference, leading to tests and confidence regions whose levels are distant from the nominal ones. The use of bootstrap rather than asympto…
The composite likelihood (CL) is amongst the computational methods used for estimation of the generalized linear mixed model (GLMM) in the context of bivariate meta-analysis of diagnostic test accuracy studies. Its advantage is that the likelihood can be derived conveniently under the assumption of independence between the random effects, but there has not been a clear analysis of the merit or necessity of this method. For synthesis of diagnostic test accuracy studies, a copula mixed model has been proposed in the biostatistics literature. This general model includes the GLMM as a special case…
This paper develops a particle filter maximum likelihood estimator for the competitive storage model. The estimator is suitable for inference problems in commodity markets where only reliable price data is available for estimation, and shocks are temporally dependent. The estimator efficiently utilizes the information present in the conditional distribution of prices when shocks are not iid. Compared to Deaton and Laroque's composite quasi-maximum likelihood estimator, simulation experiments and real-data estimation show substantial improvements in both bias and precision. Simulation experimen…
We revisit and generalize the concept of composite likelihood as a method to make a probabilistic inference by aggregation of multiple Bayesian agents, thereby defining a class of predictive models which we call composite Bayesian. This perspective gives insight to choose the weights associated with composite likelihood, either a priori or via learning; in the latter case, they may be tuned so as to minimize prediction cross-entropy, yielding an easy-to-solve convex problem. We argue that composite Bayesian inference is a middle way between generative and discriminative models that trades off …
Among many efforts to facilitate timely access to safe and effective medicines to children, increased attention has been given to extrapolation. Loosely, it is the leveraging of conclusions or available data from adults or older age groups to draw conclusions for the target pediatric population when it can be assumed that the course of the disease and the expected response to a medicinal product would be sufficiently similar in the pediatric and the reference population. Extrapolation then can be characterized as a statistical mapping of information from the reference (adults or older age grou…
The composite likelihood (CL) is amongst the computational methods used for the estimation of high-dimensional multivariate normal (MVN) copula models with discrete responses. Its computational advantage, as a surrogate likelihood method, is that is based on the independence likelihood for the univariate regression and non-regression parameters and pairwise likelihood for the correlation parameters, but the efficiency of estimating the univariate regression and non-regression parameters can be low. For a high-dimensional discrete response, we propose weighted versions of the composite likeliho…
We present methodology for constructing exact significance tests for cross tabulated data for "difficult" composite alternative hypotheses that have no natural test statistic. We construct a test for discovering Simpson's Paradox and a general test for discovering positive dependence between two ordinal variables. Our tests are Bayesian extensions of the likelihood ratio test, they are optimal with respect to the prior distribution, and are also closely related to Bayes factors and Bayesian FDR controlling testing procedures.
Institute of Computing Technology, Chinese Academy of Sciences（中国科学院计算技术研究所）；University of Chinese Academy of Sciences（中国科学院大学）；Peking University（北京大学）；Huazhong University of Science and Technology（华中科技大学）
Accurate prediction of inter-residue contacts of a protein is important to calcu- lating its tertiary structure. Analysis of co-evolutionary events among residues has been proved effective to inferring inter-residue contacts. The Markov ran- dom field (MRF) technique, although being widely used for contact prediction, suffers from the following dilemma: the actual likelihood function of MRF is accurate but time-consuming to calculate, in contrast, approximations to the actual likelihood, say pseudo-likelihood, are efficient to calculate but inaccu- rate. Thus, how to achieve both accuracy and …
A new robust stochastic volatility (SV) model having Student-t marginals is proposed. Our process is defined through a linear normal regression model driven by a latent gamma process that controls temporal dependence. This gamma process is strategically chosen to enable us to find an explicit expression for the pairwise joint density function of the Student-t response process. With this at hand, we propose a composite likelihood (CL) based inference for our model, which can be straightforwardly implemented with a low computational cost. This is a remarkable feature of our Student-t SV process …
In high-dimensional model selection problems, penalized simple least-square approaches have been extensively used. This paper addresses the question of both robustness and efficiency of penalized model selection methods, and proposes a data-driven weighted linear combination of convex loss functions, together with weighted $L_1$-penalty. It is completely data-adaptive and does not require prior knowledge of the error distribution. The weighted $L_1$-penalty is used both to ensure the convexity of the penalty term and to ameliorate the bias caused by the $L_1$-penalty. In the setting with dimen…
Fast Stochastic Nearest Neighbor Pairwise Composite Likelihood for Massive Spatial Datasets
Universidad Adolfo Ibáñez（阿道夫·伊巴涅斯大学）；Ca’ Foscari University of Venice（威尼斯卡福斯卡里大学）；Universidad Técnica Federico Santa María（弗雷德里科·圣塔玛丽亚理工大学）；Universidad del Bío-Bío（比奥比奥大学）
The last decade has seen max-stable processes emerge as a common tool for the statistical modeling of spatial extremes. However, their application is complicated due to the unavailability of the multivariate density function, and so likelihood-based methods remain far from providing a complete and flexible framework for inference. In this article we develop inferentially practical, likelihood-based methods for fitting max-stable processes derived from a composite-likelihood approach. The procedure is sufficiently reliable and versatile to permit the simultaneous modeling of marginal and depend…
High-dimensional data clustering has become and remains a challenging task for modern statistics and machine learning, with a wide range of applications. We consider in this work the powerful discriminative latent mixture model, and we extend it to the Bayesian framework. Modeling data as a mixture of Gaussians in a low-dimensional discriminative subspace, a Gaussian prior distribution is introduced over the latent group means and a family of twelve submodels are derived considering different covariance structures. Model inference is done with a variational EM algorithm, while the discriminati…
Statistical modeling of multivariate and spatial extreme events has attracted broad attention in various areas of science. Max-stable distributions and processes are the natural class of models for this purpose, and many parametric families have been developed and successfully applied. Due to complicated likelihoods, the efficient statistical inference is still an active area of research, and usually composite likelihood methods based on bivariate densities only are used. Thibaud et al. (2016, Ann. Appl. Stat., to appear) use a Bayesian approach to fit a Brown--Resnick process to extreme tempe…
Statistical analysis of max-stable processes used to model spatial extremes has been limited by the difficulty in calculating the joint likelihood function. This precludes all standard likelihood-based approaches, including Bayesian approaches. In this paper we present a Bayesian approach through the use of approximate Bayesian computing. This circumvents the need for a joint likelihood function by instead relying on simulations from the (unavailable) likelihood. This method is compared with an alternative approach based on the composite likelihood. We demonstrate that approximate Bayesian com…
The Posterior distribution of the Likelihood Ratio (PLR) is proposed by Dempster in 1974 for significance testing in the simple vs composite hypotheses case. In this hypotheses test case, classical frequentist and Bayesian hypotheses tests are irreconcilable, as emphasized by Lindley's paradox, Berger & Selke in 1987 and many others. However, Dempster shows that the PLR (with inner threshold 1) is equal to the frequentist p-value in the simple Gaussian case. In 1997, Aitkin extends this result by adding a nuisance parameter and showing its asymptotic validity under more general distributions. …
The main purpose of this paper is to introduce first a new family of empirical test statistics for testing a simple null hypothesis when the vector of parameters of interest are defined through a specific set of unbiased estimating functions. This family of test statistics is based on a distance between two probability vectors, with the first probability vector obtained by maximizing the empirical likelihood on the vector of parameters, and the second vector defined from the fixed vector of parameters under the simple null hypothesis. The distance considered for this purpose is the phi-diverge…
This paper proposes Bayesian mosaic, a parallelizable composite posterior, for scalable Bayesian inference on a broad class of multivariate discrete data models. Sampling is embarrassingly parallel since Bayesian mosaic is a multiplication of component posteriors that can be independently sampled from. Analogous to composite likelihood methods, these component posteriors are based on univariate or bivariate marginal densities. Utilizing the fact that the score functions of these densities are unbiased, we show that Bayesian mosaic is consistent and asymptotically normal under mild conditions. …
Maximum pseudolikelihood (MPL) estimators are useful alternatives to maximum likelihood (ML) estimators when likelihood functions are more difficult to manipulate than their marginal and conditional components. Furthermore, MPL estimators subsume a large number of estimation techniques including ML estimators, maximum composite marginal likelihood estimators, and maximum pairwise likelihood estimators. When considering only the estimation of discrete models (on a possibly countably infinite support), we show that a simple finiteness assumption on an entropy-based measure is sufficient for asse…
Gibbs point processes (GPPs) constitute a large and flexible class of spatial point processes with explicit dependence between the points. They can model attractive as well as repulsive point patterns. Feature selection procedures are an important topic in high-dimensional statistical modeling. In this paper, composite likelihood approach regularized with convex and non-convex penalty functions is proposed to handle statistical inference for possibly high-dimensional inhomogeneous GPPs. The composite likelihood incorporates both the pseudo-likelihood and the logistic composite likelihood. We p…
Kink model is developed to analyze the data where the regression function is twostage linear but intersects at an unknown threshold. In quantile regression with longitudinal data, previous work assumed that the unknown threshold parameters or kink points are heterogeneous across different quantiles. However, the location where kink effect happens tend to be the same across different quantiles, especially in a region of neighboring quantile levels. Ignoring such homogeneity information may lead to efficiency loss for estimation. In view of this, we propose a composite estimator for the common k…
This paper proposes a new approach for Bayesian and maximum likelihood parameter estimation for stationary Gaussian processes observed on a large lattice with missing values. We propose an MCMC approach for Bayesian inference, and a Monte Carlo EM algorithm for maximum likelihood inference. Our approach uses data augmentation and circulant embedding of the covariance matrix, and provides exact inference for the parameters and the missing data. Using simulated data and an application to satellite sea surface temperatures in the Pacific Ocean, we show that our method provides accurate inference …
