Mixtures of modified t-factor analyzers for model-based clustering,classification, and discriminant analysis

A novel family of mixture models is introduced based on modified t-factor analyzers. Modified factor analyzers were recently introduced within the Gaussian context and our work presents a more flexible and robust alternative. We introduce a family of mixtures of modified t-factor analyzers that uses this generalized version of the factor analysis covariance structure. We apply this family within three paradigms: model-based clustering; model-based classification; and model-based discriminant analysis. In addition, we apply the recently published Gaussian analogue to this family under the model-based classification and discriminant analysis paradigms for the first time. Parameter estimation is carried out within the alternating expectation-conditional maximization framework and the Bayesian information criterion is used for model selection. Two real data sets are used to compare our approach to other popular model-based approaches; in these comparisons, the chosen mixtures of modified t-factor analyzers model performs favourably. We conclude with a summary and suggestions for future work.     

Clustering gene expression time course data using mixtures of multivariate t-distributions

Clustering gene expression time course data is an important problem in bioinformatics because understanding which genes behave similarly can lead to the discovery of important biological information. Statistically, the problem of clustering time course data is a special case of the more general problem of clustering longitudinal data. In this paper, a very general and flexible model-based technique is used to cluster longitudinal data. Mixtures of multivariate t-distributions are utilized, with a linear model for the mean and a modified Cholesky-decomposed covariance structure. Constraints are placed upon the covariance structure, leading to a novel family of mixture models, including parsimonious models. In addition to model-based clustering, these models are also used for model-based classification, i.e., semi-supervised clustering. Parameters, including the component degrees of freedom, are estimated using an expectation-maximization algorithm and two different approaches to model selection are considered. The models are applied to simulated data to illustrate their efficacy; this includes a comparison with their Gaussian analogues—the use of these Gaussian analogues with a linear model for the mean is novel in itself. Our family of multivariate t mixture models is then applied to two real gene expression time course data sets and the results are discussed. We conclude with a summary, suggestions for future work, and a discussion about constraining the degrees of freedom parameter.     

A new per-field classification method using mixture discriminant analysis

In this study, a new per-field classification method is proposed for supervised classification of remotely sensed multispectral image data of an agricultural area using Gaussian mixture discriminant analysis (MDA). For the proposed per-field classification method, multivariate Gaussian mixture models constructed for control and test fields can have fixed or different number of components and each component can have different or common covariance matrix structure. The discrimination function and the decision rule of this method are established according to the average Bhattacharyya distance and the minimum values of the average Bhattacharyya distances, respectively. The proposed per-field classification method is analyzed for different structures of a covariance matrix with fixed and different number of components. Also, we classify the remotely sensed multispectral image data using the per-pixel classification method based on Gaussian MDA.     

Model-based classification using latent Gaussian mixture models

A novel model-based classification technique is introduced based on parsimonious Gaussian mixture models (PGMMs). PGMMs, which were introduced recently as a model-based clustering technique, arise from a generalization of the mixtures of factor analyzers model and are based on a latent Gaussian mixture model. In this paper, this mixture modelling structure is used for model-based classification and the particular area of application is food authenticity. Model-based classification is performed by jointly modelling data with known and unknown group memberships within a likelihood framework and then estimating parameters, including the unknown group memberships, within an alternating expectation-conditional maximization framework. Model selection is carried out using the Bayesian information criteria and the quality of the maximum a posteriori classifications is summarized using the misclassification rate and the adjusted Rand index. This new model-based classification technique gives excellent classification performance when applied to real food authenticity data on the chemical properties of olive oils from nine areas of Italy.     

Extending mixtures of multivariate <Emphasis Type="Italic">t</Emphasis>-factor analyzers

Model-based clustering typically involves the development of a family of mixture models and the imposition of these models upon data. The best member of the family is then chosen using some criterion and the associated parameter estimates lead to predicted group memberships, or clusterings. This paper describes the extension of the mixtures of multivariate t-factor analyzers model to include constraints on the degrees of freedom, the factor loadings, and the error variance matrices. The result is a family of six mixture models, including parsimonious models. Parameter estimates for this family of models are derived using an alternating expectation-conditional maximization algorithm and convergence is determined based on Aitken’s acceleration. Model selection is carried out using the Bayesian information criterion (BIC) and the integrated completed likelihood (ICL). This novel family of mixture models is then applied to simulated and real data where clustering performance meets or exceeds that of established model-based clustering methods. The simulation studies include a comparison of the BIC and the ICL as model selection techniques for this novel family of models. Application to simulated data with larger dimensionality is also explored.     

Using unlabelled data to update classification rules with applications in food authenticity studies

Summary.  An authentic food is one that is what it purports to be. Food processors and consumers need to be assured that, when they pay for a specific product or ingredient, they are receiving exactly what they pay for. Classification methods are an important tool in food authenticity studies where they are used to assign food samples of unknown type to known types. A classification method is developed where the classification rule is estimated by using both the labelled and the unlabelled data, in contrast with many classical methods which use only the labelled data for estimation. This methodology models the data as arising from a Gaussian mixture model with parsimonious covariance structure, as is done in model-based clustering. A missing data formulation of the mixture model is used and the models are fitted by using the EM and classification EM algorithms. The methods are applied to the analysis of spectra of food-stuffs recorded over the visible and near infra-red wavelength range in food authenticity studies. A comparison of the performance of model-based discriminant analysis and the method of classification proposed is given. The classification method proposed is shown to yield very good misclassification rates. The correct classification rate was observed to be as much as 15% higher than the correct classification rate for model-based discriminant analysis.     

A new family of multivariate heavy-tailed distributions with variable marginal amounts of tailweight: application to robust clustering

We propose a family of multivariate heavy-tailed distributions that allow variable marginal amounts of tailweight. The originality comes from introducing multidimensional instead of univariate scale variables for the mixture of scaled Gaussian family of distributions. In contrast to most existing approaches, the derived distributions can account for a variety of shapes and have a simple tractable form with a closed-form probability density function whatever the dimension. We examine a number of properties of these distributions and illustrate them in the particular case of Pearson type VII and t tails. For these latter cases, we provide maximum likelihood estimation of the parameters and illustrate their modelling flexibility on simulated and real data clustering examples.     

A comparative study of the K-means algorithm and the normal mixture model for clustering: Bivariate homoscedastic case

The K-means algorithm and the normal mixture model method are two common clustering methods. The K-means algorithm is a popular heuristic approach which gives reasonable clustering results if the component clusters are ball-shaped. Currently, there are no analytical results for this algorithm if the component distributions deviate from the ball-shape. This paper analytically studies how the K-means algorithm changes its classification rule as the normal component distributions become more elongated under the homoscedastic assumption and compares this rule with that of the Bayes rule from the mixture model method. We show that the classification rules of both methods are linear, but the slopes of the two classification lines change in the opposite direction as the component distributions become more elongated. The classification performance of the K-means algorithm is then compared to that of the mixture model method via simulation. The comparison, which is limited to two clusters, shows that the K-means algorithm provides poor classification performances consistently as the component distributions become more elongated while the mixture model method can potentially, but not necessarily, take advantage of this change and provide a much better classification performance.     

Model-based clustering with non-elliptically contoured distributions

The majority of the existing literature on model-based clustering deals with symmetric components. In some cases, especially when dealing with skewed subpopulations, the estimate of the number of groups can be misleading; if symmetric components are assumed we need more than one component to describe an asymmetric group. Existing mixture models, based on multivariate normal distributions and multivariate t distributions, try to fit symmetric distributions, i.e. they fit symmetric clusters. In the present paper, we propose the use of finite mixtures of the normal inverse Gaussian distribution (and its multivariate extensions). Such finite mixture models start from a density that allows for skewness and fat tails, generalize the existing models, are tractable and have desirable properties. We examine both the univariate case, to gain insight, and the multivariate case, which is more useful in real applications. EM type algorithms are described for fitting the models. Real data examples are used to demonstrate the potential of the new model in comparison with existing ones.     

Flexible mixture modeling via the multivariate t distribution with?the?Box-Cox transformation: an?alternative to?the?skew-t distribution

Cluster analysis is the automated search for groups of homogeneous observations in a data set. A popular modeling approach for clustering is based on finite normal mixture models, which assume that each cluster is modeled as a multivariate normal distribution. However, the normality assumption that each component is symmetric is often unrealistic. Furthermore, normal mixture models are not robust against outliers; they often require extra components for modeling outliers and/or give a poor representation of the data. To address these issues, we propose a new class of distributions, multivariate t distributions with the Box-Cox transformation, for mixture modeling. This class of distributions generalizes the normal distribution with the more heavy-tailed t distribution, and introduces skewness via the Box-Cox transformation. As a result, this provides a unified framework to simultaneously handle outlier identification and data transformation, two interrelated issues. We describe an Expectation-Maximization algorithm for parameter estimation along with transformation selection. We demonstrate the proposed methodology with three real data sets and simulation studies. Compared with a wealth of approaches including the skew-t mixture model, the proposed t mixture model with the Box-Cox transformation performs favorably in terms of accuracy in the assignment of observations, robustness against model misspecification, and selection of the number of components.     

A Class of Convolution‐Based Models for Spatio‐Temporal Processes with Non‐Separable Covariance Structure

Abstract. In this article, we propose a new parametric family of models for real‐valued spatio‐temporal stochastic processes S ( x , t ) and show how low‐rank approximations can be used to overcome the computational problems that arise in fitting the proposed class of models to large datasets. Separable covariance models, in which the spatio‐temporal covariance function of S ( x , t ) factorizes into a product of purely spatial and purely temporal functions, are often used as a convenient working assumption but are too inflexible to cover the range of covariance structures encountered in applications. We define positive and negative non‐separability and show that in our proposed family we can capture positive, zero and negative non‐separability by varying the value of a single parameter.     

A generalized skew two-piece skew-elliptical distribution

We present a new generalized family of skew two-piece skew-elliptical (GSTPSE) models and derive some its statistical properties. It is shown that the new family of distribution may be written as a mixture of generalized skew elliptical distributions. Also, a new representation theorem for a special case of GSTPSE-distribution is given. Next, we will focus on t kernel density and prove that it is a scale mixture of the generalized skew two-piece skew normal distributions. An explicit expression for the central moments as well as a recurrence relations for its cumulative distribution function and density are obtained. Since, this special case is a uni-/bimodal distribution, a sufficient condition for each cases is given. A real data set on heights of Australian females athletes is analysed. Finally, some concluding remarks and open problems are discussed.     

Bayesian inference in joint modelling of location and scale parameters of the t distribution for longitudinal data

This paper presents a fully Bayesian approach to multivariate t regression models whose mean vector and scale covariance matrix are modelled jointly for analyzing longitudinal data. The scale covariance structure is factorized in terms of unconstrained autoregressive and scale innovation parameters through a modified Cholesky decomposition. A computationally flexible data augmentation sampler coupled with the Metropolis-within-Gibbs scheme is developed for computing the posterior distributions of parameters. The Bayesian predictive inference for the future response vector is also investigated. The proposed methodologies are illustrated through a real example from a sleep dose–response study.     

Model-based clustering,classification, and discriminant analysis of data with mixed type

We propose a mixture of latent variables model for the model-based clustering, classification, and discriminant analysis of data comprising variables with mixed type. This approach is a generalization of latent variable analysis, and model fitting is carried out within the expectation-maximization framework. Our approach is outlined and a simulation study conducted to illustrate the effect of sample size and noise on the standard errors and the recovery probabilities for the number of groups. Our modelling methodology is then applied to two real data sets and their clustering and classification performance is discussed. We conclude with discussion and suggestions for future work.     

Curve prediction and clustering with mixtures of Gaussian process functional regression models

Shi, Wang, Murray-Smith and Titterington (Biometrics 63:714–723, 2007) proposed a Gaussian process functional regression (GPFR) model to model functional response curves with a set of functional covariates. Two main problems are addressed by their method: modelling nonlinear and nonparametric regression relationship and modelling covariance structure and mean structure simultaneously. The method gives very good results for curve fitting and prediction but side-steps the problem of heterogeneity. In this paper we present a new method for modelling functional data with ‘spatially’ indexed data, i.e., the heterogeneity is dependent on factors such as region and individual patient’s information. For data collected from different sources, we assume that the data corresponding to each curve (or batch) follows a Gaussian process functional regression model as a lower-level model, and introduce an allocation model for the latent indicator variables as a higher-level model. This higher-level model is dependent on the information related to each batch. This method takes advantage of both GPFR and mixture models and therefore improves the accuracy of predictions. The mixture model has also been used for curve clustering, but focusing on the problem of clustering functional relationships between response curve and covariates, i.e. the clustering is based on the surface shape of the functional response against the set of functional covariates. The model is examined on simulated data and real data.     

Robust inference in an heteroscedastic measurement error model

In this paper we deal with robust inference in heteroscedastic measurement error models. Rather than the normal distribution, we postulate a Student t distribution for the observed variables. Maximum likelihood estimates are computed numerically. Consistent estimation of the asymptotic covariance matrices of the maximum likelihood and generalized least squares estimators is also discussed. Three test statistics are proposed for testing hypotheses of interest with the asymptotic chi-square distribution which guarantees correct asymptotic significance levels. Results of simulations and an application to a real data set are also reported.     

Robust multivariate mixture regression models with incomplete data

Multivariate mixture regression models can be used to investigate the relationships between two or more response variables and a set of predictor variables by taking into consideration unobserved population heterogeneity. It is common to take multivariate normal distributions as mixing components, but this mixing model is sensitive to heavy-tailed errors and outliers. Although normal mixture models can approximate any distribution in principle, the number of components needed to account for heavy-tailed distributions can be very large. Mixture regression models based on the multivariate t distributions can be considered as a robust alternative approach. Missing data are inevitable in many situations and parameter estimates could be biased if the missing values are not handled properly. In this paper, we propose a multivariate t mixture regression model with missing information to model heterogeneity in regression function in the presence of outliers and missing values. Along with the robust parameter estimation, our proposed method can be used for (i) visualization of the partial correlation between response variables across latent classes and heterogeneous regressions, and (ii) outlier detection and robust clustering even under the presence of missing values. We also propose a multivariate t mixture regression model using MM-estimation with missing information that is robust to high-leverage outliers. The proposed methodologies are illustrated through simulation studies and real data analysis.     

Linear Discriminant Analysis of Multivariate Spatial–Temporal Regressions

Abstract.  We consider classification of the realization of a multivariate spatial–temporal Gaussian random field into one of two populations with different regression mean models and factorized covariance matrices. Unknown means and common feature vector covariance matrix are estimated from training samples with observations correlated in space and time, assuming spatial–temporal correlations to be known. We present the first-order asymptotic expansion of the expected error rate associated with a linear plug-in discriminant function. Our results are applied to ecological data collected from the Lithuanian Economic Zone in the Baltic Sea.     

Orthogonal Stiefel manifold optimization for eigen-decomposed covariance parameter estimation in mixture models

Within the mixture model-based clustering literature, parsimonious models with eigen-decomposed component covariance matrices have dominated for over a decade. Although originally introduced as a fourteen-member family of models, the current state-of-the-art is to utilize just ten of these models; the rationale for not using the other four models usually centers around parameter estimation difficulties. Following close examination of these four models, we find that two are actually easily implemented using existing algorithms but that two benefit from a novel approach. We present and implement algorithms that use an accelerated line search for optimization on the orthogonal Stiefel manifold. Furthermore, we show that the ‘extra’ models that these decompositions facilitate outperform the current state-of-the art when applied to two benchmark data sets.