Incremental modelling for compositional data streams

ABSTRACT

Incremental modelling of data streams is of great practical importance, as shown by its applications in advertising and financial data analysis. We propose two incremental covariance matrix decomposition methods for a compositional data type. The first method, exact incremental covariance decomposition of compositional data (C-EICD), gives an exact decomposition result. The second method, covariance-free incremental covariance decomposition of compositional data (C-CICD), is an approximate algorithm that can efficiently compute high-dimensional cases. Based on these two methods, many frequently used compositional statistical models can be incrementally calculated. We take multiple linear regression and principle component analysis as examples to illustrate the utility of the proposed methods via extensive simulation studies.     

Mixtures of general location model with factor analyzer covariance structure for clustering mixed type data

Cluster analysis is one of the most widely used method in statistical analyses, in which homogeneous subgroups are identified in a heterogeneous population. Due to the existence of the continuous and discrete mixed data in many applications, so far, some ordinary clustering methods such as, hierarchical methods, k-means and model-based methods have been extended for analysis of mixed data. However, in the available model-based clustering methods, by increasing the number of continuous variables, the number of parameters increases and identifying as well as fitting an appropriate model may be difficult. In this paper, to reduce the number of the parameters, for the model-based clustering mixed data of continuous (normal) and nominal data, a set of parsimonious models is introduced. Models in this set are extended, using the general location model approach, for modeling distribution of mixed variables and applying factor analyzer structure for covariance matrices. The ECM algorithm is used for estimating the parameters of these models. In order to show the performance of the proposed models for clustering, results from some simulation studies and analyzing two real data sets are presented.     

k-POD: A Method for k-Means Clustering of Missing Data

The k-means algorithm is often used in clustering applications but its usage requires a complete data matrix. Missing data, however, are common in many applications. Mainstream approaches to clustering missing data reduce the missing data problem to a complete data formulation through either deletion or imputation but these solutions may incur significant costs. Our k-POD method presents a simple extension of k-means clustering for missing data that works even when the missingness mechanism is unknown, when external information is unavailable, and when there is significant missingness in the data.

[Received November 2014. Revised August 2015.]     

Multiple imputation for combining confidential data owned by two agencies

Summary.  Statistical agencies that own different databases on overlapping subjects can benefit greatly from combining their data. These benefits are passed on to secondary data analysts when the combined data are disseminated to the public. Sometimes combining data across agencies or sharing these data with the public is not possible: one or both of these actions may break promises of confidentiality that have been given to data subjects. We describe an approach that is based on two stages of multiple imputation that facilitates data sharing and dissemination under restrictions of confidentiality. We present new inferential methods that properly account for the uncertainty that is caused by the two stages of imputation. We illustrate the approach by using artificial and genuine data.     

A new approach: Interrelated two-way clustering of gene expression data

The paper presents a new approach to interrelated two-way clustering of gene expression data. Clustering of genes has been effected using entropy and a correlation measure, whereas the samples have been clustered using the fuzzy C-means. The efficiency of this approach has been tested on two well known data sets: the colon cancer data set and the leukemia data set. Using this approach, we were able to identify the important co-regulated genes and group the samples efficiently at the same time.     

Clustering and classification problems in genetics through U-statistics

ABSTRACT

Genetic data are frequently categorical and have complex dependence structures that are not always well understood. For this reason, clustering and classification based on genetic data, while highly relevant, are challenging statistical problems. Here we consider a versatile U-statistics-based approach for non-parametric clustering that allows for an unconventional way of solving these problems. In this paper we propose a statistical test to assess group homogeneity taking into account multiple testing issues and a clustering algorithm based on dissimilarities within and between groups that highly speeds up the homogeneity test. We also propose a test to verify classification significance of a sample in one of two groups. We present Monte Carlo simulations that evaluate size and power of the proposed tests under different scenarios. Finally, the methodology is applied to three different genetic data sets: global human genetic diversity, breast tumour gene expression and Dengue virus serotypes. These applications showcase this statistical framework's ability to answer diverse biological questions in the high dimension low sample size scenario while adapting to the specificities of the different datatypes.     

Mixture of latent trait analyzers for model-based clustering of categorical data

Model-based clustering methods for continuous data are well established and commonly used in a wide range of applications. However, model-based clustering methods for categorical data are less standard. Latent class analysis is a commonly used method for model-based clustering of binary data and/or categorical data, but due to an assumed local independence structure there may not be a correspondence between the estimated latent classes and groups in the population of interest. The mixture of latent trait analyzers model extends latent class analysis by assuming a model for the categorical response variables that depends on both a categorical latent class and a continuous latent trait variable; the discrete latent class accommodates group structure and the continuous latent trait accommodates dependence within these groups. Fitting the mixture of latent trait analyzers model is potentially difficult because the likelihood function involves an integral that cannot be evaluated analytically. We develop a variational approach for fitting the mixture of latent trait models and this provides an efficient model fitting strategy. The mixture of latent trait analyzers model is demonstrated on the analysis of data from the National Long Term Care Survey (NLTCS) and voting in the U.S. Congress. The model is shown to yield intuitive clustering results and it gives a much better fit than either latent class analysis or latent trait analysis alone.     

A folded model for compositional data analysis

A folded type model is developed for analysing compositional data. The proposed model involves an extension of the α‐transformation for compositional data and provides a new and flexible class of distributions for modelling data defined on the simplex sample space. Despite its rather seemingly complex structure, employment of the EM algorithm guarantees efficient parameter estimation. The model is validated through simulation studies and examples which illustrate that the proposed model performs better in terms of capturing the data structure, when compared to the popular logistic normal distribution, and can be advantageous over a similar model without folding.     

Bayesian nonparametric clustering for large data sets

We propose two nonparametric Bayesian methods to cluster big data and apply them to cluster genes by patterns of gene–gene interaction. Both approaches define model-based clustering with nonparametric Bayesian priors and include an implementation that remains feasible for big data. The first method is based on a predictive recursion which requires a single cycle (or few cycles) of simple deterministic calculations for each observation under study. The second scheme is an exact method that divides the data into smaller subsamples and involves local partitions that can be determined in parallel. In a second step, the method requires only the sufficient statistics of each of these local clusters to derive global clusters. Under simulated and benchmark data sets the proposed methods compare favorably with other clustering algorithms, including k-means, DP-means, DBSCAN, SUGS, streaming variational Bayes and an EM algorithm. We apply the proposed approaches to cluster a large data set of gene–gene interactions extracted from the online search tool “Zodiac.”

     

Clustering microarray data using model-based double K-means

The microarray technology allows the measurement of expression levels of thousands of genes simultaneously. The dimension and complexity of gene expression data obtained by microarrays create challenging data analysis and management problems ranging from the analysis of images produced by microarray experiments to biological interpretation of results. Therefore, statistical and computational approaches are beginning to assume a substantial position within the molecular biology area. We consider the problem of simultaneously clustering genes and tissue samples (in general conditions) of a microarray data set. This can be useful for revealing groups of genes involved in the same molecular process as well as groups of conditions where this process takes place. The need of finding a subset of genes and tissue samples defining a homogeneous block had led to the application of double clustering techniques on gene expression data. Here, we focus on an extension of standard K-means to simultaneously cluster observations and features of a data matrix, namely double K-means introduced by Vichi (2000). We introduce this model in a probabilistic framework and discuss the advantages of using this approach. We also develop a coordinate ascent algorithm and test its performance via simulation studies and real data set. Finally, we validate the results obtained on the real data set by building resampling confidence intervals for block centroids.     

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 robust Parafac model for compositional data

Compositional data are characterized by values containing relative information, and thus the ratios between the data values are of interest for the analysis. Due to specific features of compositional data, standard statistical methods should be applied to compositions expressed in a proper coordinate system with respect to an orthonormal basis. It is discussed how three-way compositional data can be analyzed with the Parafac model. When data are contaminated by outliers, robust estimates for the Parafac model parameters should be employed. It is demonstrated how robust estimation can be done in the context of compositional data and how the results can be interpreted. A real data example from macroeconomics underlines the usefulness of this approach.     

Composite likelihood for aggregate data from clustered multistate processes under intermittent observation

Abstract

Markov processes offer a useful basis for modeling the progression of organisms through successive stages of their life cycle. When organisms are examined intermittently in developmental studies, likelihoods can be constructed based on the resulting panel data in terms of transition probability functions. In some settings however, organisms cannot be tracked individually due to a difficulty in identifying distinct individuals, and in such cases aggregate counts of the number of organisms in different stages of development are recorded at successive time points. We consider the setting in which such aggregate counts are available for each of a number of tanks in a developmental study. We develop methods which accommodate clustering of the transition rates within tanks using a marginal modeling approach followed by robust variance estimation, and through use of a random effects model. Composite likelihood is proposed as a basis of inference in both settings. An extension which incorporates mortality is also discussed. The proposed methods are shown to perform well in empirical studies and are applied in an illustrative example on the growth of the Arabidopsis thaliana plant.     

Classical and robust orthogonal regression between parts of compositional data

The different parts (variables) of a compositional data set cannot be considered independent from each other, since only the ratios between the parts constitute the relevant information to be analysed. Practically, this information can be included in a system of orthonormal coordinates. For the task of regression of one part on other parts, a specific choice of orthonormal coordinates is proposed which allows for an interpretation of the regression parameters in terms of the original parts. In this context, orthogonal regression is appropriate since all compositional parts – also the explanatory variables – are measured with errors. Besides classical (least-squares based) parameter estimation, also robust estimation based on robust principal component analysis is employed. Statistical inference for the regression parameters is obtained by bootstrap; in the robust version the fast and robust bootstrap procedure is used. The methodology is illustrated with a data set from macroeconomics.     

Modelling hierarchical clustered censored data with the hierarchical Kendall copula

This article proposes a new model for right‐censored survival data with multi‐level clustering based on the hierarchical Kendall copula model of Brechmann (2014) with Archimedean clusters. This model accommodates clusters of unequal size and multiple clustering levels, without imposing any structural conditions on the parameters or on the copulas used at various levels of the hierarchy. A step‐wise estimation procedure is proposed and shown to yield consistent and asymptotically Gaussian estimates under mild regularity conditions. The model fitting is based on multiple imputation, given that the censoring rate increases with the level of the hierarchy. To check the model assumption of Archimedean dependence, a goodness‐of test is developed. The finite‐sample performance of the proposed estimators and of the goodness‐of‐fit test is investigated through simulations. The new model is applied to data from the study of chronic granulomatous disease. The Canadian Journal of Statistics 47: 182–203; 2019 © 2019 Statistical Society of Canada     

Regression imputation with Q-mode clustering for rounded zero replacement in high-dimensional compositional data

The logratio methodology is not applicable when rounded zeros occur in compositional data. There are many methods to deal with rounded zeros. However, some methods are not suitable for analyzing data sets with high dimensionality. Recently, related methods have been developed, but they cannot balance the calculation time and accuracy. For further improvement, we propose a method based on regression imputation with Q-mode clustering. This method forms the groups of parts and builds partial least squares regression with these groups using centered logratio coordinates. We also prove that using centered logratio coordinates or isometric logratio coordinates in the response of partial least squares regression have the equivalent results for the replacement of rounded zeros. Simulation study and real example are conducted to analyze the performance of the proposed method. The results show that the proposed method can reduce the calculation time in higher dimensions and improve the quality of results.     

Mixtures of Gaussian copula factor analyzers for clustering high dimensional data

Mixtures of factor analyzers is a useful model-based clustering method which can avoid the curse of dimensionality in high-dimensional clustering. However, this approach is sensitive to both diverse non-normalities of marginal variables and outliers, which are commonly observed in multivariate experiments. We propose mixtures of Gaussian copula factor analyzers (MGCFA) for clustering high-dimensional clustering. This model has two advantages; (1) it allows different marginal distributions to facilitate fitting flexibility of the mixture model, (2) it can avoid the curse of dimensionality by embedding the factor-analytic structure in the component-correlation matrices of the mixture distribution.An EM algorithm is developed for the fitting of MGCFA. The proposed method is free of the curse of dimensionality and allows any parametric marginal distribution which fits best to the data. It is applied to both synthetic data and a microarray gene expression data for clustering and shows its better performance over several existing methods.     

Microdata disclosure by resampling – Empirical findings for business survey data

Summary: One specific problem statistical offices and research institutes are faced with when releasing microdata is the preservation of confidentiality. Traditional methods to avoid disclosure often destroy the structure of the data, and information loss is potentially high. In this paper an alternative technique of creating scientific–use files is discussed, which reproduces the characteristics of the original data quite well. It is based on Fienberg (1997, 1994) who estimates and resamples from the empirical multivariate cumulative distribution function of the data in order to get synthetic data. The procedure creates data sets – the resample – which have the same characteristics as the original survey data. The paper includes some applications of this method with (a) simulated data and (b) innovation survey data, the Mannheim Innovation Panel (MIP), and a comparison between resampling and a common method of disclosure control (disturbance with multiplicative error) with regard to confidentiality on the one hand and the appropriateness of the disturbed data for different kinds of analyses on the other. The results show that univariate distributions can be better reproduced by unweighted resampling. Parameter estimates can be reproduced quite well if the resampling procedure implements the correlation structure of the original data as a scale or if the data is multiplicatively perturbed and a correction term is used. On average, anonymization of data with multiplicatively perturbed values protects better against re–identification than the various resampling methods used.     

Model selection criteria for dual-inflated data

ABSTRACT

Inflated data are prevalent in many situations and a variety of inflated models with extensions have been derived to fit data with excessive counts of some particular responses. The family of information criteria (IC) has been used to compare the fit of models for selection purposes. Yet despite the common use in statistical applications, there are not too many studies evaluating the performance of IC in inflated models. In this study, we studied the performance of IC for data with dual-inflated data. The new zero- and K-inflated Poisson (ZKIP) regression model and conventional inflated models including Poisson regression and zero-inflated Poisson (ZIP) regression were fitted for dual-inflated data and the performance of IC were compared. The effect of sample sizes and the proportions of inflated observations towards selection performance were also examined. The results suggest that the Bayesian information criterion (BIC) and consistent Akaike information criterion (CAIC) are more accurate than the Akaike information criterion (AIC) in terms of model selection when the true model is simple (i.e. Poisson regression (POI)). For more complex models, such as ZIP and ZKIP, the AIC was consistently better than the BIC and CAIC, although it did not reach high levels of accuracy when sample size and the proportion of zero observations were small. The AIC tended to over-fit the data for the POI, whereas the BIC and CAIC tended to under-parameterize the data for ZIP and ZKIP. Therefore, it is desirable to study other model selection criteria for dual-inflated data with small sample size.