arXiv subjects

Paul D. McNicholas

Publications and source records attributed to Paul D. McNicholas.

At least 37 records · Page 2Linked to original sources

arXiv2023

Model-based clustering and classification using mixtures of multivariate skewed power exponential distributions

Families of mixtures of multivariate power exponential (MPE) distributions have been previously introduced and shown to be competitive for cluster analysis in comparison to other elliptical mixtures including mixtures of Gaussian distributions. Herein, we propose a family of mixtures of multivariate skewed power exponential distributions to combine the flexibility of the MPE distribution with the ability to model skewness. These mixtures are more robust to variations from normality and can account for skewness, varying tail weight, and peakedness of data. A generalized expectation-maximization approach combining minorization-maximization and optimization based on accelerated line search algorithms on the Stiefel manifold is used for parameter estimation. These mixtures are implemented both in the model-based clustering and classification frameworks. Both simulated and benchmark data are used for illustration and comparison to other mixture families.

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arXiv2022

Finite mixtures of matrix-variate Poisson-log normal distributions for three-way count data

Three-way data structures, characterized by three entities, the units, the variables and the occasions, are frequent in biological studies. In RNA sequencing, three-way data structures are obtained when high-throughput transcriptome sequencing data are collected for $n$ genes across $p$ conditions at $r$ occasions. Matrix variate distributions offer a natural way to model three-way data and mixtures of matrix variate distributions can be used to cluster three-way data. Clustering of gene expression data is carried out as means of discovering gene co-expression networks. In this work, a mixture of matrix variate Poisson-log normal distributions is proposed for clustering read counts from RNA sequencing. By considering the matrix variate structure, full information on the conditions and occasions of the RNA sequencing dataset is simultaneously considered, and the number of covariance parameters to be estimated is reduced. We propose three different frameworks for parameter estimation: a Markov chain Monte Carlo based approach, a variational Gaussian approximation based approach, and a hybrid approach. Various information criteria are used for model selection. The models are applied to both real and simulated data, and we demonstrate that the proposed approaches can recover the underlying cluster structure in both cases. In simulation studies where the true model parameters are known, our proposed approach shows good parameter recovery.

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arXiv2021

Model-based clustering via skewed matrix-variate cluster-weighted models

Cluster-weighted models (CWMs) extend finite mixtures of regressions (FMRs) in order to allow the distribution of covariates to contribute to the clustering process. In a matrix-variate framework, the matrix-variate normal CWM has been recently introduced. However, problems may be encountered when data exhibit skewness or other deviations from normality in the responses, covariates or both. Thus, we introduce a family of 24 matrix-variate CWMs which are obtained by allowing both the responses and covariates to be modelled by using one of four existing skewed matrix-variate distributions or the matrix-variate normal distribution. Endowed with a greater flexibility, our matrix-variate CWMs are able to handle this kind of data in a more suitable manner. As a by-product, the four skewed matrix-variate FMRs are also introduced. Maximum likelihood parameter estimates are derived using an expectation-conditional maximization algorithm. Parameter recovery, classification assessment, and the capability of the Bayesian information criterion to detect the underlying groups are investigated using simulated data. Lastly, our matrix-variate CWMs, along with the matrix-variate normal CWM and matrix-variate FMRs, are applied to two real datasets for illustrative purposes.

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arXiv2021

Four Skewed Tensor Distributions

With the rise of the "big data" phenomenon in recent years, data is coming in many different complex forms. One example of this is multi-way data that come in the form of higher-order tensors such as coloured images and movie clips. Although there has been a recent rise in models for looking at the simple case of three-way data in the form of matrices, there is a relative paucity of higher-order tensor variate methods. The most common tensor distribution in the literature is the tensor variate normal distribution; however, its use can be problematic if the data exhibit skewness or outliers. Herein, we develop four skewed tensor variate distributions which to our knowledge are the first skewed tensor distributions to be proposed in the literature, and are able to parameterize both skewness and tail weight. Properties and parameter estimation are discussed, and real and simulated data are used for illustration.

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arXiv2021

Matrix Normal Cluster-Weighted Models

Finite mixtures of regressions with fixed covariates are a commonly used model-based clustering methodology to deal with regression data. However, they assume assignment independence, i.e. the allocation of data points to the clusters is made independently of the distribution of the covariates. In order to take into account the latter aspect, finite mixtures of regressions with random covariates, also known as cluster-weighted models (CWMs), have been proposed in the univariate and multivariate literature. In this paper, the CWM is extended to matrix data, e.g. those data where a set of variables are simultaneously observed at different time points or locations. Specifically, the cluster-specific marginal distribution of the covariates, and the cluster-specific conditional distribution of the responses given the covariates, are assumed to be matrix normal. Maximum likelihood parameter estimates are derived using an ECM algorithm. Parameter recovery, classification assessment and the capability of the BIC to detect the underlying groups are analyzed on simulated data. Finally, two real data applications concerning educational indicators and the Italian non-life insurance market are presented.

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arXiv2021

Multivariate Cluster Weighted Models Using Skewed Distributions

Much work has been done in the area of the cluster weighted model (CWM), which extends the finite mixture of regression model to include modelling of the covariates. Although many types of distributions have been considered for both the response and covariates, to our knowledge skewed distributions have not yet been considered in this paradigm. Herein, a family of 24 novel CWMs are considered which allows both the covariates and response variables to be modelled using one of four skewed distributions, or the normal distribution. Parameter estimation is performed using the expectation-maximization algorithm and both simulated and real data are used for illustration.

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arXiv2020

Clustering and Semi-Supervised Classification for Clickstream Data via Mixture Models

Finite mixture models have been used for unsupervised learning for some time, and their use within the semi-supervised paradigm is becoming more commonplace. Clickstream data is one of the various emerging data types that demands particular attention because there is a notable paucity of statistical learning approaches currently available. A mixture of first-order continuous time Markov models is introduced for unsupervised and semi-supervised learning of clickstream data. This approach assumes continuous time, which distinguishes it from existing mixture model-based approaches; practically, this allows account to be taken of the amount of time each user spends on each webpage. The approach is evaluated, and compared to the discrete time approach, using simulated and real data.

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arXiv2020

Clustering Higher Order Data: An Application to Pediatric Multi-variable Longitudinal Data

Physical activity levels are an important predictor of cardiovascular health and increasingly being measured by sensors, like accelerometers. Accelerometers produce rich multivariate data that can inform important clinical decisions related to individual patients and public health. The CHAMPION study, a study of youth with chronic inflammatory conditions, aims to determine the links between heart health, inflammation, physical activity, and fitness. The accelerometer data from CHAMPION is represented as 4-dimensional arrays, and a finite mixture of multidimensional arrays model is developed for clustering. The use of model-based clustering for multidimensional arrays has thus far been limited to two-dimensional arrays, i.e., matrices or order-two tensors, and the work in this paper can also be seen as an approach for clustering D-dimensional arrays for D > 2 or, in other words, for clustering order-D tensors.

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arXiv2020

Skewed Distributions or Transformations? Modelling Skewness for a Cluster Analysis

Because of its mathematical tractability, the Gaussian mixture model holds a special place in the literature for clustering and classification. For all its benefits, however, the Gaussian mixture model poses problems when the data is skewed or contains outliers. Because of this, methods have been developed over the years for handling skewed data, and fall into two general categories. The first is to consider a mixture of more flexible skewed distributions, and the second is based on incorporating a transformation to near normality. Although these methods have been compared in their respective papers, there has yet to be a detailed comparison to determine when one method might be more suitable than the other. Herein, we provide a detailed comparison on many benchmarking datasets, as well as describe a novel method to assess cluster separation.

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arXiv2020

Defying the Circadian Rhythm: Clustering Participant Telemetry in the UK Biobank Data

The UK Biobank dataset follows over 500,000 volunteers and contains a diverse set of information related to societal outcomes. Among this vast collection, a large quantity of telemetry collected from wrist-worn accelerometers provides a snapshot of participant activity. Using this data, a population of shift workers, subjected to disrupted circadian rhythms, is analysed using a mixture model-based approach to yield protective effects from physical activity on survival outcomes. In this paper, we develop a scalable, standardized, and unique methodology that efficiently clusters a vast quantity of participant telemetry. By building upon the work of Doherty et al. (2017), we introduce a standardized, low-dimensional feature for clustering purposes. Participants are clustered using a matrix variate mixture model-based approach. Once clustered, survival analysis is performed to demonstrate distinct lifetime outcomes for individuals within each cluster. In summary, we process, cluster, and analyse a subset of UK Biobank participants to show the protective effects from physical activity on circadian disrupted individuals.

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arXiv2020

An Evolutionary Algorithm with Crossover and Mutation for Model-Based Clustering

An evolutionary algorithm (EA) is developed as an alternative to the EM algorithm for parameter estimation in model-based clustering. This EA facilitates a different search of the fitness landscape, i.e., the likelihood surface, utilizing both crossover and mutation. Furthermore, this EA represents an efficient approach to "hard" model-based clustering and so it can be viewed as a sort of generalization of the k-means algorithm, which is itself equivalent to a restricted Gaussian mixture model. The EA is illustrated on several datasets, and its performance is compared to other hard clustering approaches and model-based clustering via the EM algorithm.

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arXiv2020

Mixtures of Contaminated Matrix Variate Normal Distributions

Analysis of three-way data is becoming ever more prevalent in the literature, especially in the area of clustering and classification. Real data, including real three-way data, are often contaminated by potential outlying observations. Their detection, as well as the development of robust models insensitive to their presence, is particularly important for this type of data because of the practical issues concerning their effective visualization. Herein, the contaminated matrix variate normal distribution is discussed and then utilized in the mixture model paradigm for clustering. One key advantage of the proposed model is the ability to automatically detect potential outlying matrices by computing their \textit{a posteriori} probability to be a "good" or "bad" point. Such detection is currently unavailable using existing matrix variate methods. An expectation conditional maximization algorithm is used for parameter estimation, and both simulated and real data are used for illustration.

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arXiv2020

Detecting British Columbia Coastal Rainfall Patterns by Clustering Gaussian Processes

Functional data analysis is a statistical framework where data are assumed to follow some functional form. This method of analysis is commonly applied to time series data, where time, measured continuously or in discrete intervals, serves as the location for a function's value. Gaussian processes are a generalization of the multivariate normal distribution to function space and, in this paper, they are used to shed light on coastal rainfall patterns in British Columbia (BC). Specifically, this work addressed the question over how one should carry out an exploratory cluster analysis for the BC, or any similar, coastal rainfall data. An approach is developed for clustering multiple processes observed on a comparable interval, based on how similar their underlying covariance kernel is. This approach provides interesting insights into the BC data, and these insights can be framed in terms of El Niño and La Niña; however, the result is not simply one cluster representing El Niño years and another for La Niña years. From one perspective, the results show that clustering annual rainfall can potentially be used to identify extreme weather patterns.

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arXiv2020

Clustering Discrete-Valued Time Series

There is a need for the development of models that are able to account for discreteness in data, along with its time series properties and correlation. Our focus falls on INteger-valued AutoRegressive (INAR) type models. The INAR type models can be used in conjunction with existing model-based clustering techniques to cluster discrete-valued time series data. With the use of a finite mixture model, several existing techniques such as the selection of the number of clusters, estimation using expectation-maximization and model selection are applicable. The proposed model is then demonstrated on real data to illustrate its clustering applications.

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arXiv2019

Parsimonious Mixtures of Matrix Variate Bilinear Factor Analyzers

Over the years, data have become increasingly higher dimensional, which has prompted an increased need for dimension reduction techniques. This is perhaps especially true for clustering (unsupervised classification) as well as semi-supervised and supervised classification. Many methods have been proposed in the literature for two-way (multivariate) data and quite recently methods have been presented for three-way (matrix variate) data. One such such method is the mixtures of matrix variate bilinear factor analyzers (MMVBFA) model. Herein, we propose of total of 64 parsimonious MMVBFA models. Simulated and real data are used for illustration.

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arXiv2019

A Variational Approximations-DIC Rubric for Parameter Estimation and Mixture Model Selection Within a Family Setting

Mixture model-based clustering has become an increasingly popular data analysis technique since its introduction over fifty years ago, and is now commonly utilized within a family setting. Families of mixture models arise when the component parameters, usually the component covariance (or scale) matrices, are decomposed and a number of constraints are imposed. Within the family setting, model selection involves choosing the member of the family, i.e., the appropriate covariance structure, in addition to the number of mixture components. To date, the Bayesian information criterion (BIC) has proved most effective for model selection, and the expectation-maximization (EM) algorithm is usually used for parameter estimation. In fact, this EM-BIC rubric has virtually monopolized the literature on families of mixture models. Deviating from this rubric, variational Bayes approximations are developed for parameter estimation and the deviance information criterion for model selection. The variational Bayes approach provides an alternate framework for parameter estimation by constructing a tight lower bound on the complex marginal likelihood and maximizing this lower bound by minimizing the associated Kullback-Leibler divergence. This approach is taken on the most commonly used family of Gaussian mixture models, and real and simulated data are used to compare the new approach to the EM-BIC rubric.

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arXiv2019

Assessing and Visualizing Matrix Variate Normality

A framework for assessing the matrix variate normality of three-way data is developed. The framework comprises a visual method and a goodness of fit test based on the Mahalanobis squared distance (MSD). The MSD of multivariate and matrix variate normal estimators, respectively, are used as an assessment tool for matrix variate normality. Specifically, these are used in the form of a distance-distance (DD) plot as a graphical method for visualizing matrix variate normality. In addition, we employ the popular Kolmogorov-Smirnov goodness of fit test in the context of assessing matrix variate normality for three-way data. Finally, an appropriate simulation study spanning a large range of dimensions and data sizes shows that for various settings, the test proves itself highly robust.

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arXiv2019

Mixtures of Skewed Matrix Variate Bilinear Factor Analyzers

In recent years, data have become increasingly higher dimensional and, therefore, an increased need has arisen for dimension reduction techniques for clustering. Although such techniques are firmly established in the literature for multivariate data, there is a relative paucity in the area of matrix variate, or three-way, data. Furthermore, the few methods that are available all assume matrix variate normality, which is not always sensible if cluster skewness or excess kurtosis is present. Mixtures of bilinear factor analyzers using skewed matrix variate distributions are proposed. In all, four such mixture models are presented, based on matrix variate skew-t, generalized hyperbolic, variance-gamma, and normal inverse Gaussian distributions, respectively.

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