Comparison of clustering algorithms on generalized propensity score in observational studies: a simulation study

In observational studies, unbalanced observed covariates between treatment groups often cause biased inferences on the estimation of treatment effects. Recently, generalized propensity score (GPS) has been proposed to overcome this problem; however, a practical technique to apply the GPS is lacking. This study demonstrates how clustering algorithms can be used to group similar subjects based on transformed GPS. We compare four popular clustering algorithms: k-means clustering (KMC), model-based clustering, fuzzy c-means clustering and partitioning around medoids based on the following three criteria: average dissimilarity between subjects within clusters, average Dunn index and average silhouette width under four various covariate scenarios. Simulation studies show that the KMC algorithm has overall better performance compared with the other three clustering algorithms. Therefore, we recommend using the KMC algorithm to group similar subjects based on the transformed GPS.     

Simple Measures of Individual Cluster-Membership Certainty for Hard Partitional Clustering

We propose two probability-like measures of individual cluster-membership certainty that can be applied to a hard partition of the sample such as that obtained from the partitioning around medoids (PAM) algorithm, hierarchical clustering or k-means clustering. One measure extends the individual silhouette widths and the other is obtained directly from the pairwise dissimilarities in the sample. Unlike the classic silhouette, however, the measures behave like probabilities and can be used to investigate an individual’s tendency to belong to a cluster. We also suggest two possible ways to evaluate the hard partition using these measures. We evaluate the performance of both measures in individuals with ambiguous cluster membership, using simulated binary datasets that have been partitioned by the PAM algorithm or continuous datasets that have been partitioned by hierarchical clustering and k-means clustering. For comparison, we also present results from soft-clustering algorithms such as soft analysis clustering (FANNY) and two model-based clustering methods. Our proposed measures perform comparably to the posterior probability estimators from either FANNY or the model-based clustering methods. We also illustrate the proposed measures by applying them to Fisher’s classic dataset on irises.     

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.     

Identification of target clusters by using the restricted normal mixture model

This paper addresses the problem of identifying groups that satisfy the specific conditions for the means of feature variables. In this study, we refer to the identified groups as “target clusters” (TCs). To identify TCs, we propose a method based on the normal mixture model (NMM) restricted by a linear combination of means. We provide an expectation–maximization (EM) algorithm to fit the restricted NMM by using the maximum-likelihood method. The convergence property of the EM algorithm and a reasonable set of initial estimates are presented. We demonstrate the method's usefulness and validity through a simulation study and two well-known data sets. The proposed method provides several types of useful clusters, which would be difficult to achieve with conventional clustering or exploratory data analysis methods based on the ordinary NMM. A simple comparison with another target clustering approach shows that the proposed method is promising in the identification.     

Phase Type Distributions with Finite Support

This research is motivated by the fact that many random variables of practical interest have a finite support. For fixed a < b, we consider the distribution of a random variable X = (a + Ymod(b ? a)), where Y is a phase type (PH) random variable. We demonstrate that as we traverse for Y the entire set of PH distributions (or even any subset thereof like Coxian that is dense in the class of distributions on [0, ∞)), we obtain a class of matrix exponential distributions dense in (a, b). We call these Finite Support Phase Type Distributions (FSPH) of the first kind. A simple example shows that though dense, this class by itself is not very efficient for modeling; therefore, we introduce (and derive the EM algorithms for) two other classes of finite support phase type distributions (FSPH). The properties of denseness, connection to Markov chains, the EM algorithm, and ability to exploit matrix-based computations should all make these classes of distributions attractive not only for applied probability but also for a much wider variety of fields using statistical methodologies.     

Fuzzy clustering of probability density functions

Basing on L¹-distance and representing element of cluster, the article proposes new three algorithms in Fuzzy Clustering of probability density Functions (FCF). They are hierarchical approach, non-hierarchical approach and the algorithm to determine the optimal number of clusters and the initial partition matrix to improve the qualities of established clusters in non-hierarchical approach. With proposed algorithms, FCF has more advantageous than Non-fuzzy Clustering of probability density Functions. These algorithms are applied for recognizing images from Texture and Corel database and practical problem about studying and training marks of students at an university. Many Matlab programs are established for computation in proposed algorithms. These programs are not only used to compute effectively the numerical examples of this article but also to be applied for many different realistic problems.     

Cluster analysis using different correlation coefficients

Partitioning objects into closely related groups that have different states allows to understand the underlying structure in the data set treated. Different kinds of similarity measure with clustering algorithms are commonly used to find an optimal clustering or closely akin to original clustering. Using shrinkage-based and rank-based correlation coefficients, which are known to be robust, the recovery level of six chosen clustering algorithms is evaluated using Rand’s C values. The recovery levels using weighted likelihood estimate of correlation coefficient are obtained and compared to the results from using those correlation coefficients in applying agglomerative clustering algorithms. This work was supported by RIC(R) grants from Traditional and Bio-Medical Research Center, Daejeon University (RRC04713, 2005) by ITEP in Republic of Korea.     

Robust mixture modeling using the skew <Emphasis Type="Italic">t</Emphasis> distribution

A finite mixture model using the Student's t distribution has been recognized as a robust extension of normal mixtures. Recently, a mixture of skew normal distributions has been found to be effective in the treatment of heterogeneous data involving asymmetric behaviors across subclasses. In this article, we propose a robust mixture framework based on the skew t distribution to efficiently deal with heavy-tailedness, extra skewness and multimodality in a wide range of settings. Statistical mixture modeling based on normal, Student's t and skew normal distributions can be viewed as special cases of the skew t mixture model. We present analytically simple EM-type algorithms for iteratively computing maximum likelihood estimates. The proposed methodology is illustrated by analyzing a real data example.     

Mixture of linear mixed models using multivariate t distribution

Linear mixed models are widely used when multiple correlated measurements are made on each unit of interest. In many applications, the units may form several distinct clusters, and such heterogeneity can be more appropriately modelled by a finite mixture linear mixed model. The classical estimation approach, in which both the random effects and the error parts are assumed to follow normal distribution, is sensitive to outliers, and failure to accommodate outliers may greatly jeopardize the model estimation and inference. We propose a new mixture linear mixed model using multivariate t distribution. For each mixture component, we assume the response and the random effects jointly follow a multivariate t distribution, to conveniently robustify the estimation procedure. An efficient expectation conditional maximization algorithm is developed for conducting maximum likelihood estimation. The degrees of freedom parameters of the t distributions are chosen data adaptively, for achieving flexible trade-off between estimation robustness and efficiency. Simulation studies and an application on analysing lung growth longitudinal data showcase the efficacy of the proposed approach.     

Clustering large number of extragalactic spectra of galaxies and quasars through canopies

Abstract

Cluster analysis is the distribution of objects into different groups or more precisely the partitioning of a data set into subsets (clusters) so that the data in subsets share some common trait according to some distance measure. Unlike classification, in clustering one has to first decide the optimum number of clusters and then assign the objects into different clusters. Solution of such problems for a large number of high dimensional data points is quite complicated and most of the existing algorithms will not perform properly. In the present work a new clustering technique applicable to large data set has been used to cluster the spectra of 702248 galaxies and quasars having 1,540 points in wavelength range imposed by the instrument. The proposed technique has successfully discovered five clusters from this 702,248X1,540 data matrix.     

Clustering time-course microarray data using functional Bayesian infinite mixture model

This paper presents a new Bayesian, infinite mixture model based, clustering approach, specifically designed for time-course microarray data. The problem is to group together genes which have “similar” expression profiles, given the set of noisy measurements of their expression levels over a specific time interval. In order to capture temporal variations of each curve, a non-parametric regression approach is used. Each expression profile is expanded over a set of basis functions and the sets of coefficients of each curve are subsequently modeled through a Bayesian infinite mixture of Gaussian distributions. Therefore, the task of finding clusters of genes with similar expression profiles is then reduced to the problem of grouping together genes whose coefficients are sampled from the same distribution in the mixture. Dirichlet processes prior is naturally employed in such kinds of models, since it allows one to deal automatically with the uncertainty about the number of clusters. The posterior inference is carried out by a split and merge MCMC sampling scheme which integrates out parameters of the component distributions and updates only the latent vector of the cluster membership. The final configuration is obtained via the maximum a posteriori estimator. The performance of the method is studied using synthetic and real microarray data and is compared with the performances of competitive techniques.     

Fitting finite mixture models using iterative Monte Carlo classification

Parameters of a finite mixture model are often estimated by the expectation–maximization (EM) algorithm where the observed data log-likelihood function is maximized. This paper proposes an alternative approach for fitting finite mixture models. Our method, called the iterative Monte Carlo classification (IMCC), is also an iterative fitting procedure. Within each iteration, it first estimates the membership probabilities for each data point, namely the conditional probability of a data point belonging to a particular mixing component given that the data point value is obtained, it then classifies each data point into a component distribution using the estimated conditional probabilities and the Monte Carlo method. It finally updates the parameters of each component distribution based on the classified data. Simulation studies were conducted to compare IMCC with some other algorithms for fitting mixture normal, and mixture t, densities.     

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.”

     

A tutorial on spectral clustering

In recent years, spectral clustering has become one of the most popular modern clustering algorithms. It is simple to implement, can be solved efficiently by standard linear algebra software, and very often outperforms traditional clustering algorithms such as the k-means algorithm. On the first glance spectral clustering appears slightly mysterious, and it is not obvious to see why it works at all and what it really does. The goal of this tutorial is to give some intuition on those questions. We describe different graph Laplacians and their basic properties, present the most common spectral clustering algorithms, and derive those algorithms from scratch by several different approaches. Advantages and disadvantages of the different spectral clustering algorithms are discussed.     

Partly linear models on Riemannian manifolds

In partly linear models, the dependence of the response y on (x ^T, t) is modeled through the relationship y=x ^T β+g(t)+?, where ? is independent of (x ^T, t). We are interested in developing an estimation procedure that allows us to combine the flexibility of the partly linear models, studied by several authors, but including some variables that belong to a non-Euclidean space. The motivating application of this paper deals with the explanation of the atmospheric SO₂ pollution incidents using these models when some of the predictive variables belong in a cylinder. In this paper, the estimators of β and g are constructed when the explanatory variables t take values on a Riemannian manifold and the asymptotic properties of the proposed estimators are obtained under suitable conditions. We illustrate the use of this estimation approach using an environmental data set and we explore the performance of the estimators through a simulation study.     

Model selection in finite mixture of regression models: a Bayesian approach with innovative weighted g priors and reversible jump Markov chain Monte Carlo implementation

Finite mixture of regression (FMR) models are aimed at characterizing subpopulation heterogeneity stemming from different sets of covariates that impact different groups in a population. We address the contemporary problem of simultaneously conducting covariate selection and determining the number of mixture components from a Bayesian perspective that can incorporate prior information. We propose a Gibbs sampling algorithm with reversible jump Markov chain Monte Carlo implementation to accomplish concurrent covariate selection and mixture component determination in FMR models. Our Bayesian approach contains innovative features compared to previously developed reversible jump algorithms. In addition, we introduce component-adaptive weighted g priors for regression coefficients, and illustrate their improved performance in covariate selection. Numerical studies show that the Gibbs sampler with reversible jump implementation performs well, and that the proposed weighted priors can be superior to non-adaptive unweighted priors.     

Feature selection and machine learning with mass spectrometry data for distinguishing cancer and non-cancer samples

This is a comparative study of various clustering and classification algorithms as applied to differentiate cancer and non-cancer protein samples using mass spectrometry data. Our study demonstrates the usefulness of a feature selection step prior to applying a machine learning tool. A natural and common choice of a feature selection tool is the collection of marginal p-values obtained from t-tests for testing the intensity differences at each m/z ratio in the cancer versus non-cancer samples. We study the effect of selecting a cutoff in terms of the overall Type 1 error rate control on the performance of the clustering and classification algorithms using the significant features. For the classification problem, we also considered m/z selection using the importance measures computed by the Random Forest algorithm of Breiman. Using a data set of proteomic analysis of serum from ovarian cancer patients and serum from cancer-free individuals in the Food and Drug Administration and National Cancer Institute Clinical Proteomics Database, we undertake a comparative study of the net effect of the machine learning algorithm–feature selection tool–cutoff criteria combination on the performance as measured by an appropriate error rate measure.     

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.     

Flexible mixture modelling using the multivariate skew-t-normal distribution

This paper presents a robust probabilistic mixture model based on the multivariate skew-t-normal distribution, a skew extension of the multivariate Student’s t distribution with more powerful abilities in modelling data whose distribution seriously deviates from normality. The proposed model includes mixtures of normal, t and skew-normal distributions as special cases and provides a flexible alternative to recently proposed skew t mixtures. We develop two analytically tractable EM-type algorithms for computing maximum likelihood estimates of model parameters in which the skewness parameters and degrees of freedom are asymptotically uncorrelated. Standard errors for the parameter estimates can be obtained via a general information-based method. We also present a procedure of merging mixture components to automatically identify the number of clusters by fitting piecewise linear regression to the rescaled entropy plot. The effectiveness and performance of the proposed methodology are illustrated by two real-life examples.     

An algorithm for the Buckley–James estimator with interval-censored data

The Buckley–James estimator (BJE) [J. Buckley and I. James, Linear regression with censored data, Biometrika 66 (1979), pp. 429–436] has been extended from right-censored (RC) data to interval-censored (IC) data by Rabinowitz et al. [D. Rabinowitz, A. Tsiatis, and J. Aragon, Regression with interval-censored data, Biometrika 82 (1995), pp. 501–513]. The BJE is defined to be a zero-crossing of a modified score function H(b), a point at which H(·) changes its sign. We discuss several approaches (for finding a BJE with IC data) which are extensions of the existing algorithms for RC data. However, these extensions may not be appropriate for some data, in particular, they are not appropriate for a cancer data set that we are analysing. In this note, we present a feasible iterative algorithm for obtaining a BJE. We apply the method to our data.