- Murphy, Thomas Brendan

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# Murphy, Thomas Brendan

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- Publicationmclust 5: Clustering, Classification and Density Estimation Using Gaussian Finite Mixture Models(R Foundation for Statistical Computing, 2016-08-01)
; ; ; Finite mixture models are being used increasingly to model a wide variety of random phenomena for clustering, classification and density estimation. mclust is a powerful and popular package which allows modelling of data as a Gaussian finite mixture with different covariance structures and different numbers of mixture components, for a variety of purposes of analysis. Recently, version 5 of the package has been made available on CRAN. This updated version adds new covariance structures, dimension reduction capabilities for visualisation, model selection criteria, initialisation strategies for the EM algorithm, and bootstrap-based inference, making it a full-featured R package for data analysis via finite mixture modelling.943 - PublicationVariational Bayesian inference for the Latent Position Cluster Model(2009-12)
; Many recent approaches to modeling social networks have focussed on embedding the actors in a latent “social space”. Links are more likely for actors that are close in social space than for actors that are distant in social space. In particular, the Latent Position Cluster Model (LPCM) [1] allows for explicit modelling of the clustering that is exhibited in many network datasets. However, inference for the LPCM model via MCMC is cumbersome and scaling of this model to large or even medium size networks with many interacting nodes is a challenge. Variational Bayesian methods offer one solution to this problem. An approximate, closed form posterior is formed, with unknown variational parameters. These parameters are tuned to minimize the Kullback-Leibler divergence between the approximate variational posterior and the true posterior, which known only up to proportionality. The variational Bayesian approach is shown to give a computationally efficient way of fitting the LPCM. The approach is demonstrated on a number of data sets and it is shown to give a good fit.710 - PublicationJoint Modelling of Multiple Network ViewsLatent space models (LSM) for network data were introduced by Holf et al. (2002) under the basic assumption that each node of the network has an unknown position in a D-dimensional Euclidean latent space: generally the smaller the distance between two nodes in the latent space, the greater their probability of being connected. In this paper we propose a variational inference approach to estimate the intractable posterior of the LSM. In many cases, different network views on the same set of nodes are available. It can therefore be useful to build a model able to jointly summarise the information given by all the network views. For this purpose, we introduce the latent space joint model (LSJM) that merges the information given by multiple network views assuming that the probability of a node being connected with other nodes in each network view is explained by a unique latent variable. This model is demonstrated on the analysis of two datasets: an excerpt of 50 girls from 'Teenage Friends and Lifestyle Study' data at three time points and the Saccharomyces cerevisiae genetic and physical protein-protein interactions.
331 - PublicationSentiment analysis of online mediaA joint model for annotation bias and document classification is presented in the context of media sentiment analysis. We consider an Irish online media data set comprising online news articles with user annotations of negative, positive or irrelevant impact on the Irish economy. The joint model combines a statistical model for user annotation bias and a Naive Bayes model for the document terms. An EM algorithm is used to estimate the annotation bias model, the unobserved biases in the user annotations, the classifier parameters and the sentiment of the articles. The joint modeling of both the user biases and the classifier is demonstrated to be superior to estimation of the bias followed by the estimation of the classifier parameters.
904 - PublicationClustering ranked preference data using sociodemographic covariatesRanked preference data arise when a set of judges rank, in order of their preference, a set of objects. Such data arise in preferential voting systems and market research surveys. Covariate data associated with the judges are also often recorded. Such covariate data should be used in conjunction with preference data when drawing inferences about judges. To cluster a population of judges, the population is modelled as a collection of homogeneous groups. The Plackett-Luce model for ranked data is employed to model a judge’s ranked preferences within a group. A mixture of Plackett-Luce models is employed to model the population of judges, where each component in the mixture represents a group of judges. Mixture of experts models provide a framework in which covariates are included in mixture models. Covariates are included through the mixing proportions and the component density parameters. A mixture of experts model for ranked preference data is developed by combining a mixture of experts model and a mixture of Plackett-Luce models. Particular attention is given to the manner in which covariates enter the model. The mixing proportions and group specific parameters are potentially dependent on covariates. Model selection procedures are employed to choose optimal models. Model parameters are estimated via the ‘EMM algorithm’, a hybrid of the Expectation-Maximization and the Minorization-Maximization algorithms. Examples are provided through a menu survey and through Irish election data. Results indicate mixture modelling using covariates is insightful when examining a population of judges who express preferences.
603 - PublicationSentiment Analysis of Online MediaA joint model for annotation bias and document classification is presented in the context of media sentiment analysis. We consider an Irish online media data set comprising online news articles with user annotations of negative, positive or irrelevant impact on the Irish economy. The joint model combines a statistical model for user annotation bias and a Naive Bayes model for the document terms. An EM algorithm is used to estimate the annotation bias model, the unobserved biases in the user annotations, the classifier parameters and the sentiment of the articles. The joint modeling of both the user biases and the classifier is demonstrated to be superior to estimation of the bias followed by the estimation of the classifier parameters.
538 - PublicationMixed membership models for rank data: Investigating structure in Irish voting dataA mixed membership model is an individual level mixture model where individuals have partial membership of the profiles (or groups) that characterize a population. A mixed membership model for rank data is outlined and illustrated through the analysis of voting in the 2002 Irish general election. This particular election uses a voting system called proportional representation using a single transferable vote (PR-STV) where voters rank some or all of the candidates in order of preference. The data set considered consists of all votes in a constituency from the 2002 Irish general election. Interest lies in highlighting distinct voting profiles within the electorate and studying how voters affiliate themselves to these voting profiles. The mixed membership model for rank data is fitted to the voting data and is shown to give a concise and highly interpretable explanation of voting patterns in this election.
291 - Publication
1204 - PublicationPreferences in college applications - a nonparametric Bayesian analysis of top-10 rankings(2010-12-10)
; ; ; Applicants to degree courses in Irish colleges and universities rank up to ten degree courses from a list of over ﬁve hundred. These data provide a wealth of information concerning applicant degree choices. A Dirichlet process mixture of generalized Mallows models are used to explore data from a cohort of applicants. We ﬁnd strong and diverse clusters, which in turn gains us important insights into the workings of the system. No previously tried models or analysis technique are able to model the data with comparable accuracy.254 - PublicationRole Analysis in Networks Using Mixtures of Exponential Random Graph ModelsThis article introduces a novel and flexible framework for investigating the roles of actors within a network. Particular interest is in roles as defined by local network connectivity patterns, identified using the ego-networks extracted from the network. A mixture of exponential-family random graph models (ERGM) is developed for these ego-networks to cluster the nodes into roles. We refer to this model as the ego-ERGM. An expectation-maximization algorithm is developed to infer the unobserved cluster assignments and to estimate the mixture model parameters using a maximum pseudo-likelihood approximation. We demonstrate the flexibility and utility of the method using examples of simulated and real networks.
314Scopus© Citations 16