Nial Friel

• PhD
• Professor at University College Dublin

Significance We develop a statistical model for the evolution of the network of leading Irish company directorates over 11 years, before and after the financial crisis of 2008. We focus on company interlocks, whereby a director simultaneously sits on more than one company board. Our analysis indicates that the level of director interlockingness inc...

We propose Adaptive Incremental Mixture Markov chain Monte Carlo (AIMM), a novel approach to sample from challenging probability distributions defined on a general state-space. Typically, adaptive MCMC methods recursively update a parametric proposal kernel with a global rule; by contrast AIMM locally adapts a non-parametric kernel. AIMM is based o...

Many popular statistical models for complex phenomena are intractable, in the sense that the likelihood function cannot easily be evaluated, even up to proportionality. Bayesian estimation in this setting remains challenging, with a lack of computational methodology to fully exploit modern processing capabilities. In this paper we introduce novel c...

Monte Carlo algorithms often aim to draw from a distribution $\pi$ by simulating a Markov chain with transition kernel $P$ such that $\pi$ is invariant under $P$. However, there are many situations for which it is impractical or impossible to draw from the transition kernel $P$. For instance, this is the case with massive datasets, where is it proh...

Criminal networks arise from the attempt to balance a need of establishing frequent ties among affiliates to facilitate coordination of illegal activities, with the necessity to sparsify the overall connectivity architecture to hide from law enforcement. This efficiency-security trade-off is also combined with the creation of groups of redundant cr...

The latent position network model (LPM) is a popular approach for the statistical analysis of network data. A central aspect of this model is that it assigns nodes to random positions in a latent space, such that the probability of an interaction between each pair of individuals or nodes is determined by their distance in this latent space. A key f...

Online boards offer a platform for sharing and discussing content, where discussion emerges as a cascade of comments in response to a post. Branching point process models offer a practical approach to modelling these cascades; however, existing models do not account for apparent features of empirical data. We address this gap by illustrating the fl...

Rankings represent preferences that arise from situations where assessors arrange items, for example, in decreasing order of utility. Orderings of the item set are permutations (\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upg...

Criminal networks arise from the unique attempt to balance a need of establishing frequent ties among affiliates to facilitate the coordination of illegal activities, with the necessity to sparsify the overall connectivity architecture to hide from law enforcement. This efficiency-security tradeoff is also combined with the creation of groups of re...

The relative abundance of groups of species is often used in ecological surveys to estimate community composition, a metric that reflects patterns of commonness and rarity of biological assemblages. The focus of this paper is measurements of the abundances of four benthic groups (that live on the seafloor) at several reefs on Australia’s Great Barr...

The exponential random graph (ERGM) model is a popular statistical framework for studying the determinants of tie formations in social network data. To test scientific theories under the ERGM framework, statistical inferential techniques are generally used based on traditional significance testing using p values. This methodology has certain limita...

In this chapter, we present a review of latent position models for networks. We review the recent literature in this area and illustrate the basic aspects and properties of this modeling framework. Through several illustrative examples we highlight how the latent position model is able to capture important features of observed networks. We emphasiz...

Competitive balance is of much interest in the sports analytics literature and beyond. We develop a statistical network model based on an extension of the stochastic block model to assess the balance between teams in a league. We represent the outcome of all matches in a football season as a dense network with nodes identified by teams and categori...

The expected number of secondary infections arising from each index case, referred to as the reproduction or R$$ R $$ number, is a vital summary statistic for understanding and managing epidemic diseases. There are many methods for estimating R$$ R $$; however, few explicitly model heterogeneous disease reproduction, which gives rise to superspread...

Recent advances in computational methods for intractable models have made network data increasingly amenable to statistical analysis. Exponential random graph models (ERGMs) emerged as one of the main families of models capable of capturing the complex dependence structure of network data in a wide range of applied contexts. The Bergm package for R...

In this paper, a multivariate count distribution with Conway-Maxwell (COM)-Poisson marginals is proposed. To do this, we develop a modification of the Sarmanov method for constructing multivariate distributions. Our multivariate COM-Poisson (MultCOMP) model has desirable features such as (i) it admits a flexible covariance matrix allowing for both...

We describe the population-based susceptible-exposed-infected-removed (SEIR) model developed by the Irish Epidemiological Modelling Advisory Group (IEMAG), which advises the Irish government on COVID-19 responses. The model assumes a time-varying effective contact rate (equivalently, a time-varying reproduction number) to model the effect of non-ph...

Competitive balance is a desirable feature in any professional sports league and encapsulates the notion that there is unpredictability in the outcome of games as opposed to an imbalanced league in which the outcome of some games are more predictable than others, for example, when an apparent strong team plays against a weak team. In this paper, we...

In this paper, a multivariate count distribution with Conway-Maxwell (COM)-Poisson marginals is proposed. To do this, we develop a modification of the Sarmanov method for constructing multivariate distributions. Our multivariate COM-Poisson (MultCOMP) model has desirable features such as (i) it admits a flexible covariance matrix allowing for both...

The expected number of secondary infections arising from each index case, the reproduction number, or $R$ number is a vital summary statistic for understanding and managing epidemic diseases. There are many methods for estimating $R$; however, few of these explicitly model heterogeneous disease reproduction, which gives rise to superspreading withi...

We describe the population-based SEIR (susceptible, exposed, infected, removed) model developed by the Irish Epidemiological Modelling Advisory Group (IEMAG), which advises the Irish government on COVID-19 responses. The model assumes a time-varying effective contact rate (equivalently, a time-varying reproduction number) to model the effect of non...

Relative abundance is a common metric to estimate the composition of species in ecological surveys reflecting patterns of commonness and rarity of biological assemblages. Measurements of coral reef compositions formed by four communities along Australia's Great Barrier Reef (GBR) gathered between 2012 and 2017 are the focus of this paper. We undert...

Recent advances in computational methods for intractable models have made network data increasingly amenable to statistical analysis. Exponential random graph models (ERGMs) emerged as one of the main families of models capable of capturing the complex dependence structure of network data in a wide range of applied contexts. The Bergm package for R...

Deriving Bayesian inference for exponential random graph models (ERGMs) is a challenging “doubly intractable” problem as the normalizing constants of the likelihood and posterior density are both intractable. Markov chain Monte Carlo (MCMC) methods which yield Bayesian inference for ERGMs, such as the exchange algorithm, are asymptotically exact bu...

This paper introduces a framework for speeding up Bayesian inference conducted in presence of large datasets. We design a Markov chain whose transition kernel uses an {unknown} fraction of {fixed size} of the available data that is randomly refreshed throughout the algorithm. Inspired by the Approximate Bayesian Computation (ABC) literature, the su...

Bayesian inference for exponential random graphs (ERGMs) is a doubly intractable problem as the normalizing constants of both the likelihood and the posterior density are intractable. Markov chain Monte Carlo (MCMC) methods which yield Bayesian inference for ERGMs, such as the exchange algorithm, are asymptotically exact but computationally intensi...

In cluster analysis interest lies in probabilistically capturing partitions of individuals, items or observations into groups, such that those belonging to the same group share similar attributes or relational profiles. Bayesian posterior samples for the latent allocation variables can be effectively obtained in a wide range of clustering models, i...

The reversible jump Markov chain Monte Carlo (RJMCMC) method offers an across-model simulation approach for Bayesian estimation and model comparison, by exploring the sampling space that consists of several models of varying dimensions. The implementation of RJMCMC to models like Gibbs random fields suffers from computational difficulties: the post...

Latent position models are nowadays widely used for the analysis of networks in a variety of research fields. In fact, these models possess a number of desirable theoretical properties, and are particularly easy to interpret. However, statistical methodologies that infer latent position models generally require a computational cost which grows with...

We present a discussion of the paper "Bayesian cluster analysis: point estimation and credible balls" by Wade and Ghahramani. We believe that this paper contributes substantially to the literature on Bayesian clustering by filling in an important methodological gap, by providing a means to assess the uncertainty around a point estimate of the optim...

Latent position models are widely used for the analysis of networks in a variety of research fields. In fact, these models possess a number of desirable theoretical properties, and are particularly easy to interpret. However, statistical methodologies to fit these models generally incur a computational cost which grows with the square of the number...

The reversible jump Markov chain Monte Carlo (RJMCMC) method offers an across-model simulation approach for Bayesian estimation and model comparison, by exploring the sampling space that consists of several models of varying dimensions. The implementation of RJMCMC to models like Gibbs random fields suffers from computational difficulties: the post...

The reversible jump Markov chain Monte Carlo (RJMCMC) method offers an across-model simulation approach for Bayesian estimation and model comparison, by exploring the sampling space that consists of several models of possibly varying dimensions. A naive implementation of RJMCMC to models like Gibbs random fields suffers from computational difficult...

A spatial hidden Markov model (SHMM) is introduced to analyse the distribution of a species on an atlas, taking into account that false observations and false non-detections of the species can occur during the survey, blurring the true map of presence and absence of the species. The reconstruction of the true map is tackled as the restoration of a...

Bayesian inference of Gibbs random fields (GRFs) is often referred to as a doubly intractable problem, since the likelihood function is intractable. The exploration of the posterior distribution of such models is typically carried out with a sophisticated Markov chain Monte Carlo (MCMC) method, the exchange algorithm (Murray et al., 2006), which re...

Bayesian inference of Gibbs random fields (GRFs) is often referred to as a doubly intractable problem, since the likelihood function is intractable. The exploration of the posterior distribution of such models is typically carried out with a sophisticated Markov chain Monte Carlo (MCMC) method, the exchange algorithm (Murray et al., 2006), which re...

Bayesian inference for models with intractable likelihood functions represents a challenging suite of problems in modern statistics. In this work we analyse the Conway-Maxwell-Poisson (COM-Poisson) distribution, a two parameter generalisation of the Poisson distribution. COM-Poisson regression modelling allows the flexibility to model dispersed cou...

Bayesian inference for models with intractable likelihood functions represents a challenging suite of problems in modern statistics. In this work we analyse the Conway-Maxwell-Poisson (COM-Poisson) distribution, a two parameter generalisation of the Poisson distribution. COM-Poisson regression modelling allows the flexibility to model dispersed cou...

Exponential random graph models are an important tool in the statistical analysis of data. However, Bayesian parameter estimation for these models is extremely challenging, since evaluation of the posterior distribution typically involves the calculation of an intractable normalizing constant. This barrier motivates the consideration of tractable a...

Hamiltonian Monte Carlo (HMC) has been progressively incorporated within the statistician's toolbox as an alternative sampling method in settings when standard Metropolis-Hastings is inefficient. HMC generates a Markov chain on an augmented state space with transitions based on a deterministic differential flow derived from Hamiltonian mechanics. I...

Hamiltonian Monte Carlo (HMC) has been progressively incorporated within the statistician's toolbox as an alternative sampling method in settings when standard Metropolis-Hastings is inefficient. HMC generates a Markov chain on an augmented state space with transitions based on a deterministic differential flow derived from Hamiltonian mechanics. I...

This paper introduces a framework for speeding up Bayesian inference conducted in presence of large datasets. We design a Markov chain whose transition kernel uses an (unknown) fraction of (fixed size) of the available data that is randomly refreshed throughout the algorithm. Inspired by the Approximate Bayesian Computation (ABC) literature, the su...

Models with intractable likelihood functions arise in many areas including network analysis and spatial statistics, especially those involving Gibbs random field models. Posterior parameter estimation in these settings has been termed a doubly intractable problem because both the likelihood function and the posterior distribution are intractable. T...

Models with intractable likelihood functions arise in areas including network analysis and spatial statistics, especially those involving Gibbs random fields. Posterior parameter es timation in these settings is termed a doubly-intractable problem because both the likelihood function and the posterior distribution are intractable. The comparison of...

The widely applicable Bayesian information criterion (WBIC) is a simple and fast approximation to the statistical evidence that has received little practical consideration. Introduced to handle the problem of singular statistical models, such as latent variable models or those with a hierarchical structure, WBIC is investigated under four models of...

The latent position cluster model is a popular model for the statistical analysis of network data. This model assumes that there is an underlying latent space in which the actors follow a finite mixture distribution. Moreover, actors which are close in this latent space are more likely to be tied by an edge. This is an appealing approach since it a...

The Bergm package provides a comprehensive framework for Bayesian inference using Markov chain Monte Carlo (MCMC) algorithms. It can also supply graphical Bayesian goodness-of-fit procedures that address the issue of model adequacy. The package is simple to use and represents an attractive way of analysing network data as it offers the advantage of...

We consider the task of simultaneous clustering of the two node sets involved in a bipartite network. The approach we adopt is based on use of the exact integrated complete likelihood for the latent blockmodel. Using this allows one to infer the number of clusters as well as cluster memberships using a greedy search. This gives a model-based cluste...

Latent stochastic block models are flexible statistical models that are widely used in social network analysis. In recent years, efforts have been made to extend these models to temporal dynamic networks, whereby the connections between nodes are observed at a number of different times. In this paper we extend the original stochastic block model by...

Latent stochastic block models are flexible statistical models that are widely used in social network analysis. In recent years, efforts have been made to extend these models to temporal dynamic networks, whereby the connections between nodes are observed at a number of different times. In this paper we extend the original stochastic block model by...

The latent position cluster model is a popular model for the statistical analysis of network data. This model assumes that there is an underlying latent space in which the actors follow a finite mixture distribution. Moreover, actors which are close in this latent space are more likely to be tied by an edge. This is an appealing approach since it a...

We derive properties of latent variable models for networks, a broad class of models that includes the widely used latent position models. We characterize several features of interest, with particular focus on the degree distribution, clustering coefficient, average path length, and degree correlations. We introduce the Gaussian latent position mod...

Contributed discussion to the paper of Drton and Plummer (2017), presented before the Royal Statistical Society on 5th October 2016.

In cluster analysis interest lies in probabilistically capturing partitions of individuals, items or observations into groups, such that those belonging to the same group share similar attributes or relational profiles. Bayesian posterior samples for the latent allocation variables can be effectively obtained in a wide range of clustering models, i...

We extend the well-known and widely used exponential random graph model (ERGM) by including nodal random effects to compensate for heterogeneity in the nodes of a network. The Bayesian framework for ERGMs proposed by Caimo and Friel (2011) yields the basis of our modelling algorithm. A central question in network models is the question of model sel...

We consider the problem of Bayesian inference for changepoints where the number and position of the changepoints are both unknown. In particular, we consider product partition models where it is possible to integrate out model parameters for the regime between each changepoint, leaving a posterior distribution over a latent vector indicating the pr...

We consider the problem of Bayesian inference for changepoints where the number and position of the changepoints are both unknown. In particular, we consider product partition models where it is possible to integrate out model parameters for the regime between each changepoint, leaving a posterior distribution over a latent vector indicating the pr...

We propose Adaptive Incremental Mixture Markov chain Monte Carlo (AIMM), a novel approach to sample from challenging probability distributions defined on a general state-space. While adaptive MCMC methods usually update a parametric proposal kernel with a global rule, AIMM locally adapts a semiparametric kernel. AIMM is based on an independent Metr...

Light and Widely Applicable (LWA-) MCMC is a novel approximation of the Metropolis-Hastings kernel targeting a posterior distribution defined on a large number of observations. Inspired by Approximate Bayesian Computation, we design a Markov chain whose transition makes use of an unknown but fixed, fraction of the available data, where the random c...

Gibbs random fields play an important role in statistics, however, the resulting likelihood is typically unavailable due to an intractable normalizing constant. Composite likelihoods offer a principled means to construct useful approximations. This paper provides a mean to calibrate the posterior distribution resulting from using a composite likeli...

The widely applicable Bayesian information criterion (WBIC) is a simple and fast approximation to the model evidence that has received little practical consideration. WBIC uses the fact that the log evidence can be written as an expectation, with respect to a powered posterior proportional to the likelihood raised to a power $t^*\in{(0,1)}$, of the...

The ICL criteria has proven to be a very popular approach for clustering data through automatically choosing the number of components in a mixture model. This approach effectively maximises the complete data likelihood, thereby including the location of observations to components in the model selection criteria. However for practical implementation...

In this paper we describe the main featuress of the Bergm package for the open-source R software which provides a comprehensive framework for Bayesian analysis for exponential random graph models: tools for parameter estimation, model selection and goodness-of-fit diagnostics. We illustrate the capabilities of this package describing the algorithms...

Probabilistic k-nearest neighbour (PKNN) classification has been introduced to improve the performance of original k-nearest neighbour (KNN) classification algorithm by explicitly modelling uncertainty in the classification of each feature vector. However, an issue common to both KNN and PKNN is to select the optimal number of neighbours, $k$. The...

The Reversible Jump algorithm is one of the most widely used Markov chain Monte Carlo algorithms for Bayesian estimation and model selection. A generalized multiple-try version of this algorithm is proposed. The algorithm is based on drawing several proposals at each step and randomly choosing one of them on the basis of weights (selection probabil...

Approximate Bayesian computation has proven to be a valuable approach in the Bayesian analysis of statistical models with intractable likelihood models. At the heart of this approach is the requirement to sample from the likelihood model. However in certain contexts this requirement can result in excessive computational costs. This is certainly the...

Statistical models which involve intractable likelihood are attracting considerable interest from the statistics community. For example, approximate Bayesian computation (eg., (Marin et al. 2012)) and pseudo-marginal methods Andrieu and Roberts (2009) are two relatively recent approaches which have had a big impact and both of which are the subject...

The latent position cluster model is a popular model for the statistical analysis of network data. This approach assumes that there is an underlying latent space in which the actors follow a finite mixture distribution. Moreover, actors which are close in this latent space tend to be tied by an edge. This is an appealing approach since it allows th...

An efficient MCMC algorithm is presented to cluster the nodes of a network such that nodes with similar role in the network are clustered together. This is known as block-modeling or block-clustering. The model is the stochastic blockmodel (SBM) with block parameters integrated out. The resulting marginal distribution defines a posterior over the n...

Gibbs random fields play an important role in statistics. However they are complicated to work with due to an intractability of the likelihood function and there has been much work devoted to finding computational algorithms to allow Bayesian inference to be conducted for such so-called doubly intractable distributions. This paper extends this work...

Exponential random graph models are a class of widely used exponential family models for social networks. The topological structure of an observed network is modelled by the relative prevalence of a set of local sub-graph configurations termed network statistics. One of the key tasks in the application of these models is which network statistics to...

The statistical evidence (or marginal likelihood) is a key quantity in Bayesian statistics, allowing one to assess the probability of the data given the model under investigation. This paper focuses on refining the power posterior approach to improve estimation of the evidence. The power posterior method involves transitioning from the prior to the...

Gibbs random fields play an important role in statistics, for example the autologistic model is commonly used to model the spatial distribution of binary variables defined on a lattice. However they are complicated to work with due to an intractability of the likelihood function. It is therefore natural to consider tractable approximations to the l...

In the model-based clustering of networks, blockmodelling may be used to identify roles in the network. We identify a special case of the Stochastic Block Model (SBM) where we constrain the cluster-cluster interactions such that the density inside the clusters of nodes is expected to be greater than the density between clusters. This corresponds to...

An efficient MCMC algorithm is presented to cluster the nodes of a network such that nodes with similar role in the network are clustered together. This is known as block-modelling or block-clustering. The model is the stochastic blockmodel (SBM) with block parameters integrated out. The resulting marginal distribution defines a posterior over the...

The model evidence is a vital quantity in the comparison of statistical models under the Bayesian paradigm. This papers presents a review of commonly used methods. We outline some guidelines and offer some practical advice. The reviewed methods are compared for two examples; non-nested Gaussian linear regression and covariate subset selection in lo...

The model evidence is a vital quantity in the comparison of statistical models under the Bayesian paradigm. This paper presents a review of commonly used methods. We outline some guidelines and offer some practical advice. The reviewed methods are compared for two examples; non-nested Gaussian linear regression and covariate subset selection in log...

This paper proposes approaches for the analysis of multiple changepoint models when dependency in the data is modelled through a hierarchical Gaussian Markov random field. Integrated nested Laplace approximations are used to approximate data quantities, and an approximate filtering recursions approach is proposed for savings in compuational cost wh...

This paper proposes a new probabilistic classification algorithm using a Markov random field approach. The joint distribution of class labels is explicitly modelled using the distances between feature vectors. Intuitively, aclass label should depend more on class labels which are closer in the feature space, than those which are further away. Our a...

Bubbles is a classification image technique that randomly samples visual information from input stimuli to derive the diagnostic features that observers use in visual categorization tasks. To reach statistical significance, Bubbles performs an exhaustive and repetitive search in the stimulus space. To reduce the search trials, we developed an adapt...

This paper proposes approaches for the analysis of multiple changepoint models when dependency in the data is modelled through a hierarchical Gaussian Markov random field model. Integrated nested Laplace approximations are used to approximate data quantities, and an approximate filtering recursions approach is proposed for savings in compuational c...

Generalized Additive Models (GAMs) with age, period and cohort as possible covariates are used to predict future mortality improvements for the Irish population. The GAMs considered are the 1-dimensional age + period and age + cohort models and the 2-dimensional age-period and age-cohort models. In each case thin plate regression splines are used a...

Exponential random graph models are extremely difficult models to handle from a statistical viewpoint, since their normalising constant, which depends on model parameters, is available only in very trivial cases. We show how inference can be carried out in a Bayesian framework using a MCMC algorithm, which circumvents the need to calculate the norm...

This paper presents a Markov chain Monte Carlo method to generate approximate posterior samples in retrospective multiple changepoint problems where the number of changes is not known in advance. The method uses conjugate models whereby the marginal likelihood for the data between consecutive changepoints is tractable. Inclusion of hyperpriors give...

We introduce a Bayesian extension of the latent block model for model-based block clustering of data matrices. Our approach considers a block model where block parameters may be integrated out. The result is a posterior defined over the number of clusters in rows and columns and cluster memberships. The number of row and column clusters need not be...

The method of tempered transitions was proposed by Neal (1996) for tackling the difficulties arising when using Markov chain Monte Carlo to sample from multimodal distributions. In common with methods such as simulated tempering and Metropolis-coupled MCMC, the key idea is to utilise a series of successively easier to sample distributions to improv...

Supplementary tables. Table S1: novel variants in LD with heterozygous polymorphisms previously associated with disease. Table S2: indels in coding sequence regions. Table S3: Tajima's D values. Table S4: re-sequencing results of 26 coding indels.

Figure S1. Principal components analysis plot adapted from [15] illustrating the position of our Irish Individual with respect to other individuals of western European origin.

Figure S2. Confirmation of rs3197999 in the Irish individual via standard PCR resequencing.

Figure S3. Confirmation of the novel nonsense variant in MST1 via standard PCR followed by sequencing.

Table S5. The resulting genotype calls for chromosome 20.

Recent studies generating complete human sequences from Asian, African and European subgroups have revealed population-specific variation and disease susceptibility loci. Here, choosing a DNA sample from a population of interest due to its relative geographical isolation and genetic impact on further populations, we extend the above studies through...

Exponential random graph models are extremely difficult models to handle from a statistical viewpoint, since their normalising constant, which depends on model parameters, is available only in very trivial cases. We show how inference can be carried out in a Bayesian framework using a MCMC algorithm, which circumvents the need to calculate the norm...

The p* model is widely used in social net- work analysis. The likelihood of a network under this model is impossible to calculate for all but trivially small networks. Vari- ous approximation have been presented in the literature, and the pseudolikelihood ap- proximation is the most popular. The aim of this paper is to introduce two likelihood appr...