arXiv subjects

Isobel Claire Gormley

Publications and source records attributed to Isobel Claire Gormley.

At least 19 recordsLinked to original sources

arXiv2026

Characterising mortality dynamics across countries and time using a multi-stage clustering approach

Comparative analyses of mortality dynamics across countries have long shaped our understanding of mortality inequalities and patterns of divergence and convergence over time. However, most existing studies focus on either mortality differences across countries at a single point in time or on country trajectories, without considering both factors simultaneously. In this paper, we address this gap by introducing a multi-stage clustering framework, applied to 94 countries by sex over the period 1960-2019 using data from the World Population Prospects. Specifically, we model life-table probabilities of death using a time-dependent beta latent variable model and identify a small set of ``mortality states'' that characterise the mortality pattern of each country at any given point in time. We then cluster countries based on their sequences of mortality states. Our results reveal substantial heterogeneity in the timing and pace of transitions between mortality states, including a persistent East-West divide in Europe and distinctive Latin American patterns associated with elevated young-adult male mortality. Cross-country inequality increased for both sexes until the 1990s, before plateauing and subsequently declining. Our proposed multi-stage clustering framework provides an interpretable, time-explicit description of mortality dynamics that jointly captures within-country change and between-country differences, and can be applied to other settings where trajectories of categorical or discretised profiles are of interest.

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arXiv2026

Summarising mortality data with a time-dependent beta latent variable model

Age-specific probabilities of death provide a snapshot of population mortality at the country level at a given point in time. Due to the high dimensionality of the data, summarising mortality information is essential for various analyses, such as visualisation and clustering. We propose the use of beta latent variable (BLV) models to summarise mortality information without data transformation. A time-dependent version of the BLV model is developed by incorporating an autoregressive prior for the latent effects. This model aims to represent mortality data with a small set of $K$ latent effects while accounting for time dependence between these effects. Inference is performed using Bayesian methods, with posterior samples generated via Hamiltonian Monte Carlo. The BLV model is applied to probabilities of death from the Human Mortality Database, covering 41 countries and 23 age-specific probabilities of death over several periods. The time-dependent BLV model with $K=6$ latent effects accurately reconstructs observed mortality data, and the model parameters have intuitive and insightful interpretations. The time-dependent BLV outperforms the standard Gaussian factor analysis model applied to logit probability of death, and demonstrates that BLV models can effectively summarise mortality data.

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arXiv2025

Clustering country-level all-cause mortality data: a review

Mortality data are relevant to demography, public health, and actuarial science. Whilst clustering is increasingly used to explore patterns in such data, no study has reviewed its application to country-level all-cause mortality. This review therefore summarises recent work and addresses key questions: why clustering is used, which mortality data are analysed, which methods are most common, and what main findings emerge. To address these questions, we examine studies applying clustering to country-level all-cause mortality, focusing on mortality indices, data sources, and methodological choices, and we replicate some approaches using Human Mortality Database (HMD) data. Our analysis reveals that clustering is mainly motivated by forecasting and by studying convergence and inequality. Most studies use HMD data from developed countries and rely on k-means, hierarchical, or functional clustering. Main findings include a persistent East-West European division across applications, with clustering generally improving forecast accuracy over single-country models. Overall, this review highlights the methodological range in the literature, summarises clustering results, and identifies gaps, such as the limited evaluation of clustering quality and the underuse of data from countries outside the high-income world.

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arXiv2025

Model-based Clustering for Network Data via a Latent Shrinkage Position Cluster Model

Low-dimensional representation and clustering of network data are tasks of great interest across various fields. Latent position models are routinely used for this purpose by assuming that each node has a location in a low-dimensional latent space, and by enabling node clustering. However, these models fall short through their inability to simultaneously determine the latent space dimension and number of clusters. Here we introduce the latent shrinkage position cluster model (LSPCM), which addresses this limitation. The LSPCM posits an infinite dimensional latent space and assumes a Bayesian nonparametric shrinkage prior on the latent positions' variance parameters resulting in higher dimensions having increasingly smaller variances, aiding the identification of dimensions with non-negligible variance. Further, the LSPCM assumes the latent positions follow a sparse finite Gaussian mixture model, allowing for automatic inference on the number of clusters related to non-empty mixture components. As a result, the LSPCM simultaneously infers the effective dimension of the latent space and the number of clusters, eliminating the need to fit and compare multiple models. The performance of the LSPCM is assessed via simulation studies and demonstrated through application to two real Twitter network datasets from sporting and political contexts. Open source software is available to facilitate widespread use of the LSPCM.

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arXiv2025

Missing data imputation using a truncated Gaussian infinite factor model with application to metabolomics data

Metabolomics is the study of small molecules in biological samples. Metabolomics data are typically high-dimensional and contain highly correlated variables and frequent missing values. Both missing at random (MAR) data, due to acquisition or processing errors, and missing not at random (MNAR) data, caused by values falling below detection thresholds, are common. Thus, imputation is a critical component of downstream analysis. Existing imputation methods generally assume one type of data missingness mechanism, or impute values outside the data's physical constraints. A novel truncated Gaussian infinite factor analysis (TGIFA) model is proposed to perform statistically principled and physically realistic imputation in metabolomics data. By incorporating truncated Gaussian assumptions, TGIFA respects the data's physical constraints, while leveraging an infinite latent factor framework to capture high-dimensional dependencies without pre-specifying the number of latent factors. Our Bayesian inference approach enables uncertainty quantification in both the values of the imputed data, and the missing data mechanism. A computationally efficient exchange algorithm enables scalable posterior inference via Markov Chain Monte Carlo. We validate TGIFA through a comprehensive simulation study and demonstrate its utility in a motivating urinary metabolomics dataset, where it yields useful imputations, with associated uncertainty quantification. Open-source R code, available at https://github.com/kfinucane/TGIFA, accompanies TGIFA.

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arXiv2024

Integrated differential analysis of multi-omics data using a joint mixture model: idiffomix

Gene expression and DNA methylation are two interconnected biological processes and understanding their relationship is important in advancing understanding in diverse areas, including disease pathogenesis, environmental adaptation, developmental biology, and therapeutic responses. Differential analysis, including the identification of differentially methylated cytosine-guanine dinucleotide (CpG) sites (DMCs) and differentially expressed genes (DEGs) between two conditions, such as healthy and affected samples, can aid understanding of biological processes and disease progression. Typically, gene expression and DNA methylation data are analysed independently to identify DMCs and DEGs which are further analysed to explore relationships between them. Such approaches ignore the inherent dependencies and biological structure within these related data. A joint mixture model is proposed that integrates information from the two data types at the modelling stage to capture their inherent dependency structure, enabling simultaneous identification of DMCs and DEGs. The model leverages a joint likelihood function that accounts for the nested structure in the data, with parameter estimation performed using an expectation-maximisation algorithm. Performance of the proposed method, idiffomix, is assessed through a thorough simulation study and application to a publicly available breast cancer dataset. Several genes, identified as non-differentially expressed when the data types were modelled independently, had high likelihood of being differentially expressed when associated methylation data were integrated into the analysis. The idiffomix approach highlights the advantage of an integrated analysis via a joint mixture model over independent analyses of the two data types; genome-wide and cross-omics information is simultaneously utilised providing a more comprehensive view.

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arXiv2024

A consensus-constrained parsimonious Gaussian mixture model for clustering hyperspectral images

The use of hyperspectral imaging to investigate food samples has grown due to the improved performance and lower cost of instrumentation. Food engineers use hyperspectral images to classify the type and quality of a food sample, typically using classification methods. In order to train these methods, every pixel in each training image needs to be labelled. Typically, computationally cheap threshold-based approaches are used to label the pixels, and classification methods are trained based on those labels. However, threshold-based approaches are subjective and cannot be generalized across hyperspectral images taken in different conditions and of different foods. Here a consensus-constrained parsimonious Gaussian mixture model (ccPGMM) is proposed to label pixels in hyperspectral images using a model-based clustering approach. The ccPGMM utilizes information that is available on some pixels and specifies constraints on those pixels belonging to the same or different clusters while clustering the rest of the pixels in the image. A latent variable model is used to represent the high-dimensional data in terms of a small number of underlying latent factors. To ensure computational feasibility, a consensus clustering approach is employed, where the data are divided into multiple randomly selected subsets of variables and constrained clustering is applied to each data subset; the clustering results are then consolidated across all data subsets to provide a consensus clustering solution. The ccPGMM approach is applied to simulated datasets and real hyperspectral images of three types of puffed cereal, corn, rice, and wheat. Improved clustering performance and computational efficiency are demonstrated when compared to other current state-of-the-art approaches.

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arXiv2024

A novel family of beta mixture models for the differential analysis of DNA methylation data: an application to prostate cancer

Identifying differentially methylated cytosine-guanine dinucleotide (CpG) sites between benign and tumour samples can assist in understanding disease. However, differential analysis of bounded DNA methylation data often requires data transformation, reducing biological interpretability. To address this, a family of beta mixture models (BMMs) is proposed that (i) objectively infers methylation state thresholds and (ii) identifies differentially methylated CpG sites (DMCs) given untransformed, beta-valued methylation data. The BMMs achieve this through model-based clustering of CpG sites and by employing parameter constraints, facilitating application to different study settings. Inference proceeds via an expectation-maximisation algorithm, with an approximate maximization step providing tractability and computational feasibility. Performance of the BMMs is assessed through thorough simulation studies, and the BMMs are used for differential analyses of DNA methylation data from a prostate cancer study. Intuitive and biologically interpretable methylation state thresholds are inferred and DMCs are identified, including those related to genes such as GSTP1, RASSF1 and RARB, known for their role in prostate cancer development. Gene ontology analysis of the DMCs revealed significant enrichment in cancer-related pathways, demonstrating the utility of BMMs to reveal biologically relevant insights. An R package betaclust facilitates widespread use of BMMs.

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arXiv2024

Predicting milk traits from spectral data using Bayesian probabilistic partial least squares regression

High-dimensional spectral data -- routinely generated in dairy production -- are used to predict a range of traits in milk products. Partial least squares (PLS) regression is ubiquitously used for these prediction tasks. However, PLS regression is not typically viewed as arising from a probabilistic model, and parameter uncertainty is rarely quantified. Additionally, PLS regression does not easily lend itself to model-based modifications, coherent prediction intervals are not readily available, and the process of choosing the latent-space dimension, $\mathtt{Q}$, can be subjective and sensitive to data size. We introduce a Bayesian latent-variable model, emulating the desirable properties of PLS regression while accounting for parameter uncertainty in prediction. The need to choose $\mathtt{Q}$ is eschewed through a nonparametric shrinkage prior. The flexibility of the proposed Bayesian partial least squares (BPLS) regression framework is exemplified by considering sparsity modifications and allowing for multivariate response prediction. The BPLS regression framework is used in two motivating settings: 1) multivariate trait prediction from mid-infrared spectral analyses of milk samples, and 2) milk pH prediction from surface-enhanced Raman spectral data. The prediction performance of BPLS regression at least matches that of PLS regression. Additionally, the provision of correctly calibrated prediction intervals objectively provides richer, more informative inference for stakeholders in dairy production.

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arXiv2024

Variational Inference for the Latent Shrinkage Position Model

The latent position model (LPM) is a popular method used in network data analysis where nodes are assumed to be positioned in a $p$-dimensional latent space. The latent shrinkage position model (LSPM) is an extension of the LPM which automatically determines the number of effective dimensions of the latent space via a Bayesian nonparametric shrinkage prior. However, the LSPM reliance on Markov chain Monte Carlo for inference, while rigorous, is computationally expensive, making it challenging to scale to networks with large numbers of nodes. We introduce a variational inference approach for the LSPM, aiming to reduce computational demands while retaining the model's ability to intrinsically determine the number of effective latent dimensions. The performance of the variational LSPM is illustrated through simulation studies and its application to real-world network data. To promote wider adoption and ease of implementation, we also provide open-source code.

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arXiv2023

A Latent Shrinkage Position Model for Binary and Count Network Data

Interactions between actors are frequently represented using a network. The latent position model is widely used for analysing network data, whereby each actor is positioned in a latent space. Inferring the dimension of this space is challenging. Often, for simplicity, two dimensions are used or model selection criteria are employed to select the dimension, but this requires choosing a criterion and the computational expense of fitting multiple models. Here the latent shrinkage position model (LSPM) is proposed which intrinsically infers the effective dimension of the latent space. The LSPM employs a Bayesian nonparametric multiplicative truncated gamma process prior that ensures shrinkage of the variance of the latent positions across higher dimensions. Dimensions with non-negligible variance are deemed most useful to describe the observed network, inducing automatic inference on the latent space dimension. While the LSPM is applicable to many network types, logistic and Poisson LSPMs are developed here for binary and count networks respectively. Inference proceeds via a Markov chain Monte Carlo algorithm, where novel surrogate proposal distributions reduce the computational burden. The LSPM's properties are assessed through simulation studies, and its utility is illustrated through application to real network datasets. Open source software assists wider implementation of the LSPM.

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arXiv2021

Clustering Longitudinal Life-Course Sequences Using Mixtures of Exponential-Distance Models

Sequence analysis is an increasingly popular approach for analysing life courses represented by ordered collections of activities experienced by subjects over time. Here, we analyse a survey data set containing information on the career trajectories of a cohort of Northern Irish youths tracked between the ages of 16 and 22. We propose a novel, model-based clustering approach suited to the analysis of such data from a holistic perspective, with the aims of estimating the number of typical career trajectories, identifying the relevant features of these patterns, and assessing the extent to which such patterns are shaped by background characteristics. Several criteria exist for measuring pairwise dissimilarities among categorical sequences. Typically, dissimilarity matrices are employed as input to heuristic clustering algorithms. The family of methods we develop instead clusters sequences directly using mixtures of exponential-distance models. Basing the models on weighted variants of the Hamming distance metric permits closed-form expressions for parameter estimation. Simultaneously allowing the component membership probabilities to depend on fixed covariates and accommodating sampling weights in the clustering process yields new insights on the Northern Irish data. In particular, we find that school examination performance is the single most important predictor of cluster membership.

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arXiv2021

Infinite Mixtures of Infinite Factor Analysers

Factor-analytic Gaussian mixture models are often employed as a model-based approach to clustering high-dimensional data. Typically, the numbers of clusters and latent factors must be specified in advance of model fitting, and remain fixed. The pair which optimises some model selection criterion is then chosen. For computational reasons, models in which the number of latent factors differ across clusters are rarely considered. Here the infinite mixture of infinite factor analysers (IMIFA) model is introduced. IMIFA employs a Pitman-Yor process prior to facilitate automatic inference of the number of clusters using the stick-breaking construction and a slice sampler. Furthermore, IMIFA employs multiplicative gamma process shrinkage priors to allow cluster-specific numbers of factors, automatically inferred via an adaptive Gibbs sampler. IMIFA is presented as the flagship of a family of factor-analytic mixture models, providing flexible approaches to clustering high-dimensional data. Applications to a benchmark data set, metabolomic spectral data, and a manifold learning handwritten digit example illustrate the IMIFA model and its advantageous features. These include obviating the need for model selection criteria, reducing the computational burden associated with the search of the model space, improving clustering performance by allowing cluster-specific numbers of factors, and quantifying uncertainty in the numbers of clusters and cluster-specific factors.

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arXiv2021

Inferring food intake from multiple biomarkers using a latent variable model

Metabolomic based approaches have gained much attention in recent years due to their promising potential to deliver objective tools for assessment of food intake. In particular, multiple biomarkers have emerged for single foods. However, there is a lack of statistical tools available for combining multiple biomarkers to infer food intake. Furthermore, there is a paucity of approaches for estimating the uncertainty around biomarker based prediction of intake. Here, to facilitate inference on the relationship between multiple metabolomic biomarkers and food intake in an intervention study conducted under the A-DIET research programme, a latent variable model, multiMarker, is proposed. The proposed model draws on factor analytic and mixture of experts models, describing intake as a continuous latent variable whose value gives raise to the observed biomarker values. We employ a mixture of Gaussian distributions to flexibly model the latent variable. A Bayesian hierarchical modelling framework provides flexibility to adapt to different biomarker distributions and facilitates prediction of the latent intake along with its associated uncertainty. Simulation studies are conducted to assess the performance of the proposed multiMarker framework, prior to its application to the motivating application of quantifying apple intake.

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arXiv2019

Investigation of Parameter Uncertainty in Clustering Using a Gaussian Mixture Model Via Jackknife, Bootstrap and Weighted Likelihood Bootstrap

Mixture models are a popular tool in model-based clustering. Such a model is often fitted by a procedure that maximizes the likelihood, such as the EM algorithm. At convergence, the maximum likelihood parameter estimates are typically reported, but in most cases little emphasis is placed on the variability associated with these estimates. In part this may be due to the fact that standard errors are not directly calculated in the model-fitting algorithm, either because they are not required to fit the model, or because they are difficult to compute. The examination of standard errors in model-based clustering is therefore typically neglected. The widely used R package mclust has recently introduced bootstrap and weighted likelihood bootstrap methods to facilitate standard error estimation. This paper provides an empirical comparison of these methods (along with the jackknife method) for producing standard errors and confidence intervals for mixture parameters. These methods are illustrated and contrasted in both a simulation study and in the traditional Old Faithful data set and Thyroid data set.

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arXiv2019

Combining biomarker and self-reported dietary intake data: a review of the state of the art and an exposition of concepts

Classical approaches to assessing dietary intake are associated with measurement error. In an effort to address inherent measurement error in dietary self-reported data there is increased interest in the use of dietary biomarkers as objective measures of intake. Furthermore, there is a growing consensus of the need to combine dietary biomarker data with self-reported data. A review of state of the art techniques employed when combining biomarker and self-reported data is conducted. Two predominant methods, the calibration method and the method of triads, emerge as relevant techniques used when combining biomarker and self-reported data to account for measurement errors in dietary intake assessment. Both methods crucially assume measurement error independence. To expose and understand the performance of these methods in a range of realistic settings, their underpinning statistical concepts are unified and delineated, and thorough simulation studies conducted. Results show that violation of the methods' assumptions negatively impacts resulting inference but that this impact is mitigated when the variation of the biomarker around the true intake is small. Thus there is much scope for the further development of biomarkers and models in tandem to achieve the ultimate goal of accurately assessing dietary intake.

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arXiv2018

Mixtures of Experts Models

Mixtures of experts models provide a framework in which covariates may be included in mixture models. This is achieved by modelling the parameters of the mixture model as functions of the concomitant covariates. Given their mixture model foundation, mixtures of experts models possess a diverse range of analytic uses, from clustering observations to capturing parameter heterogeneity in cross-sectional data. This chapter focuses on delineating the mixture of experts modelling framework and demonstrates the utility and flexibility of mixtures of experts models as an analytic tool.

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arXiv2018

Clustering high dimensional mixed data to uncover sub-phenotypes:joint analysis of phenotypic and genotypic data

The LIPGENE-SU.VI.MAX study, like many others, recorded high dimensional continuous phenotypic data and categorical genotypic data. LIPGENE-SU.VI.MAX focuses on the need to account for both phenotypic and genetic factors when studying the metabolic syndrome (MetS), a complex disorder that can lead to higher risk of type 2 diabetes and cardiovascular disease. Interest lies in clustering the LIPGENE-SU.VI.MAX participants into homogeneous groups or sub-phenotypes, by jointly considering their phenotypic and genotypic data, and in determining which variables are discriminatory. A novel latent variable model which elegantly accommodates high dimensional, mixed data is developed to cluster LIPGENE-SU.VI.MAX participants using a Bayesian finite mixture model. A computationally efficient variable selection algorithm is incorporated, estimation is via a Gibbs sampling algorithm and an approximate BIC-MCMC criterion is developed to select the optimal model. Two clusters or sub-phenotypes (`healthy' and `at risk') are uncovered. A small subset of variables is deemed discriminatory which notably includes phenotypic and genotypic variables, highlighting the need to jointly consider both factors. Further, seven years after the LIPGENE-SU.VI.MAX data were collected, participants underwent further analysis to diagnose presence or absence of the MetS. The two uncovered sub-phenotypes strongly correspond to the seven year follow up disease classification, highlighting the role of phenotypic and genotypic factors in the MetS, and emphasising the potential utility of the clustering approach in early screening. Additionally, the ability of the proposed approach to define the uncertainty in sub-phenotype membership at the participant level is synonymous with the concepts of precision medicine and nutrition.

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