arXiv subjects

Arthur Leroy

Publications and source records attributed to Arthur Leroy.

7 recordsLinked to original sources

arXiv2025

Towards Gaussian processes modelling to study the late effects of radiotherapy in children and young adults with brain tumours

Survivors of childhood cancer need lifelong monitoring for side effects from radiotherapy. However, longitudinal data from routine monitoring is often infrequently and irregularly sampled, and subject to inaccuracies. Due to this, measurements are often studied in isolation, or simple relationships (e.g., linear) are used to impute missing timepoints. In this study, we investigated the potential role of Gaussian Processes (GP) modelling to make population-based and individual predictions, using insulin-like growth factor 1 (IGF-1) measurements as a test case. With training data of 23 patients with a median (range) of 4 (1-16) timepoints we identified a trend within the range of literature reported values. In addition, with 8 test cases, individual predictions were made with an average root mean squared error of 31.9 (10.1 - 62.3) ng/ml and 27.4 (0.02 - 66.1) ng/ml for two approaches. GP modelling may overcome limitations of routine longitudinal data and facilitate analysis of late effects of radiotherapy.

stat.AP↗

arXiv2024

Prospective Prediction of Body Mass Index Trajectories using Multi-task Gaussian Processes

Clinicians often investigate the body mass index (BMI) trajectories of children to assess their growth with respect to their peers, as well as to anticipate future growth and disease risk. While retrospective modelling of BMI trajectories has been an active area of research, prospective prediction of continuous BMI trajectories from historical growth data has not been well investigated. Using weight and height measurements from birth to age 10 years from a longitudinal mother-offspring cohort, we leveraged a multi-task Gaussian processes model, called MagmaClust, to derive probabilistic predictions for BMI trajectories over various forecasting periods. Experiments were conducted to evaluate the accuracy, sensitivity to missing values, and number of clusters. The results were compared with cubic B-spline regression and a parametric Jenss-Bayley mixed effects model. A downstream tool computing individual overweight probabilities was also proposed and evaluated. In all experiments, MagmaClust outperformed conventional models in prediction accuracy while correctly calibrating uncertainty regardless of the missing data amount (up to 90\% missing) or the forecasting period (from 2 to 8 years in the future). Moreover, the overweight probabilities computed from MagmaClust's uncertainty quantification exhibited high specificity ($0.94$ to $0.96$) and accuracy ($0.86$ to $0.94$) in predicting the 10-year overweight status even from age 2 years. MagmaClust provides a probabilistic non-parametric framework to prospectively predict BMI trajectories, which is robust to missing values and outperforms conventional BMI trajectory modelling approaches. It also clusters individuals to identify typical BMI patterns (early peak, adiposity rebounds) during childhood. Overall, we demonstrated its potential to anticipate BMI evolution throughout childhood, allowing clinicians to implement prevention strategies.

stat.AP↗

arXiv2023

Longitudinal prediction of DNA methylation to forecast epigenetic outcomes

Interrogating the evolution of biological changes at early stages of life requires longitudinal profiling of molecules, such as DNA methylation, which can be challenging with children. We introduce a probabilistic and longitudinal machine learning framework based on multi-mean Gaussian processes (GPs), accounting for individual and gene correlations across time. This method provides future predictions of DNA methylation status at different individual ages while accounting for uncertainty. Our model is trained on a birth cohort of children with methylation profiled at ages 0-4, and we demonstrated that the status of methylation sites for each child can be accurately predicted at ages 5-7. We show that methylation profiles predicted by multi-mean GPs can be used to estimate other phenotypes, such as epigenetic age, and enable comparison to other health measures of interest. This approach encourages epigenetic studies to move towards longitudinal design for investigating epigenetic changes during development, ageing and disease progression.

q-bio.GN↗

arXiv2023

Latent Variable Multi-output Gaussian Processes for Hierarchical Datasets

Multi-output Gaussian processes (MOGPs) have been introduced to deal with multiple tasks by exploiting the correlations between different outputs. Generally, MOGPs models assume a flat correlation structure between the outputs. However, such a formulation does not account for more elaborate relationships, for instance, if several replicates were observed for each output (which is a typical setting in biological experiments). This paper proposes an extension of MOGPs for hierarchical datasets (i.e. datasets for which the relationships between observations can be represented within a tree structure). Our model defines a tailored kernel function accounting for hierarchical structures in the data to capture different levels of correlations while leveraging the introduction of latent variables to express the underlying dependencies between outputs through a dedicated kernel. This latter feature is expected to significantly improve scalability as the number of tasks increases. An extensive experimental study involving both synthetic and real-world data from genomics and motion capture is proposed to support our claims.

cs.LG↗

arXiv2023

A Bayesian Framework for Multivariate Differential Analysis

Differential analysis is a routine procedure in the statistical analysis toolbox across many applied fields, including quantitative proteomics, the main illustration of the present paper. The state-of-the-art limma approach uses a hierarchical formulation with moderated-variance estimators for each analyte directly injected into the t-statistic. While standard hypothesis testing strategies are recognised for their low computational cost, allowing for quick extraction of the most differential among thousands of elements, they generally overlook key aspects such as handling missing values, inter-element correlations, and uncertainty quantification. The present paper proposes a fully Bayesian framework for differential analysis, leveraging a conjugate hierarchical formulation for both the mean and the variance. Inference is performed by computing the posterior distribution of compared experimental conditions and sampling from the distribution of differences. This approach provides well-calibrated uncertainty quantification at a similar computational cost as hypothesis testing by leveraging closed-form equations. Furthermore, a natural extension enables multivariate differential analysis that accounts for possible inter-element correlations. We also demonstrate that, in this Bayesian treatment, missing data should generally be ignored in univariate settings, and further derive a tailored approximation that handles multiple imputation for the multivariate setting. We argue that probabilistic statements in terms of effect size and associated uncertainty are better suited to practical decision-making. Therefore, we finally propose simple and intuitive inference criteria, such as the overlap coefficient, which express group similarity as a probability rather than traditional, and often misleading, p-values.

stat.ME↗

arXiv2022

Cluster-Specific Predictions with Multi-Task Gaussian Processes

A model involving Gaussian processes (GPs) is introduced to simultaneously handle multi-task learning, clustering, and prediction for multiple functional data. This procedure acts as a model-based clustering method for functional data as well as a learning step for subsequent predictions for new tasks. The model is instantiated as a mixture of multi-task GPs with common mean processes. A variational EM algorithm is derived for dealing with the optimisation of the hyper-parameters along with the hyper-posteriors' estimation of latent variables and processes. We establish explicit formulas for integrating the mean processes and the latent clustering variables within a predictive distribution, accounting for uncertainty on both aspects. This distribution is defined as a mixture of cluster-specific GP predictions, which enhances the performances when dealing with group-structured data. The model handles irregular grid of observations and offers different hypotheses on the covariance structure for sharing additional information across tasks. The performances on both clustering and prediction tasks are assessed through various simulated scenarios and real datasets. The overall algorithm, called MagmaClust, is publicly available as an R package.

cs.LG↗

arXiv2022

MAGMA: Inference and Prediction with Multi-Task Gaussian Processes

A novel multi-task Gaussian process (GP) framework is proposed, by using a common mean process for sharing information across tasks. In particular, we investigate the problem of time series forecasting, with the objective to improve multiple-step-ahead predictions. The common mean process is defined as a GP for which the hyper-posterior distribution is tractable. Therefore an EM algorithm is derived for handling both hyper-parameters optimisation and hyper-posterior computation. Unlike previous approaches in the literature, the model fully accounts for uncertainty and can handle irregular grids of observations while maintaining explicit formulations, by modelling the mean process in a unified GP framework. Predictive analytical equations are provided, integrating information shared across tasks through a relevant prior mean. This approach greatly improves the predictive performances, even far from observations, and may reduce significantly the computational complexity compared to traditional multi-task GP models. Our overall algorithm is called \textsc{Magma} (standing for Multi tAsk Gaussian processes with common MeAn). The quality of the mean process estimation, predictive performances, and comparisons to alternatives are assessed in various simulated scenarios and on real datasets.

stat.CO↗