Emulation‐based inference for spatial infectious disease transmission models incorporating event time uncertainty

Ensemble learning methods of inference for spatially stratified infectious disease systems

Individual level models are a class of mechanistic models that are widely used to infer infectious disease transmission dynamics. These models incorporate individual level covariate information accounting for population heterogeneity and are generally fitted in a Bayesian Markov chain Monte Carlo (MCMC) framework. However, Bayesian MCMC methods of inference are computationally expensive for large data sets. This issue becomes more severe when applied to infectious disease data collected from spatially heterogeneous populations, as the number of covariates increases. In addition, summary statistics over the global population may not capture the true spatio-temporal dynamics of disease transmission. In this study we propose to use ensemble learning methods to predict epidemic generating models instead of time consuming Bayesian MCMC method. We apply these methods to infer disease transmission dynamics over spatially clustered populations, considering the clusters as natural strata instead of a global population. We compare the performance of two tree-based ensemble learning techniques: random forest and gradient boosting. These methods are applied to the 2001 foot-and-mouth disease epidemic in the U.K. and evaluated using simulated data from a clustered population. It is shown that the spatially clustered data can help to predict epidemic generating models more accurately than the global data.

Variable screening methods in spatial infectious disease transmission models

Data-driven mathematical modelling can enrich our understanding of infectious disease spread enormously. Individual-level models of infectious disease transmission allow the incorporation of different individual-level covariates, such as spatial location, vaccination status, etc. This study aims to explore and develop methods for fitting such models when we have many potential covariates to include in the model. The aim is to enhance the performance and interpretability of models and ease the computational burden of fitting these models to data. We have applied and compared multiple variable selection methods in the context of spatial epidemic data. These include a Bayesian two-stage least absolute shrinkage and selection operator (Lasso), forward and backward stepwise selection based on the Akaike information criterion (AIC), spike-and-slab priors, and random variable selection (boosting) methods. We discuss and compare the performance of these methods via simulated datasets and UK 2001 foot-and-mouth disease data. While comparing the variable selection methods all performed consistently well except the two-stage Lasso. We conclude that the spike-and-slab prior method is to be recommended, consistently resulting in high accuracy and short computational time.