A Novel Approximate Bayesian Inference Method for Compartmental Models in Epidemiology using Stan

Abstract: Mechanistic compartmental models are widely used in epidemiology to study the dynamics of infectious disease transmission. These models have significantly contributed to designing and evaluating effective control strategies during pandemics. However, the increasing complexity and the number of parameters needed to describe rapidly evolving transmission scenarios present significant challenges for parameter estimation due to intractable likelihoods. To overcome this issue, likelihood-free methods have proven effective for accurately and efficiently fitting these models to data. In this study, we focus on approximate Bayesian computation (ABC) and synthetic likelihood methods for parameter inference. We develop a method that employs ABC to select the most informative subset of summary statistics, which are then used to construct a synthetic likelihood for posterior sampling. Posterior sampling is performed using Hamiltonian Monte Carlo as implemented in the Stan software. The proposed algorithm is demonstrated through simulation studies, showing promising results for inference in a simulated epidemic scenario.