Deep Learning Aided Laplace Based Bayesian Inference for Epidemiological Systems

Abstract

Parameter estimation and associated uncertainty quantification is an important problem in dynamical systems characterized by ordinary differential equation (ODE) models that are often nonlinear. Typically, such models have analytically intractable trajectories which result in likelihoods and posterior distributions that are similarly intractable. Bayesian inference for ODE systems via simulation methods require numerical approximations to produce inference with high accuracy at a cost of heavy computational power and slow convergence. At the same time, Artificial Neural Networks (ANN) offer tractability that can be utilized to construct an approximate but tractable likelihood and posterior distribution. In this paper we propose a hybrid approach, where Laplace-based Bayesian inference is combined with an ANN architecture for obtaining approximations to the ODE trajectories as a function of the unknown initial values and system parameters. Suitable choices of a collocation grid and customized loss functions are proposed to fine tune the ODE trajectories and Laplace approximation. The effectiveness of our proposed methods is demonstrated using an epidemiological system with non-analytical solutions, the Susceptible-Infectious-Removed (SIR) model for infectious diseases, based on simulated and real-life influenza datasets. The novelty and attractiveness of our proposed approach include (i) a new development of Bayesian inference using ANN architectures for ODE based dynamical systems, and (ii) a computationally fast posterior inference by avoiding convergence issues of benchmark Markov Chain Monte Carlo methods. These two features establish the developed approach as an accurate alternative to traditional Bayesian computational methods, with improved computational cost.