Inference in epidemiological agent-based models using ensemble-based data assimilation

TL;DR

This paper introduces a novel method combining agent-based epidemiological models with ensemble Kalman filters to improve disease spread inference and parameter estimation from real-world data, capturing individual interactions and social networks.

Contribution

It develops stochastic strategies for calibrating agent-based models using data assimilation, addressing the challenge of integrating coarse epidemiological data into detailed contact network models.

Findings

Effective calibration of agent-based models with real COVID-19 data

Improved estimation of epidemiological parameters

Demonstrated applicability on synthetic and real data

Abstract

To represent the complex individual interactions in the dynamics of disease spread informed by data, the coupling of an epidemiological agent-based model with the ensemble Kalman filter is proposed. The statistical inference of the propagation of a disease by means of ensemble-based data assimilation systems has been studied in previous work. The models used are mostly compartmental models representing the mean field evolution through ordinary differential equations. These techniques allow to monitor the propagation of the infections from data and to estimate several parameters of epidemiological interest. However, there are many important features which are based on the individual interactions that cannot be represented in the mean field equations, such as social network and bubbles, contact tracing, isolating individuals in risk, and social network-based distancing strategies. Agent-based models can describe contact networks at an individual level, including demographic attributes such as age, neighbourhood, household, workplaces, schools, entertainment places, among others. Nevertheless, these models have several unknown parameters which are thus difficult to estimate. In this work, we propose the use of ensemble-based data assimilation techniques to calibrate an agent-based model using daily epidemiological data. This raises the challenge of having to adapt the agent populations to incorporate the information provided by the coarse-grained data. To do this, two stochastic strategies to correct the model predictions are developed. The ensemble Kalman filter with perturbed observations is used for the joint estimation of the state and some key epidemiological parameters. We conduct experiments with an agent based-model designed for COVID-19 and assess the proposed methodology on synthetic data and on COVID-19 daily reports from Ciudad Aut\'onoma de Buenos Aires, Argentina.