Hybrid SINDy-EnKF in Learning Chikungunya Dynamics from Incomplete, Noisy or Partially Observed Data

Abstract

Current mechanistic models for the transmission dynamics of the Chikungunya virus (CHIKV) rely on uncertain parameters or partially observed data. This limitation challenges the use of theoretical models for understanding and forecasting disease spread. Here we present a hybrid, data-driven model framework that combines Sparse Identification of Nonlinear Dynamics (SINDy) with the Ensemble Kalman Filter (EnKF) for sequential data assimilation. Our numerical experiments show that this approach improves prediction accuracy and provides a good reconstruction of unobserved trajectories under partial observability, a common constraint in real-world epidemiological surveillance. SINDy can be applied to epidemic trajectories, recovering the underlying equations in noise-free conditions. However, standalone SINDy is highly sensitive to noise, leading to spurious terms and poor performance. Hence, we embed the identification procedure within an EnKF framework, which assimilates noisy observations to correct forecast states from the SINDy-derived model and to infer unobserved state variables.