Graph neural network surrogates to leverage mechanistic expert knowledge towards reliable and immediate pandemic response.

During the COVID-19 crisis, mechanistic models have guided evidence-based decision making. However, time-critical decisions in a dynamical environment limit the time available to gather supporting evidence. We address this bottleneck by developing a graph neural network (GNN) surrogate of an age-structured and spatially resolved mechanistic metapopulation simulation model. This combined approach complements classical modeling approaches which are mostly mechanistic and purely data-driven machine learning approaches which are often black box. Our design of experiments spans outbreak and persistent-threat regimes, up to three contact change points, and age-structured contact matrices on a spatial graph with 400 nodes representing German counties. We benchmark multiple GNN layers and identify an ARMAConv-based architecture that offers a strong accuracy–runtime trade-off. Across horizons of 30–90 day simulation and prediction, allowing up to three contact change points, the surrogate model attains 10–27% mean absolute percentage error (MAPE) while delivering (near) constant runtime with respect to the forecast horizon. Our approach accelerates evaluation by up to 28 670 times compared with the mechanistic model, allowing responsive decision support in time-critical scenarios and straightforward web integration. These results show how GNN surrogates can translate complex metapopulation models into immediate, reliable tools for pandemic response.