Seq2Seq Surrogates of Epidemic Models to Facilitate Bayesian Inference

arXiv2209.09617MaRDI QIDQ6411336FDOQ6411336

Seth R. Flaxman, Timothy M. Wolock, Peter Winskill, Azra C. Ghani, Samir Bhatt, Giovanni Charles

Publication date: 20 September 2022

Abstract: Epidemic models are powerful tools in understanding infectious disease. However, as they increase in size and complexity, they can quickly become computationally intractable. Recent progress in modelling methodology has shown that surrogate models can be used to emulate complex epidemic models with a high-dimensional parameter space. We show that deep sequence-to-sequence (seq2seq) models can serve as accurate surrogates for complex epidemic models with sequence based model parameters, effectively replicating seasonal and long-term transmission dynamics. Once trained, our surrogate can predict scenarios a several thousand times faster than the original model, making them ideal for policy exploration. We demonstrate that replacing a traditional epidemic model with a learned simulator facilitates robust Bayesian inference.

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