Papers › Scalable calibration of individual-based epidemic models through categorical approximations
Scalable calibration of individual-based epidemic models through categorical approximations
Lorenzo Rimella, Nick Whiteley, Chris Jewell, Paul Fearnhead, Michael Whitehouse
The archive published only this paper's code-link row. Authors, date and abstract are from arXiv's metadata (CC0), read from the Kaggle arXiv metadata snapshot of 2026-09-12 where its title matched the archive's; the title is the archive's.
Traditional compartmental models capture population-level dynamics but fail to characterize individual-level risk. The computational cost of exact likelihood evaluation for partially observed individual-based models, however, grows exponentially with the population size, necessitating approximate inference. Existing sampling-based methods usually require multiple simulations of the individuals in the population and rely on bespoke proposal distributions or summary statistics. We propose a deterministic approach to approximating the likelihood using categorical distributions. The approximate likelihood is amenable to automatic differentiation so that parameters can be estimated by maximization or posterior sampling using standard software libraries such as Stan or TensorFlow with little user effort. We prove the consistency of the maximum approximate likelihood estimator. We empirically test our approach on several classes of individual-based models for epidemiology: different sets of disease states, individual-specific transition rates, spatial interactions, under-reporting and misreporting. We demonstrate ground truth recovery and comparable marginal log-likelihood values at substantially reduced cost compared to competitor methods. Finally, we show the scalability and effectiveness of our approach with a real-world application on the 2001 UK Foot-and-Mouth outbreak, where the simplicity of the CAL allows us to include 162775 farms.
Code
Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.
Code Syntology ran Syntology
Not run by Syntology. Nothing on this page verifies that the listed code works.
Results from the paper archive 2025-07-28
No leaderboard rows for this paper in the archive.
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections