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Island filters for inference on metapopulation dynamics

De Edward Ionides

Apparaît dans la collection : Thematic Month Week 3: Mathematical Modeling and Statistical Analysis of Infectious Disease Outbreaks / Mois thématique Semaine 3 : Modélisation mathématique et analyses statistique des épidémies de maladies infectieuses

Low-dimensional compartment models for biological systems can be fitted to time series data using Monte Carlo particle filter methods. As dimension increases, for example when analyzing a collection of spatially coupled populations, particle filter methods rapidly degenerate. We show that many independent Monte Carlo calculations, each of which does not attempt to solve the filtering problem, can be combined to give a global filtering solution with favorable theoretical scaling properties under a weak coupling condition. The independent Monte Carlo calculations are called islands, and the operation carried out on each island is called adapted simulation, so the complete algorithm is called an adapted simulation island filter. We demonstrate this methodology and some related algorithms on a model for measles transmission within and between cities.

Informations sur la vidéo

Données de citation

  • DOI 10.24350/CIRM.V.19612403
  • Citer cette vidéo Ionides, Edward (17/02/2020). Island filters for inference on metapopulation dynamics. CIRM. Audiovisual resource. DOI: 10.24350/CIRM.V.19612403
  • URL https://dx.doi.org/10.24350/CIRM.V.19612403


  • IONIDES, Edward L., ASFAW, Kidus, PARK, Joonha, et al. Island filters for partially observed spatiotemporal systems. arXiv preprint arXiv:2002.05211, 2020. - https://arxiv.org/abs/2002.05211
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  • PARK, Joonha et IONIDES, Edward L. A guided intermediate resampling particle filter for inference on high dimensional systems. arXiv preprint arXiv:1708.08543, 2017. - https://arxiv.org/abs/1708.08543
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  • King, A. A., Nguyen, D. and Ionides, E. L. (2016). Statistical inference for partially observed Markov processes via the R package pomp, Journal of Statistical Software 69: 1–43. - http://dx.doi.org/10.18637/jss.v069.i12
  • Asfaw, K., Ionides, E. L. and King, A. A. (2019). spatPomp: R package for statistical inference for spatiotemporal partially observed Markov processes, - [https: //github.com/kidusasfaw/spatPomp](https: //github.com/kidusasfaw/spatPomp)
  • IONIDES, Edward L., NGUYEN, Dao, ATCHADÉ, Yves, et al. Inference for dynamic and latent variable models via iterated, perturbed Bayes maps. Proceedings of the National Academy of Sciences, 2015, vol. 112, no 3, p. 719-724. - https://doi.org/10.1073/pnas.1410597112
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