Tor Erlend Fjelde
Publications
Interoperability of statistical models in pandemic preparedness: principles and reality
George Nicholson, Marta Blangiardo, Mark Briers, Peter J Diggle, Tor Erlend Fjelde, Hong Ge, Robert J B Goudie, Radka Jersakova, Ruairidh E King, Brieuc C L Lehmann, Ann-Marie Mallon, Tullia Padellini, Yee Whye Teh, Chris Holmes, Sylvia Richardson, May 2022. (Stat. Sci.).
Abstract▼ URL
We present interoperability as a guiding framework for statistical modelling to assist policy makers asking multiple questions using diverse datasets in the face of an evolving pandemic response. Interoperability provides an important set of principles for future pandemic preparedness, through the joint design and deployment of adaptable systems of statistical models for disease surveillance using probabilistic reasoning. We illustrate this through case studies for inferring and characterising spatial-temporal prevalence and reproduction numbers of SARS-CoV-2 infections in England.
Couplings for Multinomial Hamiltonian Monte Carlo
Kai Xu, Tor Erlend Fjelde, Charles Sutton, Hong Ge, 13–15 Apr 2021. (In Proceedings of The 24th International Conference on Artificial Intelligence and Statistics). Edited by Arindam Banerjee, Kenji Fukumizu. PMLR. Proceedings of Machine Learning Research.
Abstract▼ URL
Hamiltonian Monte Carlo (HMC) is a popular sampling method in Bayesian inference. Recently, Heng & Jacob (2019) studied Metropolis HMC with couplings for unbiased Monte Carlo estimation, establishing a generic parallelizable scheme for HMC. However, in practice a different HMC method, multinomial HMC, is considered as the go-to method, e.g. as part of the no-U-turn sampler. In multinomial HMC, proposed states are not limited to end-points as in Metropolis HMC; instead points along the entire trajectory can be proposed. In this paper, we establish couplings for multinomial HMC, based on optimal transport for multinomial sampling in its transition. We prove an upper bound for the meeting time – the time it takes for the coupled chains to meet – based on the notion of local contractivity. We evaluate our methods using three targets: 1,000 dimensional Gaussians, logistic regression and log-Gaussian Cox point processes. Compared to Heng & Jacob (2019), coupled multinomial HMC generally attains a smaller meeting time, and is more robust to choices of step sizes and trajectory lengths, which allows re-use of existing adaptation methods for HMC. These improvements together paves the way for a wider and more practical use of coupled HMC methods.