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Hamiltonian Monte Carlo (HMC) has been widely adopted in the statistics community because of its ability to sample high-dimensional distributions much more efficiently than other Metropolis-based methods. Despite this, HMC often performs sub-optimally on distributions with high correlations or marginal variances on multiple scales because the resulting stiffness forces the leapfrog integrator in HMC to take an unreasonably small stepsize. We provide intuition as well as a formal analysis showing how these multiscale distributions limit the stepsize of leapfrog and we show how the implicit midpoint method can be used, together with Newton-Krylov iteration, to circumvent this limitation and achieve major efficiency gains. Furthermore, we offer practical guidelines for when to choose between implicit midpoint and leapfrog and what stepsize to use for each method, depending on the distribution being sampled. Unlike previous modifications to HMC, our method is generally applicable to highly non-Gaussian distributions exhibiting multiple scales. We illustrate how our method can provide a dramatic speedup over leapfrog in the context of the No-U-Turn sampler (NUTS) applied to several examples.

We present a selection criterion for the Euclidean metric adapted during warmup in a Hamiltonian Monte Carlo sampler that makes it possible for a sampler to automatically pick the metric based on the model and the availability of warmup draws. Additionally, we present a new adaptation inspired by the selection criterion that requires significantly fewer warmup draws to be effective. The effectiveness of the selection criterion and adaptation are demonstrated on a number of applied problems. An implementation for the Stan probabilistic programming language is provided., Comment: Data/code available at https://github.com/bbbales2/cmdstan-warmup