We propose a new scheme for selecting pool states for the embedded Hidden Markov Model (HMM) Markov Chain Monte Carlo (MCMC) method. This new scheme allows the embedded HMM method to be used for efficient sampling in state space models where the state can be high-dimensional. Previously, embedded HMM methods were only applied to models with a one-dimensional state space. We demonstrate that using our proposed pool state selection scheme, an embedded HMM sampler can have similar performance to a well-tuned sampler that uses a combination of Particle Gibbs with Backward Sampling (PGBS) and Metropolis updates. The scaling to higher dimensions is made possible by selecting pool states locally near the current value of the state sequence. The proposed pool state selection scheme also allows each iteration of the embedded HMM sampler to take time linear in the number of the pool states, as opposed to quadratic as in the original embedded HMM sampler. We also consider a model with a multimodal posterior, and show how a technique we term ``mirroring'' can be used to efficiently move between the modes. We show that the embedded HMM sampler with mirroring performs significantly better for this multimodal example than a sampler combining PGBS and Metropolis updates.
Technical report, 18 February 2016, 21 pages: pdf.
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