Computational Methods for Complex Stochastic Systems: Alternatives to MCMC

Paul Fearnhead


We consider analysis of complex stochastic models based upon partial information. MCMC and reversible jump MCMC are often the methods of choice for such problems, but in some situations they can be difficult to implement; and suffer from problems such as poor mixing, and the difficulty of diagnosing convergence. Here we review various alternatives to MCMC methods: importance sampling, the forward-backward algorithm, and sequential Monte Carlo (SMC). We discuss how to design good proposal densities for importance sampling, show some of the range of models for which the forward-backward algorithm can be applied, and show how resampling ideas from SMC can be used to improve the efficiency of the other two methods. We demonstrate these methods on a range of examples, including estimating the transition density of a diffusion and of a discrete-state continuous-time Markov chain; inferring structure in population genetics; and segmenting genetic divergence data.


Diffusions, Forward-Backward Algorithm, Importance Sampling, Missing Data, Particle Filter, Population Genetics


Code for Example 2: [LV_IS.R][LV_Example.R]

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