Accelerating Markov Chain Monte Carlo Simulation by Differential Evolution with Self-Adaptive Randomized Subspace Sampling

Markov chain Monte Carlo (MCMC) methods have found widespread use in many fields of study to estimate the average properties of complex systems, and for posterior inference in a Bayesian framework. Existing theory and experiments prove convergence of well constructed MCMC schemes to the appropriate limiting distribution under a variety of different conditions. In practice, however this convergence is often observed to be disturbingly slow. This is frequently caused by an inappropriate selection of the proposal distribution used to generate trial moves in the Markov Chain. Here we show that significant improvements to the efficiency of MCMC simulation can be made by using a self-adaptive Differential Evolution learning strategy within a population-based evolutionary framework. This scheme, entitled DiffeRential Evolution Adaptive Metropolis or DREAM, runs multiple different chains simultaneously for global exploration, and automatically tunes the scale and orientation of the proposal distribution in randomized subspaces during the search. Ergodicity of the algorithm is proved, and various examples involving nonlinearity, high-dimensionality, and multimodality show that DREAM is generally superior to other adaptive MCMC sampling approaches. The DREAM scheme significantly enhances the applicability of MCMC simulation to complex, multi-modal search problems.

[1]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[2]  W. K. Hastings,et al.  Monte Carlo Sampling Methods Using Markov Chains and Their Applications , 1970 .

[3]  B. M. Hill,et al.  Bayesian Inference in Statistical Analysis , 1974 .

[4]  Adrian F. M. Smith,et al.  Sampling-Based Approaches to Calculating Marginal Densities , 1990 .

[5]  S. Sorooshian,et al.  Effective and efficient global optimization for conceptual rainfall‐runoff models , 1992 .

[6]  D. Rubin,et al.  Inference from Iterative Simulation Using Multiple Sequences , 1992 .

[7]  Walter R. Gilks,et al.  Adaptive Direction Sampling , 1994 .

[8]  L. Tierney Markov Chains for Exploring Posterior Distributions , 1994 .

[9]  Bin Yu,et al.  Regeneration in Markov chain samplers , 1995 .

[10]  Berend Smit,et al.  Understanding molecular simulation: from algorithms to applications , 1996 .

[11]  Siddhartha Chib,et al.  Markov Chain Monte Carlo Simulation Methods in Econometrics , 1996, Econometric Theory.

[12]  A. Gelman,et al.  Weak convergence and optimal scaling of random walk Metropolis algorithms , 1997 .

[13]  George Kuczera,et al.  Monte Carlo assessment of parameter uncertainty in conceptual catchment models: the Metropolis algorithm , 1998 .

[14]  G. Roberts,et al.  Adaptive Markov Chain Monte Carlo through Regeneration , 1998 .

[15]  J. Felsenstein,et al.  Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. , 1999, Genetics.

[16]  L Tierney,et al.  Some adaptive monte carlo methods for Bayesian inference. , 1999, Statistics in medicine.

[17]  Heikki Haario,et al.  Adaptive proposal distribution for random walk Metropolis algorithm , 1999, Comput. Stat..

[18]  Didier Chauveau,et al.  Improving convergence of the Hastings-MetropolisAlgorithm with a learning proposal , 1999 .

[19]  Berend Smit,et al.  Understanding Molecular Simulation , 2001 .

[20]  Peter Beerli,et al.  Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[21]  John P. Huelsenbeck,et al.  MRBAYES: Bayesian inference of phylogenetic trees , 2001, Bioinform..

[22]  R. Nielsen,et al.  Distinguishing migration from isolation: a Markov chain Monte Carlo approach. , 2001, Genetics.

[23]  H. Haario,et al.  An adaptive Metropolis algorithm , 2001 .

[24]  D. Chauveau,et al.  Improving Convergence of the Hastings–Metropolis Algorithm with an Adaptive Proposal , 2002 .

[25]  S. Sorooshian,et al.  A Shuffled Complex Evolution Metropolis algorithm for optimization and uncertainty assessment of hydrologic model parameters , 2002 .

[26]  P. Moral,et al.  Sequential Monte Carlo samplers , 2002, cond-mat/0212648.

[27]  C. Millar,et al.  Rates of Evolution in Ancient DNA from Adélie Penguins , 2002, Science.

[28]  Anatoly Zhigljavsky,et al.  Self-regenerative Markov chain Monte Carlo with adaptation , 2003 .

[29]  Y. Tse,et al.  Estimation of hyperbolic diffusion using the Markov chain Monte Carlo method , 2004 .

[30]  D. Frenkel Speed-up of Monte Carlo simulations by sampling of rejected states. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[31]  Art B Owen,et al.  A quasi-Monte Carlo Metropolis algorithm. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[32]  Heikki Haario,et al.  Componentwise adaptation for high dimensional MCMC , 2005, Comput. Stat..

[33]  Cajo J. F. ter Braak,et al.  A Markov Chain Monte Carlo version of the genetic algorithm Differential Evolution: easy Bayesian computing for real parameter spaces , 2006, Stat. Comput..

[34]  Heikki Haario,et al.  DRAM: Efficient adaptive MCMC , 2006, Stat. Comput..

[35]  Jasper A Vrugt,et al.  Improved evolutionary optimization from genetically adaptive multimethod search , 2007, Proceedings of the National Academy of Sciences.

[36]  A. Gelman,et al.  Adaptively Scaling the Metropolis Algorithm Using Expected Squared Jumped Distance , 2007 .

[37]  Cajo J. F. ter Braak,et al.  Differential Evolution Markov Chain with snooker updater and fewer chains , 2008, Stat. Comput..

[38]  José M. Bernardo,et al.  Bayesian Statistics , 2011, International Encyclopedia of Statistical Science.