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README.md

  • Files:

    • Files with names mcmc_XXX_sampler.R, where XXX = {lme, variable_selection, mix}, represent the MCMC sampler that uses the full data for sampling.
    • Files with names sub_XXX_sampler.R, where XXX = {lme, variable_selection, mix}, represent the MCMC sampler modified using stochastic approximation.
    • Subset posterior samples of parameters are obtained using sub_XXX_sampler.R.
    • The two samplers with XXX = lme are for linear mixed-effects models.
    • The two samplers with XXX = variable_selection are for variable selection using the GDP prior in linear regression models.
    • The two samplers with XXX = mix are for fitting mixture of multivariate Gaussians, where the number of mixture components is known apriori.
    • File pie_sampler.R includes the 'pie' function that that implements the univariate and multivariate versions of the PIE algorithm for combining parameter samples obtained from the $k$ subset posterior distributions.
    • File submit.R shows how to implement any distributed Bayesian sampling algorithm for linear mixed-effects model on an SGE cluster.
  • Comments:

    • A generic approach to implement any distributed Bayesian sampling algorithm is as follows:
      1. Randomly split the samples into $k$ subsets.
      2. Use sub_XXX_sampler.R files to run $k$ subset posterior sampling algorithms in parallel (on a cluster or across different threads of a multicore processor).
      3. Store the posterior samples from every subset.
      4. Import the subset posterior samples and use the 'pie' function in pie_sampler.R file to combine the collection of $k$ subset posterior samples.
    • Our future work seeks to combine steps 3. and 4. into a single step.
    • The four steps outlined previously are easily implemented on a cluster. The submit.R file shows how to do this on a SGE cluster through a qsub files.
  • Citations:

    1. Li, C., Srivastava, S., & Dunson, D. B. (2017). Simple, scalable and accurate posterior interval estimation. Biometrika, online print asx033.
    2. Srivastava, S., Cevher, V., Tranh-Dinh, Q., and Dunson, D.B. (2015). WASP: Scalable Bayes via barycenters of subset posteriors. In Artificial Intelligence and Statistics (pp. 912-920).
    3. Srivastava, S., Li, C., & Dunson, D. B. (2015). Scalable Bayes via barycenter in Wasserstein space. arXiv preprint arXiv:1508.05880.
  • Contact:

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WASP and PIE algorithms of Sanvesh Srivastava, Cheng Li, and David Dunson (2015, 2017)

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