Oftentimes, researchers must decide which parameterized model best fits the system they are observing. This type of model selection is a challenging problem, whose challenges are further compounded when inferring the associated parameters for each model. The Reversible Jump Markov Chain Monte Carlo (RJMCMC) method is a trans-dimensional Bayesian algorithm that can be used to simultaneously infer the joint distribution o both the model and model-parameter space. CU-MSDSp offers a generalized, parallel implementation of RJMCMC that provides researchers with an accessible, flexible, and objectively reliable approach to inference on the joint model and model parameter space.
- Provide an accessible, extendable, reliable RJMCMC software implementation for users to carry out in parallel.
CU-MSDSp begins an analysis by infering model paramter distributions for each competing model, in order that these results may subsequently be used to infer the model space probabilities. Specifically, CU-MSDSp first independently forms converged approximations for each of the competing model's parameter joint posterior distribution using the Stan API interface. The collection of samples corresponding to the converged joint posteriors is referred to as "gold standard chains". These gold standard chains are then used in a parallel RJMCMC algorithm, via Message Passing Interace (MPI), to assess the model probabilities. A schematic of this algorithm is shown below:
We assume that users have a general background in Bayesian Statistics and Markov Chain Monte Carlo (MCMC) methods. While not necessary, we beleive it beneficial to have some understanding of RJMCMC and refer readers to [Green RJMCMC](how to cite) for more details on this trans-dimensional algorithm.
- Python Dependicies (can be installed from here)
- Matplotlib
- Seaborn
- Numpy
- C Dependencies
- Bash *bc command
- cmdstan- See here for installation instruction and dependencies.
We now walk through a cannoical example used in RJMCMC literature: deciding if a Poisson or Negative Binomial distribution best fits a collection of observational data. The following steps are required to implement CU-MSDSp:
-
Define Data Specify the germane observational data within the data directory using JSON format (labeled as data.json). These data will be referenced by the models written for the Stan API. An example data.json file is in within the data directory to aid users.
-
Define Models As mentioned prevoiusly, users must define ther models using the stan language. These models should be placed in the models directory as modelname.stan. The poisson.stan and negativeBinomial.stan are already defined in the models directory, as an example.
-
Define A Config File A config file is required to run CU-MSDSp. This config file specifies the location of cmdstan directory (for example in ~/.cmdstan), the number of cores needed for the Stan API, the number of chains, samples to run, etc. This is specified as setup.config in the home directory of CU-MSDSp.
-
Run CU-MSDSp CU-RJMCMp is run in bash as follows:
sh runParallel.shCU-MSDSp will output the samples for each gold standard chain in the goldStandardChains directory. These results are produced by cmdstan. The results of model selection are collected within the modelSelection directory. The chain samples, as well as the corresponding acceptance probability from the simualation, are included within modelSelection. We note that users can check MCMC congergence diagnostics by using some of the built-in capabilities of cmdstan. Finally a mapping of the model name and model index will be provided in the home directory as modelIndex.txt
- Visualize Results Some basic visualization are built into CU-MSDSp. Specifically, parameter histogram and parameter trace plots are provided for each model. In addition, the distribtuion of the model probabilities and the acceptance probabilites are also visualized. The plotting function is specified in the config file, but can be run seperately by
python plotMCMCResults.pyAll results are stored in the pics directory.
Please see our paper [Software X Paper](A link) for more details on the numerical underpinnings of CU-MSDSp. In addition to the paper, we present our derivation and proof of the theoretical foundation that shows that the parallel approach used in CU-MSDSp leads to the same joint model and model-parameter distribution as the standard RJMCMC.