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A general-purpose approximate Bayesian calculation

Project description

Approximate Bayesian calculation (ABC)

This package conducts ABC on a given model and parameters. Basically, ABayesianC does the following:

  • Sample uniformly from the n-dimensional space of the free parameters

  • Create a parameter set for each of sample set

  • Run the given model for each parameter set and collect the error value

  • Choose the best fits by the rejection algorithm

Getting started

Quick start

pip install --upgrade ABayesianC

# inside your script, e.g. test.py

from ABayesianC import tools

obj = tools.ABC(settings = settings, free_params = free_params)

obj.sample()

obj.run()

obj.postprocess()

More on it

The module receives two inputs from users. First, the free parameters' list that is a python dictionary containing the names and bounds (min and max) of each free parameter, as shown below:

free_params = {
    'p_name_1': [1.1,4.3], # [min,max]/ Prior
    'p_name_2': [6.4,23.1]
}

Second, the settings variable that is another python dictionary containing:

settings = {
    "MPI_flag": True, # whether to use MPI or not
    "sample_n": 10000,  # Sample number
    "top_n": 100, # Number of top selected samples, i.e. posterior
    "output_path": "outputs", # Relative output directory to save the results
    "replica_n":3 #  number of replica run for each param set
    "model": Model # the model that receives the parameter set and returns the error value

}

The provided model must:

  • receive a parameter set as argument
  • has a function named run
  • the run function runs the model and returns back the error/fitness value

Parallel run

To run the constructed script, e.g. test.py, in parallel, commain in terminal,

mpiexec -n available_cpu_core python test.py

available_cpu_core is the CPU core number that user intend to allocate for this process. For more info, see MPI for Python.

Outputs

Among the library outputs are:

  • samples.txt: the samples in the n-dimensional space of the free parameters
  • distances.txt: the distances/errors/fitness values obtained for each parameter set
  • best_distances.txt: the best n distances. n is defined in the settings
  • posterior.json: the posteriors extracted for each free parameter using top n best fit
  • medians.json: the medians of the posteriors for each free parameter. These values can be considered as inferred values.

Install

Using pip manager:

  • pip install --upgrade ABayesianC

Or, download the package and in the root folder, command:

  • python3 setup.py install

Authors

  • Jalil Nourisa

Useful links

MPI for Python.

Contributing to ABayesianC

In case of encountering a problem, pls report it as an issue or contant the author (jalil.nourisa@gmail.com)

Project details


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