Create Bayesian Network and learn parameters with Python3.x

python-3.x machine-learning scikit-learn probability bayesian-networks
Spu picture Spu · Feb 10, 2015 · Viewed 24.8k times · Source

I'm searching for the most appropriate tool for python3.x on Windows to create a Bayesian Network, learn its parameters from data and perform the inference.

The network structure I want to define myself as follows: enter image description here

It is taken from this paper.

All the variables are discrete (and can take only 2 possible states) except "Size" and "GraspPose", which are continuous and should be modeled as Mixture of Gaussians.

Authors use Expectation-Maximization algorithm to learn the parameters for conditional probability tables and Junction-Tree algorithm to compute the exact inference.

As I understand all is realised in MatLab with Bayes Net Toolbox by Murphy.

I tried to search something similar in python and here are my results:

  1. Python Bayesian Network Toolbox http://sourceforge.net/projects/pbnt.berlios/ (http://pbnt.berlios.de/). Web-site doesn't work, project doesn't seem to be supported.
  2. BayesPy https://github.com/bayespy/bayespy I think this is what I actually need, but I fail to find some examples similar to my case, to understand how to approach construction of the network structure.

  3. PyMC seems to be a powerful module, but I have problems with importing it on Windows 64, python 3.3. I get error when I install development version

    WARNING (theano.configdefaults): g++ not detected ! Theano will be unable to execute optimized C-implementations (for both CPU and GPU) and will default to Python implementations. Performance will be severely degraded. To remove this warning, set Theano flags cxx to an empty string.

UPDATE:

  1. libpgm (http://pythonhosted.org/libpgm/). Exactly what I need, unfortunately not supported by python 3.x
  2. Very interesting actively developing library: PGMPY. Unfortunately continuous variables and learning from data is not supported yet. https://github.com/pgmpy/pgmpy/

Any advices and concrete examples will be highly appreciated.

Answer

James Atwood picture James Atwood · Oct 20, 2015

It looks like pomegranate was recently updated to include Bayesian Networks. I haven't tried it myself, but the interface looks nice and sklearn-ish.

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