NOTE: pomegranate does not yet work with networkx 2.0. If you have problems, please downgrade networkx and try again.
pomegranate is a package for probabilistic and graphical models for Python, implemented in cython for speed. It grew out of the YAHMM package, where many of the components used could be rearranged to do other cool things. It currently supports:
- Probability Distributions
- General Mixture Models
- Hidden Markov Models
- Naive Bayes
- Bayes Classifiers
- Markov Chains
- Discrete Bayesian Networks
To support the above algorithms, it has efficient implementations of the following:
- Kmeans
- Factor Graphs
See the tutorial below, or the more in depth tutorials in the tutorials folder with examples in IPython notebooks. See the website for further information.
No good project is done alone, and so I'd like to thank all the previous contributors to YAHMM, and all the current contributors to pomegranate, including the graduate students who share my office I annoy on a regular basis by bouncing ideas off of.
Installation
Dependencies
pomegranate requires:
- Cython (only if building from source)
- NumPy
- SciPy
- NetworkX
- joblib
To run the tests, you also must have nose installed.
User Installation
pomegranate is now pip installable! Install using pip install pomegranate. pomegranate can also be installed with conda, using conda install pomegranate. Wheels have been built for Windows versions for quick installations without the need for a C++ compiler. NOTE: If you are on OSX and python 2.7 you may encounter an error using pip on versions above 0.7.3. Please install those versions from GitHub or use 0.7.3.
You can get the bleeding edge from GitHub using the following:
git clone https://github.com/jmschrei/pomegranate.git
cd pomegranate
python setup.py install
Lastly, you can also download the zip and manually move the files into your site-packages folder (or your PYTHON_PATH, if you've changed it).
To build from source on Windows machines, you may need to download a C++ compiler. For Python 2 this minimal version of Visual Studio 2008 works well: https://www.microsoft.com/en-us/download/details.aspx?id=44266. For Python 3 this version of the Visual Studio Build Tools has been reported to work: http://go.microsoft.com/fwlink/?LinkId=691126.
If those do no work, it has been suggested that https://wiki.python.org/moin/WindowsCompilers may provide more information. Note that your compiler version must fit your python version. Run python --version to tell which python version you use. Don't forget to select the appropriate Windows version API you'd like to use. If you get an error message "ValueError: Unknown MS Compiler version 1900" remove your Python's Lib/distutils/distutil.cfg and retry. See http://stackoverflow.com/questions/34135280/valueerror-unknown-ms-compiler-version-1900 for details.
Some users with python 3.6 have reported getting the following error after download: ModuleNotFoundError: No module named 'pomegranate.utils'. A reported solution is to uninstall and reinstall without cached files using the following:
pip uninstall pomegranate
pip install pomegranate --no-cache-dir
If that doesn't work for you, you may need to downgrade your version of numpy to 1.11.3 and try the above again.
Some users on Macs have seen the following error when downloading: MarkovChain.so: unknown file type, first eight bytes: 0x7F 0x45 0x4C 0x46 0x02 0x01 0x01 0x00. This can be fixed by removing the .so files from the pomegranate installation or by building pomegranate from source.
If you have identified any other issues, please report them on the issue tracker.
Installing on Fedora Release 25 onwards
Installing on root path for all users
Install dependencies and pomegranate via pip3:
$ sudo dnf install -y python3-virtualenv python3-scipy python3-numpy python3-networkx python3-Cython
$ sudo pip3 install --no-cache-dir pomegranate
Installing inside a virtualenv
Install dependencies, create a virtualenv and install pomegranate via pip3:
$ sudo dnf install -y python3-virtualenv python3-scipy python3-numpy python3-networkx python3-Cython
$ virtualenv env3 --python=python3.5 --system-site-packages
$ source env3/bin/activate
(env3) $ pip3 install wheel nose cython numpy scipy networkx
(env3) $ pip3 install --no-cache-dir pomegranate
Verifying the installation
Our setup is done, so now we can check that pomegranate is ready to use:
$ python -c 'from pomegranate import *; print(NormalDistribution(0, 1).probability(0))'
0.398942280402
If you don't see the output above, or any other error is encountered, please feel free to file an issue.
Contributing
If you would like to contribute a feature then fork the master branch (fork the release if you are fixing a bug). Be sure to run the tests before changing any code. You'll need to have nosetests installed. The following command will run all the tests:
python setup.py test
Let us know what you want to do just in case we're already working on an implementation of something similar. This way we can avoid any needless duplication of effort. Also, please don't forget to add tests for any new functions.
Tutorial
Please take a look at the tutorials folder, which includes several tutorials on how to effectively use pomegranate!