Tuesday, 30 June 2015

CPython Integration in Weka

Continuing the interoperability in Weka that was started with R integration a few years ago, we now have integration with Python. Whilst Weka has had the ability to do Python scripting via Jython for quite some time, the latest effort adds CPython integration in the form of a "wekaPython" package that can be installed via Weka's package manager. This opens the door to all the highly optimised scientific libraries in Python - such as numpy, scipy, pandas and scikit-learn - that have components written in C or Fortran. Scikit-learn is a relatively new machine learning library that is increasing in popularity very rapidly (see the latest KDNuggets software poll).

Like the R integration in Weka, the CPython support allows for general scripting via a Knowledge Flow Python scripting step. This allows arbitrary scripts to be executed and one or more variables to be extracted from the Python runtime. Weka instances are transferred into Python as pandas data frames, and pandas data frames can be extracted from Python and converted back into instances. Furthermore, arbitrary variables can be extracted in textual form, and matlibplot graphics can be extracted as PNG images.

The package also provides a wrapper classifier and wrapper clusterer for the supervised and unsupervised learning algorithms implemented in scikit-learn. This allows the scikit-learn algorithms to be used and evaluated within Weka's framework, just like the MLRClassifier from the RPlugin package allows ML algorithms from R to be used. With both RPlugin and wekaPython installed it is quite cool to run comparisons between implementations in the different frameworks - e.g. here is a quick comparison on some UCI datasets (using Weka's Experiment environment to run a 10x10 fold cross-validation) between random forest implementations in Weka, R and scikit-learn. All default settings were used except for the number of trees, which was set to 500 for each implementation. Since scikit-learn only handles numeric input variables, both Weka's random forest and the MLRClassifier running R random forest were wrapped in the FilteredClassifier to apply unsupervised nominal to binary encoding (one hot encoding) so that all three implementations received the same input:


This classifier wraps the majority of the supervised learning algorithms in scikit-learn. The wrapper supports retrieving the underlying model from python (as a pickled string) so that the ScikitLearnClassifier can be serialised and used for prediction at a later date.


This clusterer wraps clustering algorithms in scikit-learn. It basically functions in exactly the same way as the ScikitLearnClassifier, which allows it to be used in any Weka UI or from Weka's command line interface.

Under the hood

The underlying integration works via a micro-server written in python that is launched by Weka automatically. Communication is done over plain sockets and messages are stored in JSON structures. Datasets are transmitted as plain CSV and image data as base64 encoded PNG.

wekaPython works with both Python 2.7.x and 3.x. As it relies on a few new features in core Weka, a snapshot build of the development version (3.7) of Weka is required until Weka 3.7.13 is released. Numpy, pandas, matplotlib and scikit-learn must be installed in python for the wekaPython package to operate. Anaconda is a nice python distribution that comes with all the requirements (and lots more).