Using the meka wrapper

Setting up MEKA

In order to use the python interface to MEKA you need to have JAVA and MEKA installed. Paths to both are passed to the class’s constructor.

The current version supports meka 1.9.1+

The currently officially released MEKA version is 1.9.0 from 2015 and has a bug that prevents the wrapper from working. Please download a compiled 1.9.1+ snapshot instead of using the 1.9.0 version, unzip it to <meka_directory> and use <meka_directory>/lib/ as the MEKA classpath for the constructor.

Note that you will need to have liac-arff installed if you want to use the MEKA wrapper, you can get them using: pip install liac-arff.

An example path to java might be: /usr/bin/java, an example classpath to meka can be: /opt/meka-1.9.1-SNAPSHOT/lib/. In Python 2.7 the pip package whichcraft is used to detect the location of java executables if no path is provided to the constructor. You can install it via pip install whichcraft. In Python 3 whichcraft is not used.

Using the wrapper

Starting from scikit-multilearn 0.0.2 the meka wrapper is available from skmultilearn.ext (ext as in external) and is a fully scikit-compatible multi-label classifier. Please note that rel

To use the interface class start with importing skmultilearn’s module, then create an object of the Meka class using the constructor and run the interface such as in the example:

from sklearn.datasets import make_multilabel_classification
from sklearn.model_selection import train_test_split
from sklearn.metrics import hamming_loss
from skmultilearn.ext import Meka

X, y = make_multilabel_classification(sparse = True,
    return_indicator = 'sparse')

X_train, X_test, y_train, y_test = train_test_split(X,

meka = Meka(
    meka_classifier = "meka.classifiers.multilabel.LC",
    weka_classifier = "weka.classifiers.bayes.NaiveBayes",
    meka_classpath = "/opt/meka-1.9/lib/",
    java_command = '/usr/bin/java'), y_train)

predictions = meka.predict(X_test)

metrics.hamming_loss(y_test, predictions)


  • meka_classifier is the MEKA classifier class selected from the MEKA API
  • weka_classifier is the WEKA classifier class selected from the WEKA API
  • java_command is the path to java, if not provided, the wrapper will try to import the whichcraft module to find java in the system PATH
  • meka_classpath is the path to where meka.jar and weka.jar are located, usually they come together in meka releases, so this points to the lib subfolder of the folder where meka-<version> file was unzipped. If not provided the path is taken from environmental variable: MEKA_CLASSPATH

A good introduction to selecting MEKA or WEKA classifiers can be found on MEKA’s Methods page.

Remember that if you use MEKA, apart from citing scikit-multilearn, you should also cite both MEKA and WEKA papers:

    author = {Read, Jesse and Reutemann, Peter and Pfahringer, Bernhard and Holmes, Geoff},
    title = {{MEKA}: A Multi-label/Multi-target Extension to {Weka}},
    journal = {Journal of Machine Learning Research},
    year = {2016},
    volume = {17},
    number = {21},
    pages = {1--5},
    url = {},

    author = {Hall, Mark and Frank, Eibe and Holmes, Geoffrey and Pfahringer, Bernhard and Reutemann, Peter and Witten, Ian H.},
    title = {The WEKA Data Mining Software: An Update},
    journal = {SIGKDD Explor. Newsl.},
    issue_date = {June 2009},
    volume = {11},
    number = {1},
    month = nov,
    year = {2009},
    issn = {1931-0145},
    pages = {10--18},
    numpages = {9},
    url = {},
    doi = {10.1145/1656274.1656278},
    acmid = {1656278},
    publisher = {ACM},
    address = {New York, NY, USA},

Handling errors

MEKA is handled through a subprocess and while MEKA is a wonderful library, its error reporting system is more targeted at reading output in the terminal. In case of error we wull issue an exception with the output MEKA provided. You can always check the output / errors of MEKA as they are stored in the classes’s output and error properties. For example in the above example where the MEKA classifier instance is named meka - you can access the properties under meka.output``or ``meka.error.