vishalbelsare / grakel

A scikit-learn compatible library for graph kernels

GraKeL: A library for graph kernels

grakel is a library compatible with the project of scikit-learn

Installing grakel

The grakel library requires:

• Python [>=2.7, >=3.5]
• NumPy [>=1.8.2]
• SciPy [>=0.13.3]
• Cython [>=0.27.3]
• cvxopt [>=1.2.0] [optional: lovasz]
• future [>=0.16.0] (for python 2.7)

Installing Dependencies

For installing dependencies the procedure is the well known:

(sudo) pip install extension>=extension_version

or

(sudo) pip install -r requirements.txt

where (sudo) depends on if pip has superuser privilages.

Installing the development-version

To install the development-version from pip execute:

$ (sudo) pip install grakel-dev

whereas to install it from conda:

$ conda install grakel-dev

Usage

To learn how to use the GraKeL api as a user, please read the documentation on sections Introduction and A longer introduction (in case your are full of curiosity).

Testing

In order for the following to work you first need to build the package cython extension locally by executing:

$ python setup.py build_ext -i

To test the package, execute:

$ nosetests

for executing unit_tests or use a testing-interface for testing the kernel module:

$ python  grakel/tests/test_kernels.py --help
usage: test_kernels.py [-h] [--verbose] [--problematic] [--slow]
                       [--ignore_warnings] [--dataset DATASET] [--normalize]
                       [--develop | --all | --main]

A test file for all kernels

optional arguments:
  -h, --help         show this help message and exit
  --verbose          print kernels with their outputs on stdout
  --problematic      allow execution of problematic test cases in development
  --slow             allow execution of slow test cases in development
  --ignore_warnings  ignore warnings produced by kernel executions
  --dataset DATASET  chose the datset you want the tests to be executed
  --normalize        normalize the kernel output
  --develop          execute only tests connected with current development
  --all              execute all tests
  --main             execute the main tests [default]

for testing graph_kernels:

$ python grakel/tests/test_graph_kernel.py --help
usage: test_graph_kernels.py [-h] [--verbose] [--problematic] [--slow]
                             [--normalize] [--ignore_warnings]
                             [--dataset DATASET] [--develop | --all | --main]

A test file for all kernels

optional arguments:
  -h, --help         show this help message and exit
  --verbose          print kernels with their outputs on stdout
  --problematic      allow execution of problematic test cases in development
  --slow             allow execution of slow test cases in development
  --normalize        normalize the kernel output
  --ignore_warnings  ignore warnings produced by kernel executions
  --dataset DATASET  chose the datset you want the tests to be executed
  --develop          execute only tests connected with current development
  --all              execute all tests
  --main             execute the main tests [default]

and for testing the Graph class:

$ python grakel/tests/test_graph.py --help
usage: test_graph.py [-h] [--verbose] [--ignore_warnings]

A test file for all `Graph` type objects

optional arguments:
  -h, --help         show this help message and exit
  --verbose          verbose outputs on stdout
  --ignore_warnings  ignore warnings produced by kernel executions

You can also execute the kernel test locally through a test-main-function as

$ python -m grakel.tests

Contributing

For learning how to integrate your own kernel, please read section Write your own kernel inside the package documentation. For contributing to the GraKeL project, please read section contributing inside the package documentation.

Citation

If you use GraKeL in a scientific publication, please cite our paper:

@article{siglidis2018grakel,
  title={GraKeL: A Graph Kernel Library in Python},
  author={Siglidis, Giannis and Nikolentzos, Giannis and Limnios, Stratis and Giatsidis, Christos and Skianis, Konstantinos and Vazirgiannis, Michalis},
  journal={arXiv preprint arXiv:1806.02193},
  year={2018}
}