Python3 implementation of the paper Optimal Transport for structured data with application on graphs
Fused Gromov-Wasserstein (FGW) is a distance between labeled graphs based on Optimal Transport. It is applicable between graphs with different number of nodes and with any type of label/feature on the nodes.
It computes a soft assignment of the nodes wrt their features and the graphs' structures. It can be used for visualisation, classification and barycenter of multiple graphs.
In the paper we also used this implementation of the Patchy-San Convolutional Network framework PSCN
Feel free to ask if any question
If you use this toolbox in your research and find it useful, please cite FGW using the following bibtex reference:
@InProceedings{vay2019fgw,
title = {Optimal Transport for structured data with application on graphs},
author = {Titouan, Vayer and Courty, Nicolas and Tavenard, Romain and Laetitia, Chapel and Flamary, R{\'e}mi},
booktitle = {Proceedings of the 36th International Conference on Machine Learning},
pages = {6275--6284},
year = {2019},
editor = {Chaudhuri, Kamalika and Salakhutdinov, Ruslan},
volume = {97},
series = {Proceedings of Machine Learning Research},
address = {Long Beach, California, USA},
month = {09--15 Jun},
publisher = {PMLR},
pdf = {http://proceedings.mlr.press/v97/titouan19a/titouan19a.pdf},
url = {http://proceedings.mlr.press/v97/titouan19a.html}
}
- For graph tools networkx Networkx (>=2.0)
- For the classification using Graph Kernels using GraKel GraKel (>=0.1a5)
- For Optimal transport Python Optimal Transport POT (>=0.5.1)
- Sklearn (>=0.20.0)
- Numpy (>=1.11)
- Scipy (>=1.0)
- Cython (>=0.23)
- Matplotlib (>=1.5)
All the data used in the paper came from the Benchmark Data Sets for Graph Kernels [3]
- FGW between structured objects with a cost M between features and structure matrices C1,C2:
- Comparing labeled graphs using FGW:
- Methods for graphs barycenter using FGW:
- Nested cross validation used in the paper (for e.g):
python3 nested_cv_fgw.py -dn mutag -d ../data -r ../results -ni 10 -no 50 -fea hamming_dist -st shortest_path -cva True -wl 2
- Some demos are presented in the notebooks ("examples" folder):
- FGW_on_1D_measure.ipynb: illustrates the difference between Wasserstein/ Gromov-Wasserstein and Fused Gromov-Wasserstein distances on 1D measures
- graphs_barycenter.ipynb: simple computation of barycenter of multiple labeled graphs
- train_example.ipynb: simple classification on the Mutag dataset using FGW
- graphs_transport.ipynb: illustrates how use FGW between labeled graphs and to plot the soft assignment of their nodes
- clustering_example.ipynb: k-means clustering of labeled graphs with FGW
- cleaning of k-means of multiple graphs
- Add other methods for graph kernels
[1] Flamary Rémi and Courty Nicolas POT Python Optimal Transport library
[2] Siglidis, Giannis and Nikolentzos, Giannis and Limnios, Stratis and Giatsidis, Christos and Skianis, Konstantinos and Vazirgiannis, Michali. GraKeL: A Graph Kernel Library in Python
[3] Kristian Kersting and Nils M. Kriege and Christopher Morris and Petra Mutzel and Marion Neumann Benchmark Data Sets for Graph Kernels