diff --git a/README.md b/README.md index 62759a4..4547735 100644 --- a/README.md +++ b/README.md @@ -65,27 +65,27 @@ The docs of the library can be found [here](https://graphkit-learn.readthedocs.i ### 1 List of graph kernels * Based on walks - * [The common walk kernel](gklearn/kernels/common_walk.py) [1] + * [The common walk kernel](https://github.com/jajupmochi/graphkit-learn/tree/master/gklearn/kernels/common_walk.py) [1] * Exponential * Geometric - * [The marginalized kenrel](gklearn/kernels/marginalized.py) + * [The marginalized kenrel](https://github.com/jajupmochi/graphkit-learn/tree/master/gklearn/kernels/marginalized.py) * With tottering [2] * Without tottering [7] - * [The generalized random walk kernel](gklearn/kernels/random_walk.py) [3] - * [Sylvester equation](gklearn/kernels/sylvester_equation.py) + * [The generalized random walk kernel](https://github.com/jajupmochi/graphkit-learn/tree/master/gklearn/kernels/random_walk.py) [3] + * [Sylvester equation](https://github.com/jajupmochi/graphkit-learn/tree/master/gklearn/kernels/sylvester_equation.py) * Conjugate gradient * Fixed-point iterations - * [Spectral decomposition](gklearn/kernels/spectral_decomposition.py) + * [Spectral decomposition](https://github.com/jajupmochi/graphkit-learn/tree/master/gklearn/kernels/spectral_decomposition.py) * Based on paths - * [The shortest path kernel](gklearn/kernels/shortest_path.py) [4] - * [The structural shortest path kernel](gklearn/kernels/structural_sp.py) [5] - * [The path kernel up to length h](gklearn/kernels/path_up_to_h.py) [6] + * [The shortest path kernel](https://github.com/jajupmochi/graphkit-learn/tree/master/gklearn/kernels/shortest_path.py) [4] + * [The structural shortest path kernel](https://github.com/jajupmochi/graphkit-learn/tree/master/gklearn/kernels/structural_sp.py) [5] + * [The path kernel up to length h](https://github.com/jajupmochi/graphkit-learn/tree/master/gklearn/kernels/path_up_to_h.py) [6] * The Tanimoto kernel * The MinMax kernel * Non-linear kernels - * [The treelet kernel](gklearn/kernels/treelet.py) [10] - * [Weisfeiler-Lehman kernel](gklearn/kernels/weisfeiler_lehman.py) [11] - * [Subtree](gklearn/kernels/weisfeiler_lehman.py#L479) + * [The treelet kernel](https://github.com/jajupmochi/graphkit-learn/tree/master/gklearn/kernels/treelet.py) [10] + * [Weisfeiler-Lehman kernel](https://github.com/jajupmochi/graphkit-learn/tree/master/gklearn/kernels/weisfeiler_lehman.py) [11] + * [Subtree](https://github.com/jajupmochi/graphkit-learn/tree/master/gklearn/kernels/weisfeiler_lehman.py#L479) A demo of computing graph kernels can be found on [Google Colab](https://colab.research.google.com/drive/17Q2QCl9CAtDweGF8LiWnWoN2laeJqT0u?usp=sharing) and in the [`examples`](https://github.com/jajupmochi/graphkit-learn/blob/master/gklearn/examples/compute_graph_kernel.py) folder. @@ -97,7 +97,7 @@ A demo of generating graph preimages can be found on [Google Colab](https://cola ### 4 Interface to `GEDLIB` -[`GEDLIB`](https://github.com/dbblumenthal/gedlib) is an easily extensible C++ library for (suboptimally) computing the graph edit distance between attributed graphs. [A Python interface](gklearn/gedlib) for `GEDLIB` is integrated in this library, based on [`gedlibpy`](https://github.com/Ryurin/gedlibpy) library. +[`GEDLIB`](https://github.com/dbblumenthal/gedlib) is an easily extensible C++ library for (suboptimally) computing the graph edit distance between attributed graphs. [A Python interface](https://github.com/jajupmochi/graphkit-learn/tree/master/gklearn/gedlib) for `GEDLIB` is integrated in this library, based on [`gedlibpy`](https://github.com/Ryurin/gedlibpy) library. ### 5 Computation optimization methods diff --git a/requirements.txt b/requirements.txt index e67a6a3..f0a7cbc 100644 --- a/requirements.txt +++ b/requirements.txt @@ -5,7 +5,8 @@ networkx>=2.2 scikit-learn>=0.20.0 tabulate>=0.8.2 tqdm>=4.26.0 -control>=0.8.2 # for generalized random walk kernels only. +control>=0.8.2; matplotlib>=3.1.0 # for generalized random walk kernels only. +control<0.8.2; matplotlib<3.1.0 cvxpy>=1.0.31 # for preimage. Does not work for "pip install graphkit-learn". # -e https://files.pythonhosted.org/packages/11/d0/d900870dc2d02ea74961b90c353666c6528a33ea61a10aa59a0d5574ae59/cvxpy-1.0.31.tar.gz # for preimage. cvxopt>=1.2.5 # for preimage. diff --git a/requirements_pypi.txt b/requirements_pypi.txt index 6eb403a..64b0652 100644 --- a/requirements_pypi.txt +++ b/requirements_pypi.txt @@ -1,11 +1,12 @@ numpy>=1.16.2 scipy>=1.1.0 -matplotlib>=3.1.0 +matplotlib>=3.0.0 networkx>=2.2 scikit-learn>=0.20.0 tabulate>=0.8.2 tqdm>=4.26.0 -control>=0.8.2 # for generalized random walk kernels only. +control>=0.8.2; matplotlib>=3.1.0 # for generalized random walk kernels only. +control<0.8.2; matplotlib<3.1.0 # cvxpy>=1.0.31 # for preimage. Does not work for "pip install graphkit-learn". # -e https://files.pythonhosted.org/packages/11/d0/d900870dc2d02ea74961b90c353666c6528a33ea61a10aa59a0d5574ae59/cvxpy-1.0.31.tar.gz # for preimage. cvxopt>=1.2.5 # for preimage.