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@@ -62,20 +62,20 @@ The docs of the library can be found [here](https://graphkit-learn.readthedocs.i


## Main contents ## Main contents


### List of graph kernels
### 1 List of graph kernels


* Based on walks * Based on walks
* The common walk kernel [1]
* [The common walk kernel](https://github.com/jajupmochi/graphkit-learn/blob/master/gklearn/kernels/common_walk.py) [1]
* Exponential * Exponential
* Geometric * Geometric
* [The marginalized kenrel](https://github.com/jajupmochi/graphkit-learn/blob/master/gklearn/kernels/marginalized.py) * [The marginalized kenrel](https://github.com/jajupmochi/graphkit-learn/blob/master/gklearn/kernels/marginalized.py)
* With tottering [2] * With tottering [2]
* Without tottering [7] * Without tottering [7]
* The generalized random walk kernel [3]
* Sylvester equation
* [The generalized random walk kernel](gklearn/kernels/random_walk.py) [3]
* [Sylvester equation](gklearn/kernels/sylvester_equation.py)
* Conjugate gradient * Conjugate gradient
* Fixed-point iterations * Fixed-point iterations
* Spectral decomposition
* [Spectral decomposition](gklearn/kernels/spectral_decomposition.py)
* Based on paths * Based on paths
* [The shortest path kernel](https://github.com/jajupmochi/graphkit-learn/blob/master/gklearn/kernels/shortest_path.py) [4] * [The shortest path kernel](https://github.com/jajupmochi/graphkit-learn/blob/master/gklearn/kernels/shortest_path.py) [4]
* [The structural shortest path kernel](https://github.com/jajupmochi/graphkit-learn/blob/master/gklearn/kernels/structural_sp.py) [5] * [The structural shortest path kernel](https://github.com/jajupmochi/graphkit-learn/blob/master/gklearn/kernels/structural_sp.py) [5]
@@ -89,17 +89,17 @@ The docs of the library can be found [here](https://graphkit-learn.readthedocs.i


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. 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.


### Graph Edit Distances
### 2 Graph Edit Distances


### Graph preimage methods
### 3 Graph preimage methods


A demo of generating graph preimages can be found on [Google Colab](https://colab.research.google.com/drive/1PIDvHOcmiLEQ5Np3bgBDdu0kLOquOMQK?usp=sharing) and in the [`examples`](https://github.com/jajupmochi/graphkit-learn/blob/master/gklearn/examples/median_preimege_generator.py) folder. A demo of generating graph preimages can be found on [Google Colab](https://colab.research.google.com/drive/1PIDvHOcmiLEQ5Np3bgBDdu0kLOquOMQK?usp=sharing) and in the [`examples`](https://github.com/jajupmochi/graphkit-learn/blob/master/gklearn/examples/median_preimege_generator.py) folder.


### Interface to `GEDLIB`
### 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](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. [`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.


### Computation optimization methods
### 5 Computation optimization methods


* Python’s `multiprocessing.Pool` module is applied to perform **parallelization** on the computations of all kernels as well as the model selection. * Python’s `multiprocessing.Pool` module is applied to perform **parallelization** on the computations of all kernels as well as the model selection.
* **The Fast Computation of Shortest Path Kernel (FCSP) method** [8] is implemented in *the random walk kernel*, *the shortest path kernel*, as well as *the structural shortest path kernel* where FCSP is applied on both vertex and edge kernels. * **The Fast Computation of Shortest Path Kernel (FCSP) method** [8] is implemented in *the random walk kernel*, *the shortest path kernel*, as well as *the structural shortest path kernel* where FCSP is applied on both vertex and edge kernels.


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