├── .gitignore ├── AUTHORS.md ├── LICENSE.md ├── README.md ├── Tutorial ├── README.md ├── data.mutag ├── demo_grid_search.py ├── demo_mutag.py ├── mutag.label ├── mutag.list ├── mutag │ ├── mutag_1.graphml │ ├── mutag_10.graphml │ ├── mutag_100.graphml │ ├── mutag_101.graphml │ ├── mutag_102.graphml │ ├── mutag_103.graphml │ ├── mutag_104.graphml │ ├── mutag_105.graphml │ ├── mutag_106.graphml │ ├── mutag_107.graphml │ ├── mutag_108.graphml │ ├── mutag_109.graphml │ ├── mutag_11.graphml │ ├── mutag_110.graphml │ ├── mutag_111.graphml │ ├── mutag_112.graphml │ ├── mutag_113.graphml │ ├── mutag_114.graphml │ ├── mutag_115.graphml │ ├── mutag_116.graphml │ ├── mutag_117.graphml │ ├── mutag_118.graphml │ ├── mutag_119.graphml │ ├── mutag_12.graphml │ ├── mutag_120.graphml │ ├── mutag_121.graphml │ ├── mutag_122.graphml │ ├── mutag_123.graphml │ ├── mutag_124.graphml │ ├── mutag_125.graphml │ ├── mutag_126.graphml │ ├── mutag_127.graphml │ ├── mutag_128.graphml │ ├── mutag_129.graphml │ ├── mutag_13.graphml │ ├── mutag_130.graphml │ ├── mutag_131.graphml │ ├── mutag_132.graphml │ ├── mutag_133.graphml │ ├── mutag_134.graphml │ ├── mutag_135.graphml │ ├── mutag_136.graphml │ ├── mutag_137.graphml │ ├── mutag_138.graphml │ ├── mutag_139.graphml │ ├── mutag_14.graphml │ ├── mutag_140.graphml │ ├── mutag_141.graphml │ ├── mutag_142.graphml │ ├── mutag_143.graphml │ ├── mutag_144.graphml │ ├── mutag_145.graphml │ ├── mutag_146.graphml │ ├── mutag_147.graphml │ ├── mutag_148.graphml │ ├── mutag_149.graphml │ ├── mutag_15.graphml │ ├── mutag_150.graphml │ ├── mutag_151.graphml │ ├── mutag_152.graphml │ ├── mutag_153.graphml │ ├── mutag_154.graphml │ ├── mutag_155.graphml │ ├── mutag_156.graphml │ ├── mutag_157.graphml │ ├── mutag_158.graphml │ ├── mutag_159.graphml │ ├── mutag_16.graphml │ ├── mutag_160.graphml │ ├── mutag_161.graphml │ ├── mutag_162.graphml │ ├── mutag_163.graphml │ ├── mutag_164.graphml │ ├── mutag_165.graphml │ ├── mutag_166.graphml │ ├── mutag_167.graphml │ ├── mutag_168.graphml │ ├── mutag_169.graphml │ ├── mutag_17.graphml │ ├── mutag_170.graphml │ ├── mutag_171.graphml │ ├── mutag_172.graphml │ ├── mutag_173.graphml │ ├── mutag_174.graphml │ ├── mutag_175.graphml │ ├── mutag_176.graphml │ ├── mutag_177.graphml │ ├── mutag_178.graphml │ ├── mutag_179.graphml │ ├── mutag_18.graphml │ ├── mutag_180.graphml │ ├── mutag_181.graphml │ ├── mutag_182.graphml │ ├── mutag_183.graphml │ ├── mutag_184.graphml │ ├── mutag_185.graphml │ ├── mutag_186.graphml │ ├── mutag_187.graphml │ ├── mutag_188.graphml │ ├── mutag_19.graphml │ ├── mutag_2.graphml │ ├── mutag_20.graphml │ ├── mutag_21.graphml │ ├── mutag_22.graphml │ ├── mutag_23.graphml │ ├── mutag_24.graphml │ ├── mutag_25.graphml │ ├── mutag_26.graphml │ ├── mutag_27.graphml │ ├── mutag_28.graphml │ ├── mutag_29.graphml │ ├── mutag_3.graphml │ ├── mutag_30.graphml │ ├── mutag_31.graphml │ ├── mutag_32.graphml │ ├── mutag_33.graphml │ ├── mutag_34.graphml │ ├── mutag_35.graphml │ ├── mutag_36.graphml │ ├── mutag_37.graphml │ ├── mutag_38.graphml │ ├── mutag_39.graphml │ ├── mutag_4.graphml │ ├── mutag_40.graphml │ ├── mutag_41.graphml │ ├── mutag_42.graphml │ ├── mutag_43.graphml │ ├── mutag_44.graphml │ ├── mutag_45.graphml │ ├── mutag_46.graphml │ ├── mutag_47.graphml │ ├── mutag_48.graphml │ ├── mutag_49.graphml │ ├── mutag_5.graphml │ ├── mutag_50.graphml │ ├── mutag_51.graphml │ ├── mutag_52.graphml │ ├── mutag_53.graphml │ ├── mutag_54.graphml │ ├── mutag_55.graphml │ ├── mutag_56.graphml │ ├── mutag_57.graphml │ ├── mutag_58.graphml │ ├── mutag_59.graphml │ ├── mutag_6.graphml │ ├── mutag_60.graphml │ ├── mutag_61.graphml │ ├── mutag_62.graphml │ ├── mutag_63.graphml │ ├── mutag_64.graphml │ ├── mutag_65.graphml │ ├── mutag_66.graphml │ ├── mutag_67.graphml │ ├── mutag_68.graphml │ ├── mutag_69.graphml │ ├── mutag_7.graphml │ ├── mutag_70.graphml │ ├── mutag_71.graphml │ ├── mutag_72.graphml │ ├── mutag_73.graphml │ ├── mutag_74.graphml │ ├── mutag_75.graphml │ ├── mutag_76.graphml │ ├── mutag_77.graphml │ ├── mutag_78.graphml │ ├── mutag_79.graphml │ ├── mutag_8.graphml │ ├── mutag_80.graphml │ ├── mutag_81.graphml │ ├── mutag_82.graphml │ ├── mutag_83.graphml │ ├── mutag_84.graphml │ ├── mutag_85.graphml │ ├── mutag_86.graphml │ ├── mutag_87.graphml │ ├── mutag_88.graphml │ ├── mutag_89.graphml │ ├── mutag_9.graphml │ ├── mutag_90.graphml │ ├── mutag_91.graphml │ ├── mutag_92.graphml │ ├── mutag_93.graphml │ ├── mutag_94.graphml │ ├── mutag_95.graphml │ ├── mutag_96.graphml │ ├── mutag_97.graphml │ ├── mutag_98.graphml │ └── mutag_99.graphml ├── mutag_pydata.npy └── mutag_pydata.py └── src ├── GKextCPy ├── GKextCPy.cpp ├── GKextCPy.h ├── GKextCPy.i ├── GKextCPy.py ├── GKextCPy_wrap.cxx ├── MANIFEST ├── MANIFEST.in ├── README.md ├── eigen.i ├── numpy.i └── setup.py └── graphkernels ├── MANIFEST.in ├── graphkernels ├── __init__.py ├── data.mutag ├── kernels.py └── utilities.py └── setup.py /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | ._.DS_Store 3 | ._* 4 | 5 | *.o 6 | *.pyc 7 | *.so 8 | 9 | *.egg-info 10 | dist 11 | -------------------------------------------------------------------------------- /AUTHORS.md: -------------------------------------------------------------------------------- 1 | # Core developers 2 | 3 | - [Elisabetta 4 | Ghisu](https://www.bsse.ethz.ch/mlcb/people/person-detail.MTkyOTcz.TGlzdC83NjcsLTEyNjQ4MzU1MTY=.html) 5 | - [Mahito Sugiyama](https://mahito.info/index_e.html) 6 | -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- 1 | Copyright (c) 2018 the `graphkernels` authors 2 | 3 | Permission is hereby granted, free of charge, to any person obtaining a copy 4 | of this software and associated documentation files (the "Software"), to deal 5 | in the Software without restriction, including without limitation the rights 6 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 7 | copies of the Software, and to permit persons to whom the Software is 8 | furnished to do so, subject to the following conditions: 9 | 10 | The above copyright notice and this permission notice shall be included in all 11 | copies or substantial portions of the Software. 12 | 13 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 14 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 15 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 16 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 17 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 18 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 19 | SOFTWARE. 20 | -------------------------------------------------------------------------------- /Tutorial/README.md: -------------------------------------------------------------------------------- 1 | # Tutorial: how to compute graph kernels 2 | 3 | This is a tutorial for computing various kernel matrices using the 4 | *graphkernels* package. An example script is given in 5 | [`demo_mutag.py`](demo_mutag.py). 6 | 7 | The file `demo_mutag.py` can be executed as 8 | 9 | python demo_mutag.py 10 | 11 | The script will compute all the available kernels on the benchmark MUTAG dataset. 12 | 13 | The data that the graph kernels functions require as input, should be 14 | a list of [igraph](http://igraph.org) objects, as provided in the file [`data.mutag`](data.mutag). 15 | This example file is available here in the tutorial, but is also 16 | included in the downloadable package. 17 | 18 | # Kernel computation in Python 19 | 20 | Threee main steps are required in Python to compute a kernel matrix. 21 | 22 | 1. Import the packages 23 | 24 | ```python 25 | import numpy as np 26 | 27 | import graphkernels.kernels as gk 28 | ``` 29 | 30 | 2. Load the data 31 | 32 | mutag_list = np.load('data.mutag') 33 | 34 | 3. Compute the kernels: example with the WL kernels 35 | 36 | K_wl = gk.CalculateWLKernel(mutag_list, par = 3) 37 | 38 | The matrix `K_wl` is the kernel matrix, obtained with the WL kernel, and therefore is a square matrix of size equal to the number of samples. 39 | The `par` here represents the number of iterations of the WL kernels. Note that if no parameters is provided, a default value is used. 40 | 41 | # List of Graph Kernels 42 | 43 | Here is a complete list of all the graph kernels that can be computed with our package, the python functions to use and corresponding kernels parameters. 44 | 45 | 46 | | Graph Kernel | Function | Par | 47 | | ------------- |:-------------:| -----:| 48 | | Linear kernel between edge histograms | CalculateEdgeHistKernel | None | 49 | | Linear kernel between vertex histograms | CalculateVertexHistKernel| None | 50 | | Linear kernel between vertex-edge histograms | CalculateVertexEdgeHistKernel | None | 51 | | Linear kernel combination (V + λVE) | CalculateVertexVertexEdgeHistKernel | λ | 52 | | Gaussian RBF kernel between vertex histograms | CalculateVertexHistGaussKernel | σ | 53 | | Gaussian RBF kernel between edge histograms | CalculateEdgeHistGaussKernel | σ | 54 | | Gaussian RBF kernel between vertex-edge histograms | CalculateVertexEdgeHistGaussKernel | σ | 55 | | Geometric random walk kernel | CalculateGeometricRandomWalkKernel | λ | 56 | | Exponential random walk kernel | CalculateExponentialRandomWalkKernel | β | 57 | | k-step random walk kernel | CalculateKStepRandomWalkKernel | λ0, λ1, ..., λk | 58 | | Shortest path kernel | CalculateShortestPathKernel | None | 59 | | Weisfeiler-Lehman subtree kernel | CalculateWLKernel | h | 60 | | Graphlet kernel | CalculateGraphletKernel | k | 61 | | Graphlet kernel with connected graphlets | CalculateConnectedGraphletKernel | k | 62 | 63 | -------------------------------------------------------------------------------- /Tutorial/data.mutag: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eghisu/GraphKernels/c158d4eb706c477683ca74e21dba22d3a17c5c9e/Tutorial/data.mutag -------------------------------------------------------------------------------- /Tutorial/demo_mutag.py: -------------------------------------------------------------------------------- 1 | """ 2 | In this demo we show how to 3 | calculate the kernel matrices 4 | on the MUTAG data 5 | """ 6 | 7 | import graphkernels.kernels as gk 8 | 9 | import IPython as ip 10 | import numpy as np 11 | 12 | # Load data 13 | # comment next line if data.mutag is in a different folder 14 | mutag_list = np.load("graphkernels/data.mutag") 15 | 16 | # Uncomment next line if data.mutag is in your current folder 17 | #mutag_list = np.load("data.mutag") 18 | 19 | ### ALL KERNELS COMPUTE 20 | K1 = gk.CalculateEdgeHistKernel(mutag_list) 21 | K2 = gk.CalculateVertexHistKernel(mutag_list) 22 | K3 = gk.CalculateVertexEdgeHistKernel(mutag_list) 23 | K4 = gk.CalculateVertexVertexEdgeHistKernel(mutag_list) 24 | K5 = gk.CalculateEdgeHistGaussKernel(mutag_list) 25 | K6 = gk.CalculateVertexHistGaussKernel(mutag_list) 26 | K7 = gk.CalculateVertexEdgeHistGaussKernel(mutag_list) 27 | K8 = gk.CalculateGeometricRandomWalkKernel(mutag_list) 28 | K9 = gk.CalculateExponentialRandomWalkKernel(mutag_list) 29 | K10 = gk.CalculateKStepRandomWalkKernel(mutag_list) 30 | K11 = gk.CalculateWLKernel(mutag_list) 31 | K12 = gk.CalculateConnectedGraphletKernel(mutag_list, 4) 32 | K13 = gk.CalculateGraphletKernel(mutag_list, 4) 33 | K14 = gk.CalculateShortestPathKernel(mutag_list) 34 | 35 | -------------------------------------------------------------------------------- /Tutorial/mutag.label: -------------------------------------------------------------------------------- 1 | 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 | 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/Tutorial/mutag/mutag_148.graphml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | 9 | 10 | 11 | 3 12 | 13 | 14 | 3 15 | 16 | 17 | 6 18 | 19 | 20 | 3 21 | 22 | 23 | 3 24 | 25 | 26 | 3 27 | 28 | 29 | 3 30 | 31 | 32 | 3 33 | 34 | 35 | 3 36 | 37 | 38 | 6 39 | 40 | 41 | 6 42 | 43 | 44 | 7 45 | 46 | 47 | 7 48 | 49 | 50 | 47 51 | 52 | 53 | 50 54 | 55 | 56 | 50 57 | 58 | 59 | 113 60 | 61 | 62 | 47 63 | 64 | 65 | 47 66 | 67 | 68 | 47 69 | 70 | 71 | 47 72 | 73 | 74 | 50 75 | 76 | 77 | 47 78 | 79 | 80 | 47 81 | 82 | 83 | 50 84 | 85 | 86 | 117 87 | 88 | 89 | 117 90 | 91 | 92 | 93 | -------------------------------------------------------------------------------- /Tutorial/mutag/mutag_149.graphml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | 9 | 10 | 11 | 3 12 | 13 | 14 | 6 15 | 16 | 17 | 3 18 | 19 | 20 | 3 21 | 22 | 23 | 3 24 | 25 | 26 | 3 27 | 28 | 29 | 3 30 | 31 | 32 | 3 33 | 34 | 35 | 3 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3 15 | 16 | 17 | 3 18 | 19 | 20 | 3 21 | 22 | 23 | 3 24 | 25 | 26 | 3 27 | 28 | 29 | 3 30 | 31 | 32 | 3 33 | 34 | 35 | 3 36 | 37 | 38 | 3 39 | 40 | 41 | 6 42 | 43 | 44 | 6 45 | 46 | 47 | 7 48 | 49 | 50 | 7 51 | 52 | 53 | 47 54 | 55 | 56 | 47 57 | 58 | 59 | 50 60 | 61 | 62 | 47 63 | 64 | 65 | 47 66 | 67 | 68 | 47 69 | 70 | 71 | 47 72 | 73 | 74 | 47 75 | 76 | 77 | 47 78 | 79 | 80 | 47 81 | 82 | 83 | 47 84 | 85 | 86 | 50 87 | 88 | 89 | 50 90 | 91 | 92 | 117 93 | 94 | 95 | 117 96 | 97 | 98 | 99 | -------------------------------------------------------------------------------- /Tutorial/mutag/mutag_161.graphml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | 9 | 10 | 11 | 3 12 | 13 | 14 | 3 15 | 16 | 17 | 3 18 | 19 | 20 | 3 21 | 22 | 23 | 3 24 | 25 | 26 | 3 27 | 28 | 29 | 4 30 | 31 | 32 | 6 33 | 34 | 35 | 7 36 | 37 | 38 | 7 39 | 40 | 41 | 6 42 | 43 | 44 | 7 45 | 46 | 47 | 7 48 | 49 | 50 | 47 51 | 52 | 53 | 47 54 | 55 | 56 | 47 57 | 58 | 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12 | 13 | 14 | 3 15 | 16 | 17 | 3 18 | 19 | 20 | 3 21 | 22 | 23 | 3 24 | 25 | 26 | 3 27 | 28 | 29 | 3 30 | 31 | 32 | 3 33 | 34 | 35 | 3 36 | 37 | 38 | 3 39 | 40 | 41 | 3 42 | 43 | 44 | 3 45 | 46 | 47 | 6 48 | 49 | 50 | 7 51 | 52 | 53 | 7 54 | 55 | 56 | 47 57 | 58 | 59 | 47 60 | 61 | 62 | 47 63 | 64 | 65 | 47 66 | 67 | 68 | 47 69 | 70 | 71 | 47 72 | 73 | 74 | 47 75 | 76 | 77 | 47 78 | 79 | 80 | 47 81 | 82 | 83 | 47 84 | 85 | 86 | 47 87 | 88 | 89 | 47 90 | 91 | 92 | 50 93 | 94 | 95 | 47 96 | 97 | 98 | 117 99 | 100 | 101 | 117 102 | 103 | 104 | 105 | -------------------------------------------------------------------------------- /Tutorial/mutag/mutag_169.graphml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | 9 | 10 | 11 | 3 12 | 13 | 14 | 7 15 | 16 | 17 | 3 18 | 19 | 20 | 3 21 | 22 | 23 | 3 24 | 25 | 26 | 3 27 | 28 | 29 | 3 30 | 31 | 32 | 3 33 | 34 | 35 | 6 36 | 37 | 38 | 3 39 | 40 | 41 | 3 42 | 43 | 44 | 3 45 | 46 | 47 | 6 48 | 49 | 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| 97 | 98 | 117 99 | 100 | 101 | 117 102 | 103 | 104 | 47 105 | 106 | 107 | 108 | -------------------------------------------------------------------------------- /Tutorial/mutag/mutag_27.graphml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | 9 | 10 | 11 | 3 12 | 13 | 14 | 3 15 | 16 | 17 | 3 18 | 19 | 20 | 3 21 | 22 | 23 | 3 24 | 25 | 26 | 3 27 | 28 | 29 | 3 30 | 31 | 32 | 3 33 | 34 | 35 | 3 36 | 37 | 38 | 3 39 | 40 | 41 | 6 42 | 43 | 44 | 7 45 | 46 | 47 | 7 48 | 49 | 50 | 6 51 | 52 | 53 | 7 54 | 55 | 56 | 7 57 | 58 | 59 | 47 60 | 61 | 62 | 47 63 | 64 | 65 | 47 66 | 67 | 68 | 47 69 | 70 | 71 | 47 72 | 73 | 74 | 47 75 | 76 | 77 | 47 78 | 79 | 80 | 47 81 | 82 | 83 | 47 84 | 85 | 86 | 50 87 | 88 | 89 | 47 90 | 91 | 92 | 47 93 | 94 | 95 | 50 96 | 97 | 98 | 117 99 | 100 | 101 | 117 102 | 103 | 104 | 117 105 | 106 | 107 | 117 108 | 109 | 110 | 111 | -------------------------------------------------------------------------------- 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16 | 17 | 3 18 | 19 | 20 | 3 21 | 22 | 23 | 3 24 | 25 | 26 | 3 27 | 28 | 29 | 3 30 | 31 | 32 | 3 33 | 34 | 35 | 3 36 | 37 | 38 | 3 39 | 40 | 41 | 3 42 | 43 | 44 | 3 45 | 46 | 47 | 6 48 | 49 | 50 | 7 51 | 52 | 53 | 7 54 | 55 | 56 | 6 57 | 58 | 59 | 47 60 | 61 | 62 | 47 63 | 64 | 65 | 47 66 | 67 | 68 | 47 69 | 70 | 71 | 50 72 | 73 | 74 | 47 75 | 76 | 77 | 47 78 | 79 | 80 | 47 81 | 82 | 83 | 47 84 | 85 | 86 | 47 87 | 88 | 89 | 47 90 | 91 | 92 | 47 93 | 94 | 95 | 47 96 | 97 | 98 | 50 99 | 100 | 101 | 47 102 | 103 | 104 | 117 105 | 106 | 107 | 117 108 | 109 | 110 | 111 | -------------------------------------------------------------------------------- /Tutorial/mutag/mutag_30.graphml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | 9 | 10 | 11 | 3 12 | 13 | 14 | 3 15 | 16 | 17 | 3 18 | 19 | 20 | 3 21 | 22 | 23 | 3 24 | 25 | 26 | 3 27 | 28 | 29 | 3 30 | 31 | 32 | 3 33 | 34 | 35 | 3 36 | 37 | 38 | 3 39 | 40 | 41 | 3 42 | 43 | 44 | 3 45 | 46 | 47 | 6 48 | 49 | 50 | 7 51 | 52 | 53 | 7 54 | 55 | 56 | 47 57 | 58 | 59 | 47 60 | 61 | 62 | 47 63 | 64 | 65 | 47 66 | 67 | 68 | 47 69 | 70 | 71 | 47 72 | 73 | 74 | 47 75 | 76 | 77 | 47 78 | 79 | 80 | 50 81 | 82 | 83 | 47 84 | 85 | 86 | 47 87 | 88 | 89 | 47 90 | 91 | 92 | 47 93 | 94 | 95 | 47 96 | 97 | 98 | 47 99 | 100 | 101 | 117 102 | 103 | 104 | 117 105 | 106 | 107 | 108 | -------------------------------------------------------------------------------- /Tutorial/mutag/mutag_32.graphml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | 9 | 10 | 11 | 3 12 | 13 | 14 | 3 15 | 16 | 17 | 3 18 | 19 | 20 | 3 21 | 22 | 23 | 6 24 | 25 | 26 | 6 27 | 28 | 29 | 3 30 | 31 | 32 | 3 33 | 34 | 35 | 3 36 | 37 | 38 | 6 39 | 40 | 41 | 7 42 | 43 | 44 | 7 45 | 46 | 47 | 47 48 | 49 | 50 | 47 51 | 52 | 53 | 47 54 | 55 | 56 | 47 57 | 58 | 59 | 47 60 | 61 | 62 | 50 63 | 64 | 65 | 116 66 | 67 | 68 | 113 69 | 70 | 71 | 47 72 | 73 | 74 | 47 75 | 76 | 77 | 50 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| 46 | 47 | 47 48 | 49 | 50 | 47 51 | 52 | 53 | 47 54 | 55 | 56 | 47 57 | 58 | 59 | 50 60 | 61 | 62 | 47 63 | 64 | 65 | 50 66 | 67 | 68 | 47 69 | 70 | 71 | 116 72 | 73 | 74 | 113 75 | 76 | 77 | 47 78 | 79 | 80 | 117 81 | 82 | 83 | 117 84 | 85 | 86 | 87 | -------------------------------------------------------------------------------- /Tutorial/mutag/mutag_53.graphml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | 9 | 10 | 11 | 3 12 | 13 | 14 | 3 15 | 16 | 17 | 3 18 | 19 | 20 | 3 21 | 22 | 23 | 3 24 | 25 | 26 | 3 27 | 28 | 29 | 6 30 | 31 | 32 | 7 33 | 34 | 35 | 7 36 | 37 | 38 | 3 39 | 40 | 41 | 3 42 | 43 | 44 | 3 45 | 46 | 47 | 47 48 | 49 | 50 | 47 51 | 52 | 53 | 47 54 | 55 | 56 | 47 57 | 58 | 59 | 47 60 | 61 | 62 | 47 63 | 64 | 65 | 47 66 | 67 | 68 | 47 69 | 70 | 71 | 50 72 | 73 | 74 | 117 75 | 76 | 77 | 117 78 | 79 | 80 | 47 81 | 82 | 83 | 47 84 | 85 | 86 | 87 | -------------------------------------------------------------------------------- /Tutorial/mutag/mutag_55.graphml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | 9 | 10 | 11 | 3 12 | 13 | 14 | 6 15 | 16 | 17 | 6 18 | 19 | 20 | 3 21 | 22 | 23 | 3 24 | 25 | 26 | 3 27 | 28 | 29 | 3 30 | 31 | 32 | 3 33 | 34 | 35 | 3 36 | 37 | 38 | 3 39 | 40 | 41 | 6 42 | 43 | 44 | 7 45 | 46 | 47 | 7 48 | 49 | 50 | 50 51 | 52 | 53 | 116 54 | 55 | 56 | 113 57 | 58 | 59 | 113 60 | 61 | 62 | 47 63 | 64 | 65 | 47 66 | 67 | 68 | 47 69 | 70 | 71 | 47 72 | 73 | 74 | 47 75 | 76 | 77 | 47 78 | 79 | 80 | 47 81 | 82 | 83 | 50 84 | 85 | 86 | 117 87 | 88 | 89 | 117 90 | 91 | 92 | 93 | -------------------------------------------------------------------------------- /Tutorial/mutag/mutag_68.graphml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | 9 | 10 | 11 | 3 12 | 13 | 14 | 3 15 | 16 | 17 | 3 18 | 19 | 20 | 3 21 | 22 | 23 | 3 24 | 25 | 26 | 3 27 | 28 | 29 | 6 30 | 31 | 32 | 7 33 | 34 | 35 | 7 36 | 37 | 38 | 6 39 | 40 | 41 | 7 42 | 43 | 44 | 7 45 | 46 | 47 | 2 48 | 49 | 50 | 47 51 | 52 | 53 | 47 54 | 55 | 56 | 47 57 | 58 | 59 | 47 60 | 61 | 62 | 46 63 | 64 | 65 | 47 66 | 67 | 68 | 50 69 | 70 | 71 | 47 72 | 73 | 74 | 50 75 | 76 | 77 | 117 78 | 79 | 80 | 117 81 | 82 | 83 | 117 84 | 85 | 86 | 117 87 | 88 | 89 | 90 | -------------------------------------------------------------------------------- /Tutorial/mutag/mutag_81.graphml: -------------------------------------------------------------------------------- 1 | 2 | 6 | 7 | 8 | 9 | 10 | 11 | 3 12 | 13 | 14 | 3 15 | 16 | 17 | 3 18 | 19 | 20 | 3 21 | 22 | 23 | 3 24 | 25 | 26 | 3 27 | 28 | 29 | 6 30 | 31 | 32 | 7 33 | 34 | 35 | 7 36 | 37 | 38 | 6 39 | 40 | 41 | 7 42 | 43 | 44 | 7 45 | 46 | 47 | 47 48 | 49 | 50 | 47 51 | 52 | 53 | 47 54 | 55 | 56 | 47 57 | 58 | 59 | 50 60 | 61 | 62 | 47 63 | 64 | 65 | 47 66 | 67 | 68 | 50 69 | 70 | 71 | 117 72 | 73 | 74 | 117 75 | 76 | 77 | 117 78 | 79 | 80 | 117 81 | 82 | 83 | 84 | -------------------------------------------------------------------------------- /Tutorial/mutag_pydata.npy: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eghisu/GraphKernels/c158d4eb706c477683ca74e21dba22d3a17c5c9e/Tutorial/mutag_pydata.npy -------------------------------------------------------------------------------- /Tutorial/mutag_pydata.py: -------------------------------------------------------------------------------- 1 | 2 | """ 3 | Converting mutag to list format 4 | """ 5 | 6 | from igraph import Graph 7 | import numpy as np 8 | 9 | mutag_list = [] 10 | 11 | n_graphs = 188 12 | for i in xrange(n_graphs): 13 | 14 | g_cur = Graph.Read_GraphML("/home/eghisu/projects/gk_python_wrapper/gk_python_c/data/mutag/mutag_%d.graphml" % (i+1)) 15 | mutag_list.append(g_cur) 16 | 17 | 18 | np.save("/home/eghisu/projects/gk_python_wrapper/gk_python_c/data/mutag_pydata", mutag_list) -------------------------------------------------------------------------------- /src/GKextCPy/MANIFEST: -------------------------------------------------------------------------------- 1 | # file GENERATED by distutils, do NOT edit 2 | .DS_Store 3 | ._.DS_Store 4 | ._GKextCPy.i 5 | GKextCPy.cpp 6 | GKextCPy.h 7 | GKextCPy.i 8 | GKextCPy.py 9 | GKextCPy_wrap.cxx 10 | MANIFEST 11 | MANIFEST.in 12 | eigen.i 13 | numpy.i 14 | setup.py 15 | -------------------------------------------------------------------------------- /src/GKextCPy/MANIFEST.in: -------------------------------------------------------------------------------- 1 | # file GENERATED by distutils, do NOT edit 2 | 3 | include * 4 | -------------------------------------------------------------------------------- /src/GKextCPy/README.md: -------------------------------------------------------------------------------- 1 | # GKextCPY 2 | 3 | `GKextCPy` is a python extension building the wrapper from C++ to Python and necesssary to compile the graphkernels package. 4 | 5 | # Installation 6 | 7 | If you install the `graphkernels` package this extension is automatically installed for you. However, you can install it independently via pip: 8 | 9 | `pip install GKextCPy` 10 | 11 | # References 12 | 13 | The interface files which allow the wrapping of eigen and numpy (files numpy.i and eigen.i) are imported from the `PyMesh` project at https://github.com/qnzhou/PyMesh/tree/master/eigen_wrapper 14 | -------------------------------------------------------------------------------- /src/GKextCPy/setup.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | """ 4 | setup.py file for SWIG 5 | """ 6 | 7 | from setuptools import setup, Extension 8 | 9 | import subprocess 10 | import sys 11 | 12 | # Solve the chicken-and-egg problem of requiring packages *before* the 13 | # script has been parsed. 14 | for package in ['numpy', 'pkgconfig']: 15 | # Inside a `virtualenv`, we are *not* allowed to install packages as 16 | # a regular user. 17 | if hasattr(sys, 'real_prefix'): 18 | subprocess.check_call([sys.executable, '-m', 'pip', 'install', package]) 19 | else: 20 | subprocess.check_call([sys.executable, '-m', 'pip', 'install', '--user', package]) 21 | 22 | def get_include_dirs(): 23 | import pkgconfig 24 | import numpy 25 | 26 | if not pkgconfig.exists('eigen3'): 27 | raise Exception('Missing `eigen3` library. Please install it using the package manager of your operating system') 28 | 29 | np_include_dir = numpy.get_include() 30 | 31 | # We have to throw away the `-I` part of the `pkgconfig` output 32 | # because it is not part of the include directory. 33 | eigen3_include_dir = pkgconfig.cflags('eigen3')[2:] 34 | 35 | return [np_include_dir, eigen3_include_dir] 36 | 37 | GKextCPy_module = Extension('_GKextCPy', 38 | sources = ['GKextCPy_wrap.cxx', 'GKextCPy.cpp'], 39 | swig_opts = ['-c++'], 40 | extra_compile_args = ['-std=c++11', '-O3'], 41 | include_dirs = get_include_dirs() 42 | ) 43 | 44 | setup(name = 'GKextCPy', 45 | version = '0.4.1', 46 | author = 'Elisabetta Ghisu', 47 | description = """Graph Kernels: building the extension Python module. This is a wrapper package from C++ to Python.""", 48 | ext_modules = [GKextCPy_module], 49 | py_modules = ['GKextCPy'], 50 | setup_requires = ['pkgconfig', 'numpy'], 51 | install_requires = ['pkgconfig', 'numpy'], 52 | license = 'ETH Zurich', 53 | ) 54 | -------------------------------------------------------------------------------- /src/graphkernels/MANIFEST.in: -------------------------------------------------------------------------------- 1 | include graphkernels/data.mutag 2 | -------------------------------------------------------------------------------- /src/graphkernels/graphkernels/__init__.py: -------------------------------------------------------------------------------- 1 | from .kernels import * 2 | from .utilities import * 3 | -------------------------------------------------------------------------------- /src/graphkernels/graphkernels/data.mutag: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/eghisu/GraphKernels/c158d4eb706c477683ca74e21dba22d3a17c5c9e/src/graphkernels/graphkernels/data.mutag -------------------------------------------------------------------------------- /src/graphkernels/graphkernels/utilities.py: -------------------------------------------------------------------------------- 1 | """ 2 | Utility funcitons for the graph kernels package 3 | """ 4 | 5 | #################### 6 | ## Import packages 7 | #################### 8 | 9 | import numpy as np 10 | import igraph 11 | 12 | import GKextCPy as gkCpy 13 | 14 | 15 | 16 | ################################## 17 | ## Extract graphs information from 18 | ## an igraph object 19 | ################################### 20 | 21 | def GetGraphInfo(g): 22 | 23 | # matrix of edges 24 | E = np.zeros(shape = (len(g.es),2)) 25 | for i in range(len(g.es)): 26 | E[i,:] = g.es[i].tuple 27 | ## there are multiple edge attributes 28 | if len(g.es.attributes()) > 1: 29 | print("There are multiple edge attributes! The first attribute %s is used" % g.es.attributes()[0]) 30 | 31 | ## an edge attribute is missing 32 | if len(g.es.attributes()) == 0: 33 | g.es["label"] = 1 34 | 35 | e_attr_name = g.es.attributes()[0] 36 | e_attr_values = np.asarray(g.es[e_attr_name]).reshape(len(g.es),1) 37 | E = np.hstack((E,e_attr_values)) 38 | 39 | #if len(g.vs.attributes()) > 1: 40 | # print("There are multiple vertex attributes! The first attribute %s (or the label) is used" % g.vs.attributes()[0]) 41 | 42 | if len(g.vs.attributes()) == 0: 43 | g.vs["label"] = 1 44 | 45 | # Default to using a 'label' attribute of the graph if it is 46 | # present. This also accounts for the case where there are 2 47 | # or more attributes. 48 | if 'label' in g.vs.attributes(): 49 | v_attr_name = 'label' 50 | else: 51 | v_attr_name = g.vs.attributes()[0] 52 | 53 | v_attr_values = np.asarray(g.vs[v_attr_name]).reshape(len(g.vs),1).astype(int) 54 | 55 | res = dict([('edge', E), ('vlabel', v_attr_values), ('vsize', len(g.vs)), ('esize', len(g.es)), ('maxdegree', g.maxdegree())]) 56 | 57 | return res 58 | 59 | 60 | 61 | 62 | ############################## 63 | ## Given a list of graphs 64 | ## Extract graph information 65 | ## Convert in the desired input 66 | ## for graphkernels package 67 | ############################## 68 | 69 | def GetGKInput(G): 70 | 71 | E = gkCpy.VecMatrixXi() 72 | V_label = gkCpy.IntIntVector() 73 | V_count = gkCpy.IntVector() 74 | E_count = gkCpy.IntVector() 75 | D_max = gkCpy.IntVector() 76 | 77 | for i in range(len(G)): 78 | 79 | g_info = GetGraphInfo(G[i]) 80 | E.append(g_info['edge']) 81 | V_label.append(gkCpy.IntVector(g_info['vlabel'].reshape(-1).tolist())) 82 | V_count.append(g_info['vsize']) 83 | E_count.append(g_info['esize']) 84 | D_max.append(g_info['maxdegree']) 85 | 86 | return E, V_label, V_count, E_count, D_max 87 | 88 | 89 | 90 | def GetAdjMatList(G): 91 | 92 | adj_mat = gkCpy.VecMatrixXi() 93 | adj_list = gkCpy.IntIntIntVector() 94 | 95 | for i in range(len(G)): 96 | 97 | # get adjacency matrix of graph i 98 | am_cur = G[i].get_adjacency() 99 | am_cur = np.array(am_cur.data) 100 | adj_mat.append(am_cur) 101 | 102 | # get adjacency list of graph i 103 | al_cur = np.asarray(G[i].get_adjlist()) 104 | 105 | for j in range(len(al_cur)): 106 | al_cur[j] = gkCpy.IntVector(al_cur[j]) 107 | 108 | adj_list.append(gkCpy.IntIntVector(al_cur)) 109 | 110 | return adj_mat, adj_list 111 | 112 | 113 | 114 | 115 | 116 | 117 | 118 | -------------------------------------------------------------------------------- /src/graphkernels/setup.py: -------------------------------------------------------------------------------- 1 | from setuptools import setup 2 | 3 | setup(name = 'graphkernels', 4 | version = '0.2.1', 5 | description = 'Package for computing graph kernels', 6 | url = 'https://github.com/eghisu/GraphKernels/tree/master/graphkernels', 7 | author = 'Elisabetta Ghisu', 8 | author_email = 'elisabetta.ghisu@bsse.ethz.ch', 9 | license = 'ETH Zurich', 10 | packages = ['graphkernels'], 11 | 12 | install_requires = ['GKextCPy','python-igraph', 'numpy'], 13 | package_data={'graphkernels': ['data.mutag']}, 14 | ) # maybe to check github url 15 | --------------------------------------------------------------------------------