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1. add wl subtree kernel. 

2. update datasets.
v0.1
jajupmochi 6 years ago
parent
6222e1984f
commit
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37 changed files with 22835 additions and 610 deletions
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README.md View File

@@ -44,6 +44,8 @@ Simply clone this repository and voilà! Then check [`notebooks`](https://github
* The MinMax kernel
* Non-linear kernels
* The treelet kernel [10]
* Weisfeiler-Lehman kernel [11]
* Subtree

## Computation optimization methods

@@ -92,6 +94,8 @@ Linlin Jia, Benoit Gaüzère, and Paul Honeine. Graph Kernels Based on Linear Pa

[10] Gaüzere, B., Brun, L., Villemin, D., 2012. Two new graphs kernels in chemoinformatics. Pattern Recognition Letters 33, 2038–2047.

[11] Shervashidze, N., Schweitzer, P., Leeuwen, E.J.v., Mehlhorn, K., Borgwardt, K.M., 2011. Weisfeiler-lehman graph kernels. Journal of Machine Learning Research 12, 2539–2561.

## Authors

* [Linlin Jia](https://github.com/jajupmochi), LITIS, INSA Rouen Normandie


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datasets/MUTAG/README View File

@@ -1,68 +0,0 @@
=== Introduction ===

This folder contains 6 data sets of undirected labeled graphs in Matlab format for graph
classification: MUTAG, PTC, NCI1, NCI109, ENZYMES, and D&D.

=== Usage ===

For each data set X, the Matlab command
load X
loads into the memory a struct array containing graphs, and a column vector lx containing
a class label for each graph.
X(i).am is the adjacency matrix of the i'th graph,
X(i).al is the adjacency list of the i'th graph,
X(i).nl.values is a column vector of node labels for the i'th graph,
X(i).el (not always available) contains edge labels for the i'th graph.

Example:
typing "load MUTAG" in MATLAB
loads a 188 element array of graph structures, called MUTAG, and a column of 188 numbers,
each of which indicates the class that the corresponding graph belongs to.

=== Description ===

MUTAG (Debnath et al., 1991) is a data set of 188 mutagenic aromatic and heteroaromatic
nitro compounds labeled according to whether or not they have a mutagenic effect on the
Gram-negative bacterium Salmonella typhimurium.

PTC (Toivonen et al., 2003) contains 344 chemical compounds tested for carcinogenicity
in mice and rats. The classification task is to predict the carcinogenicity of compounds.

NCI1 and NCI109 represent two balanced subsets of data sets of chemical compounds screened
for activity against non-small cell lung cancer and ovarian cancer cell lines respectively
(Wale and Karypis (2006) and http://pubchem.ncbi.nlm.nih.gov).

ENZYMES is a data set of protein tertiary structures obtained from (Borgwardt et al.,
2005) consisting of 600 enzymes from the BRENDA enzyme database (Schomburg et al., 2004).
In this case the task is to correctly assign each enzyme to one of the 6 EC top-level
classes.

D&D is a data set of 1178 protein structures (Dobson and Doig, 2003). Each protein is
represented by a graph, in which the nodes are amino acids and two nodes are connected
by an edge if they are less than 6 Angstroms apart. The prediction task is to classify
the protein structures into enzymes and non-enzymes.

=== References ===

K. M. Borgwardt, C. S. Ong, S. Schoenauer, S. V. N. Vishwanathan, A. J. Smola, and H. P.
Kriegel. Protein function prediction via graph kernels. Bioinformatics, 21(Suppl 1):i47–i56,
Jun 2005.

A. K. Debnath, R. L. Lopez de Compadre, G. Debnath, A. J. Shusterman, and C. Hansch.
Structure-activity relationship of mutagenic aromatic and heteroaromatic nitro compounds.
Correlation with molecular orbital energies and hydrophobicity. J Med Chem, 34: 786–797,
1991.

P. D. Dobson and A. J. Doig. Distinguishing enzyme structures from non-enzymes without
alignments. J Mol Biol, 330(4):771–783, Jul 2003.

I. Schomburg, A. Chang, C. Ebeling, M. Gremse, C. Heldt, G. Huhn, and D. Schomburg. Brenda,
the enzyme database: updates and major new developments. Nucleic Acids Research, 32D:431–433,
2004.

H. Toivonen, A. Srinivasan, R.D. King, S. Kramer, and C. Helma (2003). Statistical
evaluation of the predictive toxicology challenge 2000-2001. Bioinformatics, 19(10):1183–1193.

N. Wale and G. Karypis. Comparison of descriptor spaces for chemical compound retrieval and
classification. In Proc. of ICDM, pages 678–689, Hong Kong, 2006.


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datasets/MUTAG/README.txt View File

@@ -0,0 +1,85 @@
README for dataset MUTAG


=== Usage ===

This folder contains the following comma separated text files
(replace DS by the name of the dataset):

n = total number of nodes
m = total number of edges
N = number of graphs

(1) DS_A.txt (m lines)
sparse (block diagonal) adjacency matrix for all graphs,
each line corresponds to (row, col) resp. (node_id, node_id)

(2) DS_graph_indicator.txt (n lines)
column vector of graph identifiers for all nodes of all graphs,
the value in the i-th line is the graph_id of the node with node_id i

(3) DS_graph_labels.txt (N lines)
class labels for all graphs in the dataset,
the value in the i-th line is the class label of the graph with graph_id i

(4) DS_node_labels.txt (n lines)
column vector of node labels,
the value in the i-th line corresponds to the node with node_id i

There are OPTIONAL files if the respective information is available:

(5) DS_edge_labels.txt (m lines; same size as DS_A_sparse.txt)
labels for the edges in DD_A_sparse.txt

(6) DS_edge_attributes.txt (m lines; same size as DS_A.txt)
attributes for the edges in DS_A.txt

(7) DS_node_attributes.txt (n lines)
matrix of node attributes,
the comma seperated values in the i-th line is the attribute vector of the node with node_id i

(8) DS_graph_attributes.txt (N lines)
regression values for all graphs in the dataset,
the value in the i-th line is the attribute of the graph with graph_id i


=== Description of the dataset ===

The MUTAG dataset consists of 188 chemical compounds divided into two
classes according to their mutagenic effect on a bacterium.

The chemical data was obtained form http://cdb.ics.uci.edu and converted
to graphs, where vertices represent atoms and edges represent chemical
bonds. Explicit hydrogen atoms have been removed and vertices are labeled
by atom type and edges by bond type (single, double, triple or aromatic).
Chemical data was processed using the Chemistry Development Kit (v1.4).

Node labels:

0 C
1 N
2 O
3 F
4 I
5 Cl
6 Br

Edge labels:

0 aromatic
1 single
2 double
3 triple


=== Previous Use of the Dataset ===

Kriege, N., Mutzel, P.: Subgraph matching kernels for attributed graphs. In: Proceedings
of the 29th International Conference on Machine Learning (ICML-2012) (2012).


=== References ===

Debnath, A.K., Lopez de Compadre, R.L., Debnath, G., Shusterman, A.J., and Hansch, C.
Structure-activity relationship of mutagenic aromatic and heteroaromatic nitro compounds.
Correlation with molecular orbital energies and hydrophobicity. J. Med. Chem. 34(2):786-797 (1991).

+ 5
- 7
notebooks/run_commonwalkkernel.ipynb View File

@@ -73,20 +73,18 @@
" {'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',\n",
" 'task': 'regression'}, # node symb\n",
" {'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression',\n",
" 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt', }, \n",
" 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt'}, \n",
" # contains single node graph, node symb\n",
" {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds', }, # node/edge symb\n",
" {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds', }, # unlabeled\n",
" {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat',\n",
" 'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}, # node/edge symb\n",
" {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds'}, # node/edge symb\n",
" {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds'}, # unlabeled\n",
" {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG_A.txt'}, # node/edge symb\n",
" {'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'},\n",
" # node nsymb\n",
" {'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},\n",
" # node symb/nsymb\n",
"# {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},\n",
"# # node/edge symb\n",
"# {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat',\n",
"# 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}}, # node symb\n",
"# {'name': 'D&D', 'dataset': '../datasets/DD/DD_A.txt'}, # node symb\n",
"\n",
" # {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb\n",
" # # # {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb\n",


+ 6
- 8
notebooks/run_commonwalkkernel.py View File

@@ -15,20 +15,18 @@ dslist = [
{'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',
'task': 'regression'}, # node symb
{'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression',
'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt', },
'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt'},
# contains single node graph, node symb
{'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds', }, # node/edge symb
{'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds', }, # unlabeled
{'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat',
'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}, # node/edge symb
{'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds'}, # node/edge symb
{'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds'}, # unlabeled
{'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG_A.txt'}, # node/edge symb
{'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'},
# node nsymb
{'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},
# node symb/nsymb
# {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},
# # node/edge symb
# {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat',
# 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}}, # node symb
# {'name': 'D&D', 'dataset': '../datasets/DD/DD_A.txt'}, # node symb

# {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb
# # # {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb
@@ -82,4 +80,4 @@ for ds in dslist:
n_jobs=multiprocessing.cpu_count(),
read_gm_from_file=False,
verbose=True)
print()
print()

+ 5
- 7
notebooks/run_marginalizedkernel.ipynb View File

@@ -104,20 +104,18 @@
" {'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',\n",
" 'task': 'regression'}, # node symb\n",
" {'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression',\n",
" 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt', }, \n",
" 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt'}, \n",
" # contains single node graph, node symb\n",
" {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds', }, # node/edge symb\n",
" {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds', }, # unlabeled\n",
" {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat',\n",
" 'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}, # node/edge symb\n",
" {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds'}, # node/edge symb\n",
" {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds'}, # unlabeled\n",
" {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG_A.txt'}, # node/edge symb\n",
" {'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'},\n",
" # node nsymb\n",
" {'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},\n",
" # node symb/nsymb\n",
"# {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},\n",
"# # node/edge symb\n",
"# {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat',\n",
"# 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}}, # node symb\n",
"# {'name': 'D&D', 'dataset': '../datasets/DD/DD_A.txt'}, # node symb\n",
"\n",
" # {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb\n",
" # # # {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb\n",


+ 5
- 7
notebooks/run_marginalizedkernel.py View File

@@ -15,20 +15,18 @@ dslist = [
{'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',
'task': 'regression'}, # node symb
{'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression',
'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt', },
'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt'},
# contains single node graph, node symb
{'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds', }, # node/edge symb
{'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds', }, # unlabeled
{'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat',
'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}, # node/edge symb
{'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds'}, # node/edge symb
{'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds'}, # unlabeled
{'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG_A.txt'}, # node/edge symb
{'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'},
# node nsymb
{'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},
# node symb/nsymb
# {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},
# # node/edge symb
# {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat',
# 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}}, # node symb
# {'name': 'D&D', 'dataset': '../datasets/DD/DD_A.txt'}, # node symb

# {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb
# # # {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb


+ 5
- 7
notebooks/run_randomwalkkernel.ipynb View File

@@ -219,20 +219,18 @@
" {'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',\n",
" 'task': 'regression'}, # node symb\n",
" {'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression',\n",
" 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt', }, \n",
" 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt'}, \n",
" # contains single node graph, node symb\n",
" {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds', }, # node/edge symb\n",
" {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds', }, # unlabeled\n",
" {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat',\n",
" 'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}, # node/edge symb\n",
" {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds'}, # node/edge symb\n",
" {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds'}, # unlabeled\n",
" {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG_A.txt'}, # node/edge symb\n",
" {'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'},\n",
" # node nsymb\n",
" {'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},\n",
" # node symb/nsymb\n",
"# {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},\n",
"# # node/edge symb\n",
"# {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat',\n",
"# 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}}, # node symb\n",
"# {'name': 'D&D', 'dataset': '../datasets/DD/DD_A.txt'}, # node symb\n",
"\n",
" # {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb\n",
" # # # {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb\n",


+ 7
- 8
notebooks/run_randomwalkkernel.py View File

@@ -20,20 +20,18 @@ dslist = [
{'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',
'task': 'regression'}, # node symb
{'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression',
'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt', },
'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt'},
# contains single node graph, node symb
{'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds', }, # node/edge symb
{'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds', }, # unlabeled
{'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat',
'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}, # node/edge symb
{'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds'}, # node/edge symb
{'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds'}, # unlabeled
{'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG_A.txt'}, # node/edge symb
{'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'},
# node nsymb
{'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},
# node symb/nsymb
# {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},
# # node/edge symb
# {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat',
# 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}}, # node symb
# {'name': 'D&D', 'dataset': '../datasets/DD/DD_A.txt'}, # node symb

# {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb
# # # {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb
@@ -65,6 +63,7 @@ dslist = [
estimator = randomwalkkernel
param_grid = [{'C': np.logspace(-10, 10, num=41, base=10)},
{'alpha': np.logspace(-10, 10, num=41, base=10)}]
gaussiankernel = functools.partial(gaussiankernel, gamma=0.5)

for ds in dslist:
print()
@@ -108,4 +107,4 @@ for ds in dslist:
n_jobs=multiprocessing.cpu_count(),
read_gm_from_file=False,
verbose=True)
print()
print()

+ 5
- 8
notebooks/run_spkernel.ipynb View File

@@ -171,21 +171,18 @@
" {'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',\n",
" 'task': 'regression'}, # node symb\n",
" {'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression',\n",
" 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt', }, \n",
" 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt'}, \n",
" # contains single node graph, node symb\n",
" {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds', }, # node/edge symb\n",
" {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds', }, # unlabeled\n",
" {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat',\n",
" 'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}, # node/edge symb\n",
" {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds'}, # node/edge symb\n",
" {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds'}, # unlabeled\n",
" {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG_A.txt'}, # node/edge symb\n",
" {'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'},\n",
" # node nsymb\n",
" {'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},\n",
" # node symb/nsymb\n",
"\n",
"# {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},\n",
"# # node/edge symb\n",
"# {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat',\n",
"# 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}}, # node symb\n",
"# {'name': 'D&D', 'dataset': '../datasets/DD/DD_A.txt'}, # node symb\n",
"#\n",
"# {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb\n",
"# {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb\n",


+ 6
- 9
notebooks/run_spkernel.py View File

@@ -11,21 +11,18 @@ dslist = [
{'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',
'task': 'regression'}, # node symb
{'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression',
'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt', },
'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt'},
# contains single node graph, node symb
{'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds', }, # node/edge symb
{'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds', }, # unlabeled
{'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat',
'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}, # node/edge symb
{'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds'}, # node/edge symb
{'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds'}, # unlabeled
{'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG_A.txt'}, # node/edge symb
{'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'},
# node nsymb
{'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},
# node symb/nsymb

# {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},
# # node/edge symb
# {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat',
# 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}}, # node symb
# {'name': 'D&D', 'dataset': '../datasets/DD/DD_A.txt'}, # node symb
#
# {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb
# {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb
@@ -79,4 +76,4 @@ for ds in dslist:
n_jobs=multiprocessing.cpu_count(),
read_gm_from_file=False,
verbose=True)
print()
print()

+ 5
- 7
notebooks/run_structuralspkernel.ipynb View File

@@ -124,20 +124,18 @@
" {'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',\n",
" 'task': 'regression'}, # node symb\n",
" {'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression',\n",
" 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt', }, \n",
" 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt'}, \n",
" # contains single node graph, node symb\n",
" {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds', }, # node/edge symb\n",
" {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds', }, # unlabeled\n",
" {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat',\n",
" 'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}, # node/edge symb\n",
" {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds'}, # node/edge symb\n",
" {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds'}, # unlabeled\n",
" {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG_A.txt'}, # node/edge symb\n",
" {'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'},\n",
" # node nsymb\n",
" {'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},\n",
" # node symb/nsymb\n",
"# {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},\n",
"# # node/edge symb\n",
"# {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat',\n",
"# 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}}, # node symb\n",
"# {'name': 'D&D', 'dataset': '../datasets/DD/DD_A.txt'}, # node symb\n",
"\n",
" # {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb\n",
" # # # {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb\n",


+ 6
- 8
notebooks/run_structuralspkernel.py View File

@@ -17,20 +17,18 @@ dslist = [
{'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',
'task': 'regression'}, # node symb
{'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression',
'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt', },
'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt'},
# contains single node graph, node symb
{'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds', }, # node/edge symb
{'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds', }, # unlabeled
{'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat',
'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}, # node/edge symb
{'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds'}, # node/edge symb
{'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds'}, # unlabeled
{'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG_A.txt'}, # node/edge symb
{'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'},
# node nsymb
{'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},
# node symb/nsymb
# {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},
# # node/edge symb
# {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat',
# 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}}, # node symb
# {'name': 'D&D', 'dataset': '../datasets/DD/DD_A.txt'}, # node symb

# {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb
# # # {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb
@@ -86,4 +84,4 @@ for ds in dslist:
n_jobs=multiprocessing.cpu_count(),
read_gm_from_file=False,
verbose=True)
print()
print()

+ 5
- 7
notebooks/run_treeletkernel.ipynb View File

@@ -100,20 +100,18 @@
" {'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',\n",
" 'task': 'regression'}, # node symb\n",
" {'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression',\n",
" 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt', }, \n",
" 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt'}, \n",
" # contains single node graph, node symb\n",
" {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds', }, # node/edge symb\n",
" {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds', }, # unlabeled\n",
" {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat',\n",
" 'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}, # node/edge symb\n",
" {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds'}, # node/edge symb\n",
" {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds'}, # unlabeled\n",
" {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG_A.txt'}, # node/edge symb\n",
"# {'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'},\n",
"# # node nsymb\n",
" {'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},\n",
" # node symb/nsymb\n",
"# {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},\n",
"# # node/edge symb\n",
"# {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat',\n",
"# 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}}, # node symb\n",
"# {'name': 'D&D', 'dataset': '../datasets/DD/DD_A.txt'}, # node symb\n",
"\n",
" # {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb\n",
" # # # {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb\n",


+ 9
- 11
notebooks/run_treeletkernel.py View File

@@ -1,7 +1,7 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Oct 5 19:19:33 2018
Created on Mon Mar 21 11:19:33 2019

@author: ljia
"""
@@ -10,26 +10,24 @@ from libs import *
import multiprocessing

from pygraph.kernels.treeletKernel import treeletkernel
from pygraph.utils.kernels import gaussiankernel, polynomialkernel
from pygraph.utils.kernels import gaussiankernel, linearkernel, polynomialkernel

dslist = [
{'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',
'task': 'regression'}, # node symb
{'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression',
'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt', },
'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt'},
# contains single node graph, node symb
{'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds', }, # node/edge symb
{'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds', }, # unlabeled
{'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat',
'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}, # node/edge symb
{'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds'}, # node/edge symb
{'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds'}, # unlabeled
{'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG_A.txt'}, # node/edge symb
# {'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'},
# # node nsymb
{'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},
# node symb/nsymb
# {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},
# # node/edge symb
# {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat',
# 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}}, # node symb
# {'name': 'D&D', 'dataset': '../datasets/DD/DD_A.txt'}, # node symb

# {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb
# # # {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb
@@ -59,7 +57,7 @@ dslist = [
# {'name': 'PTC_MR', 'dataset': '../datasets/PTC/Train/MR.ds',},
]
estimator = treeletkernel
param_grid_precomputed = {'sub_kernel': [gaussiankernel, polynomialkernel]}
param_grid_precomputed = {'sub_kernel': [gaussiankernel, linearkernel, polynomialkernel]}
param_grid = [{'C': np.logspace(-10, 10, num=41, base=10)},
{'alpha': np.logspace(-10, 10, num=41, base=10)}]

@@ -80,4 +78,4 @@ for ds in dslist:
n_jobs=multiprocessing.cpu_count(),
read_gm_from_file=False,
verbose=True)
print()
print()

+ 6
- 14
notebooks/run_untilhpathkernel.ipynb View File

@@ -227,13 +227,7 @@
"the gram matrix with parameters {'compute_method': 'trie', 'depth': 1.0, 'k_func': 'tanimoto', 'n_jobs': 8, 'verbose': True} is: \n",
"\n",
"\n",
"getting paths: 150it [00:00, 27568.71it/s]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"getting paths: 150it [00:00, 27568.71it/s]\n",
"calculating kernels: 11325it [00:00, 780628.98it/s]\n",
"\n",
" --- kernel matrix of path kernel up to 2 of size 150 built in 0.2590019702911377 seconds ---\n",
@@ -265,20 +259,18 @@
" {'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',\n",
" 'task': 'regression'}, # node symb\n",
" {'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression',\n",
" 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt', }, \n",
" 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt'}, \n",
" # contains single node graph, node symb\n",
" {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds', }, # node/edge symb\n",
" {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds', }, # unlabeled\n",
" {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat',\n",
" 'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}, # node/edge symb\n",
" {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds'}, # node/edge symb\n",
" {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds'}, # unlabeled\n",
" {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG_A.txt'}, # node/edge symb\n",
" {'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'},\n",
" # node nsymb\n",
" {'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},\n",
" # node symb/nsymb\n",
"# {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},\n",
"# # node/edge symb\n",
"# {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat',\n",
"# 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}}, # node symb\n",
"# {'name': 'D&D', 'dataset': '../datasets/DD/DD_A.txt'}, # node symb\n",
"\n",
" # {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb\n",
" # # # {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb\n",


+ 6
- 8
notebooks/run_untilhpathkernel.py View File

@@ -15,20 +15,18 @@ dslist = [
{'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',
'task': 'regression'}, # node symb
{'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression',
'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt', },
'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt'},
# contains single node graph, node symb
{'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds', }, # node/edge symb
{'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds', }, # unlabeled
{'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG.mat',
'extra_params': {'am_sp_al_nl_el': [0, 0, 3, 1, 2]}}, # node/edge symb
{'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds'}, # node/edge symb
{'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds'}, # unlabeled
{'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG_A.txt'}, # node/edge symb
{'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'},
# node nsymb
{'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},
# node symb/nsymb
# {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},
# # node/edge symb
# {'name': 'D&D', 'dataset': '../datasets/D&D/DD.mat',
# 'extra_params': {'am_sp_al_nl_el': [0, 1, 2, 1, -1]}}, # node symb
# {'name': 'D&D', 'dataset': '../datasets/DD/DD_A.txt'}, # node symb

# {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb
# # # {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb
@@ -81,4 +79,4 @@ for ds in dslist:
n_jobs=multiprocessing.cpu_count(),
read_gm_from_file=False,
verbose=True)
print()
print()

+ 144
- 0
notebooks/run_weisfeilerlehmankernel.ipynb View File

@@ -0,0 +1,144 @@
{
"cells": [
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"MUTAG\n",
"\n",
"--- This is a classification problem ---\n",
"\n",
"\n",
"1. Loading dataset from file...\n",
"\n",
"2. Calculating gram matrices. This could take a while...\n",
"\n",
" --- Weisfeiler-Lehman subtree kernel matrix of size 188 built in 0.14636015892028809 seconds ---\n",
"\n",
"the gram matrix with parameters {'base_kernel': 'subtree', 'height': 0.0, 'n_jobs': 8, 'verbose': True} is: \n",
"\n",
"\n",
"\n",
" --- Weisfeiler-Lehman subtree kernel matrix of size 188 built in 0.2917311191558838 seconds ---\n",
"\n",
"the gram matrix with parameters {'base_kernel': 'subtree', 'height': 1.0, 'n_jobs': 8, 'verbose': True} is: \n",
"\n",
"\n"
]
}
],
"source": [
"#!/usr/bin/env python3\n",
"# -*- coding: utf-8 -*-\n",
"\"\"\"\n",
"Created on Mon Mar 21 11:19:33 2019\n",
"\n",
"@author: ljia\n",
"\"\"\"\n",
"\n",
"from libs import *\n",
"import multiprocessing\n",
"\n",
"from pygraph.kernels.weisfeilerLehmanKernel import weisfeilerlehmankernel\n",
"from pygraph.utils.kernels import gaussiankernel, polynomialkernel\n",
"\n",
"\n",
"dslist = [\n",
" {'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',\n",
" 'task': 'regression'}, # node symb\n",
" {'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression',\n",
" 'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt'}, \n",
" # contains single node graph, node symb\n",
" {'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds'}, # node/edge symb\n",
" {'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds'}, # unlabeled\n",
" {'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG_A.txt'}, # node/edge symb\n",
" {'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'},\n",
" # node nsymb\n",
" {'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},\n",
" # node symb/nsymb\n",
"# {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},\n",
"# # node/edge symb\n",
" {'name': 'D&D', 'dataset': '../datasets/DD/DD_A.txt'}, # node symb\n",
"\n",
" # {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb\n",
" # # # {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb\n",
" # # # {'name': 'COX2', 'dataset': '../datasets/COX2_txt/COX2_A_sparse.txt'}, # node symb/nsymb\n",
" # {'name': 'Fingerprint', 'dataset': '../datasets/Fingerprint/Fingerprint_A.txt'},\n",
" #\n",
" # # {'name': 'DHFR', 'dataset': '../datasets/DHFR_txt/DHFR_A_sparse.txt'}, # node symb/nsymb\n",
" # # {'name': 'SYNTHETIC', 'dataset': '../datasets/SYNTHETIC_txt/SYNTHETIC_A_sparse.txt'}, # node symb/nsymb\n",
" # # {'name': 'MSRC9', 'dataset': '../datasets/MSRC_9_txt/MSRC_9_A.txt'}, # node symb\n",
" # # {'name': 'MSRC21', 'dataset': '../datasets/MSRC_21_txt/MSRC_21_A.txt'}, # node symb\n",
" # # {'name': 'FIRSTMM_DB', 'dataset': '../datasets/FIRSTMM_DB/FIRSTMM_DB_A.txt'}, # node symb/nsymb ,edge nsymb\n",
"\n",
" # # {'name': 'PROTEINS', 'dataset': '../datasets/PROTEINS_txt/PROTEINS_A_sparse.txt'}, # node symb/nsymb\n",
" # # {'name': 'PROTEINS_full', 'dataset': '../datasets/PROTEINS_full_txt/PROTEINS_full_A_sparse.txt'}, # node symb/nsymb\n",
"# {'name': 'AIDS', 'dataset': '../datasets/AIDS/AIDS_A.txt'}, # node symb/nsymb, edge symb\n",
" {'name': 'NCI1', 'dataset': '../datasets/NCI1/NCI1.mat',\n",
" 'extra_params': {'am_sp_al_nl_el': [1, 1, 2, 0, -1]}}, # node symb\n",
" {'name': 'NCI109', 'dataset': '../datasets/NCI109/NCI109.mat',\n",
" 'extra_params': {'am_sp_al_nl_el': [1, 1, 2, 0, -1]}}, # node symb\n",
" # {'name': 'NCI-HIV', 'dataset': '../datasets/NCI-HIV/AIDO99SD.sdf',\n",
" # 'dataset_y': '../datasets/NCI-HIV/aids_conc_may04.txt',}, # node/edge symb\n",
"\n",
" # # not working below\n",
" # {'name': 'PTC_FM', 'dataset': '../datasets/PTC/Train/FM.ds',},\n",
" # {'name': 'PTC_FR', 'dataset': '../datasets/PTC/Train/FR.ds',},\n",
" # {'name': 'PTC_MM', 'dataset': '../datasets/PTC/Train/MM.ds',},\n",
" # {'name': 'PTC_MR', 'dataset': '../datasets/PTC/Train/MR.ds',},\n",
"]\n",
"estimator = weisfeilerlehmankernel\n",
"param_grid_precomputed = {'base_kernel': ['subtree'], \n",
" 'height': np.linspace(0, 10, 11)}\n",
"param_grid = [{'C': np.logspace(-10, 4, num=29, base=10)},\n",
" {'alpha': np.logspace(-10, 10, num=41, base=10)}]\n",
"\n",
"for ds in dslist:\n",
" print()\n",
" print(ds['name'])\n",
" model_selection_for_precomputed_kernel(\n",
" ds['dataset'],\n",
" estimator,\n",
" param_grid_precomputed,\n",
" (param_grid[1] if ('task' in ds and ds['task']\n",
" == 'regression') else param_grid[0]),\n",
" (ds['task'] if 'task' in ds else 'classification'),\n",
" NUM_TRIALS=30,\n",
" datafile_y=(ds['dataset_y'] if 'dataset_y' in ds else None),\n",
" extra_params=(ds['extra_params'] if 'extra_params' in ds else None),\n",
" ds_name=ds['name'],\n",
" n_jobs=multiprocessing.cpu_count(),\n",
" read_gm_from_file=False,\n",
" verbose=True)\n",
" print()"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.6.7"
}
},
"nbformat": 4,
"nbformat_minor": 2
}

+ 81
- 0
notebooks/run_weisfeilerlehmankernel.py View File

@@ -0,0 +1,81 @@
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Mar 21 11:19:33 2019

@author: ljia
"""

from libs import *
import multiprocessing

from pygraph.kernels.weisfeilerLehmanKernel import weisfeilerlehmankernel
from pygraph.utils.kernels import gaussiankernel, polynomialkernel


dslist = [
{'name': 'Acyclic', 'dataset': '../datasets/acyclic/dataset_bps.ds',
'task': 'regression'}, # node symb
{'name': 'Alkane', 'dataset': '../datasets/Alkane/dataset.ds', 'task': 'regression',
'dataset_y': '../datasets/Alkane/dataset_boiling_point_names.txt'},
# contains single node graph, node symb
{'name': 'MAO', 'dataset': '../datasets/MAO/dataset.ds'}, # node/edge symb
{'name': 'PAH', 'dataset': '../datasets/PAH/dataset.ds'}, # unlabeled
{'name': 'MUTAG', 'dataset': '../datasets/MUTAG/MUTAG_A.txt'}, # node/edge symb
{'name': 'Letter-med', 'dataset': '../datasets/Letter-med/Letter-med_A.txt'},
# node nsymb
{'name': 'ENZYMES', 'dataset': '../datasets/ENZYMES_txt/ENZYMES_A_sparse.txt'},
# node symb/nsymb
# {'name': 'Mutagenicity', 'dataset': '../datasets/Mutagenicity/Mutagenicity_A.txt'},
# # node/edge symb
{'name': 'D&D', 'dataset': '../datasets/DD/DD_A.txt'}, # node symb
#
# {'name': 'COIL-DEL', 'dataset': '../datasets/COIL-DEL/COIL-DEL_A.txt'}, # edge symb, node nsymb
# # # {'name': 'BZR', 'dataset': '../datasets/BZR_txt/BZR_A_sparse.txt'}, # node symb/nsymb
# # # {'name': 'COX2', 'dataset': '../datasets/COX2_txt/COX2_A_sparse.txt'}, # node symb/nsymb
# {'name': 'Fingerprint', 'dataset': '../datasets/Fingerprint/Fingerprint_A.txt'},
#
# # {'name': 'DHFR', 'dataset': '../datasets/DHFR_txt/DHFR_A_sparse.txt'}, # node symb/nsymb
# # {'name': 'SYNTHETIC', 'dataset': '../datasets/SYNTHETIC_txt/SYNTHETIC_A_sparse.txt'}, # node symb/nsymb
# # {'name': 'MSRC9', 'dataset': '../datasets/MSRC_9_txt/MSRC_9_A.txt'}, # node symb
# # {'name': 'MSRC21', 'dataset': '../datasets/MSRC_21_txt/MSRC_21_A.txt'}, # node symb
# # {'name': 'FIRSTMM_DB', 'dataset': '../datasets/FIRSTMM_DB/FIRSTMM_DB_A.txt'}, # node symb/nsymb ,edge nsymb

# # {'name': 'PROTEINS', 'dataset': '../datasets/PROTEINS_txt/PROTEINS_A_sparse.txt'}, # node symb/nsymb
# # {'name': 'PROTEINS_full', 'dataset': '../datasets/PROTEINS_full_txt/PROTEINS_full_A_sparse.txt'}, # node symb/nsymb
# {'name': 'AIDS', 'dataset': '../datasets/AIDS/AIDS_A.txt'}, # node symb/nsymb, edge symb
{'name': 'NCI1', 'dataset': '../datasets/NCI1/NCI1_A.txt'}, # node symb
{'name': 'NCI109', 'dataset': '../datasets/NCI109/NCI109_A.txt'}, # node symb
# {'name': 'NCI-HIV', 'dataset': '../datasets/NCI-HIV/AIDO99SD.sdf',
# 'dataset_y': '../datasets/NCI-HIV/aids_conc_may04.txt',}, # node/edge symb

# # not working below
# {'name': 'PTC_FM', 'dataset': '../datasets/PTC/Train/FM.ds',},
# {'name': 'PTC_FR', 'dataset': '../datasets/PTC/Train/FR.ds',},
# {'name': 'PTC_MM', 'dataset': '../datasets/PTC/Train/MM.ds',},
# {'name': 'PTC_MR', 'dataset': '../datasets/PTC/Train/MR.ds',},
]
estimator = weisfeilerlehmankernel
param_grid_precomputed = {'base_kernel': ['subtree'],
'height': np.linspace(0, 10, 11)}
param_grid = [{'C': np.logspace(-10, 4, num=29, base=10)},
{'alpha': np.logspace(-10, 10, num=41, base=10)}]

for ds in dslist:
print()
print(ds['name'])
model_selection_for_precomputed_kernel(
ds['dataset'],
estimator,
param_grid_precomputed,
(param_grid[1] if ('task' in ds and ds['task']
== 'regression') else param_grid[0]),
(ds['task'] if 'task' in ds else 'classification'),
NUM_TRIALS=30,
datafile_y=(ds['dataset_y'] if 'dataset_y' in ds else None),
extra_params=(ds['extra_params'] if 'extra_params' in ds else None),
ds_name=ds['name'],
n_jobs=multiprocessing.cpu_count(),
read_gm_from_file=False,
verbose=True)
print()

+ 3
- 17
preimage/iam.py View File

@@ -16,7 +16,7 @@ import librariesImport, script
sys.path.insert(0, "../")
from pygraph.utils.graphfiles import saveDataset
from pygraph.utils.graphdataset import get_dataset_attributes
from pygraph.utils.utils import graph_isIdentical
from pygraph.utils.utils import graph_isIdentical, get_node_labels, get_edge_labels
#from pygraph.utils.utils import graph_deepcopy


@@ -158,9 +158,9 @@ def GED(g1, g2, lib='gedlib'):
script.PyRestartEnv()
script.PyLoadGXLGraph('ged_tmp/', 'ged_tmp/tmp.xml')
listID = script.PyGetGraphIds()
script.PySetEditCost("CHEM_2")
script.PySetEditCost("CHEM_1")
script.PyInitEnv()
script.PySetMethod("BIPARTITE", "")
script.PySetMethod("IPFP", "")
script.PyInitMethod()
g = listID[0]
h = listID[1]
@@ -173,20 +173,6 @@ def GED(g1, g2, lib='gedlib'):
return dis, pi_forward, pi_backward


def get_node_labels(Gn, node_label):
nl = set()
for G in Gn:
nl = nl | set(nx.get_node_attributes(G, node_label).values())
return nl


def get_edge_labels(Gn, edge_label):
el = set()
for G in Gn:
el = el | set(nx.get_edge_attributes(G, edge_label).values())
return el


# --------------------------- These are tests --------------------------------#
def test_iam_with_more_graphs_as_init(Gn, G_candidate, c_ei=3, c_er=3, c_es=1,


+ 22
- 21
pygraph/kernels/marginalizedKernel.py View File

@@ -65,6 +65,7 @@ def marginalizedkernel(*args,
# pre-process
n_iteration = int(n_iteration)
Gn = args[0][:] if len(args) == 1 else [args[0].copy(), args[1].copy()]
Gn = [g.copy() for g in Gn]
ds_attrs = get_dataset_attributes(
Gn,
@@ -215,37 +216,37 @@ def _marginalizedkernel_do(g1, g2, node_label, edge_label, p_quit, n_iteration):
R_inf = {} # dict to save all the R_inf for all pairs of nodes
# initial R_inf, the 1st iteration.
for node1 in g1.nodes(data=True):
for node2 in g2.nodes(data=True):
for node1 in g1.nodes():
for node2 in g2.nodes():
# R_inf[(node1[0], node2[0])] = r1
if len(g1[node1[0]]) > 0:
if len(g2[node2[0]]) > 0:
R_inf[(node1[0], node2[0])] = r1
if len(g1[node1]) > 0:
if len(g2[node2]) > 0:
R_inf[(node1, node2)] = r1
else:
R_inf[(node1[0], node2[0])] = p_quit
R_inf[(node1, node2)] = p_quit
else:
if len(g2[node2[0]]) > 0:
R_inf[(node1[0], node2[0])] = p_quit
if len(g2[node2]) > 0:
R_inf[(node1, node2)] = p_quit
else:
R_inf[(node1[0], node2[0])] = 1
R_inf[(node1, node2)] = 1
# compute all transition probability first.
t_dict = {}
if n_iteration > 1:
for node1 in g1.nodes(data=True):
neighbor_n1 = g1[node1[0]]
for node1 in g1.nodes():
neighbor_n1 = g1[node1]
# the transition probability distribution in the random walks
# generating step (uniform distribution over the vertices adjacent
# to the current vertex)
if len(neighbor_n1) > 0:
p_trans_n1 = (1 - p_quit) / len(neighbor_n1)
for node2 in g2.nodes(data=True):
neighbor_n2 = g2[node2[0]]
for node2 in g2.nodes():
neighbor_n2 = g2[node2]
if len(neighbor_n2) > 0:
p_trans_n2 = (1 - p_quit) / len(neighbor_n2)
for neighbor1 in neighbor_n1:
for neighbor2 in neighbor_n2:
t_dict[(node1[0], node2[0], neighbor1, neighbor2)] = \
t_dict[(node1, node2, neighbor1, neighbor2)] = \
p_trans_n1 * p_trans_n2 * \
deltakernel(g1.node[neighbor1][node_label],
g2.node[neighbor2][node_label]) * \
@@ -258,20 +259,20 @@ def _marginalizedkernel_do(g1, g2, node_label, edge_label, p_quit, n_iteration):
R_inf_old = R_inf.copy()

# calculate R_inf for each pair of nodes
for node1 in g1.nodes(data=True):
neighbor_n1 = g1[node1[0]]
for node1 in g1.nodes():
neighbor_n1 = g1[node1]
# the transition probability distribution in the random walks
# generating step (uniform distribution over the vertices adjacent
# to the current vertex)
if len(neighbor_n1) > 0:
for node2 in g2.nodes(data=True):
neighbor_n2 = g2[node2[0]]
for node2 in g2.nodes():
neighbor_n2 = g2[node2]
if len(neighbor_n2) > 0:
R_inf[(node1[0], node2[0])] = r1
R_inf[(node1, node2)] = r1
for neighbor1 in neighbor_n1:
for neighbor2 in neighbor_n2:
R_inf[(node1[0], node2[0])] += \
(t_dict[(node1[0], node2[0], neighbor1, neighbor2)] * \
R_inf[(node1, node2)] += \
(t_dict[(node1, node2, neighbor1, neighbor2)] * \
R_inf_old[(neighbor1, neighbor2)]) # ref [1] equation (8)

# add elements of R_inf up and calculate kernel


+ 1
- 0
pygraph/kernels/randomWalkKernel.py View File

@@ -58,6 +58,7 @@ def randomwalkkernel(*args,
"""
compute_method = compute_method.lower()
Gn = args[0] if len(args) == 1 else [args[0], args[1]]
Gn = [g.copy() for g in Gn]

eweight = None
if edge_weight == None:


+ 1
- 0
pygraph/kernels/spKernel.py View File

@@ -54,6 +54,7 @@ def spkernel(*args,
"""
# pre-process
Gn = args[0] if len(args) == 1 else [args[0], args[1]]
Gn = [g.copy() for g in Gn]
weight = None
if edge_weight is None:
if verbose:


+ 1
- 0
pygraph/kernels/structuralspKernel.py View File

@@ -74,6 +74,7 @@ def structuralspkernel(*args,
"""
# pre-process
Gn = args[0] if len(args) == 1 else [args[0], args[1]]
Gn = [g.copy() for g in Gn]
weight = None
if edge_weight is None:
if verbose:


+ 7
- 4
pygraph/kernels/treeletKernel.py View File

@@ -1,6 +1,8 @@
"""
@author: linlin
@references: Gaüzère B, Brun L, Villemin D. Two new graphs kernels in chemoinformatics. Pattern Recognition Letters. 2012 Nov 1;33(15):2038-47.
@references:
[1] Gaüzère B, Brun L, Villemin D. Two new graphs kernels in
chemoinformatics. Pattern Recognition Letters. 2012 Nov 1;33(15):2038-47.
"""

import sys
@@ -50,6 +52,7 @@ def treeletkernel(*args,
"""
# pre-process
Gn = args[0] if len(args) == 1 else [args[0], args[1]]
Gn = [g.copy() for g in Gn]
Kmatrix = np.zeros((len(Gn), len(Gn)))
ds_attrs = get_dataset_attributes(Gn,
attr_names=['node_labeled', 'edge_labeled', 'is_directed'],
@@ -76,13 +79,13 @@ def treeletkernel(*args,
else:
chunksize = 100
canonkeys = [[] for _ in range(len(Gn))]
getps_partial = partial(wrapper_get_canonkeys, node_label, edge_label,
get_partial = partial(wrapper_get_canonkeys, node_label, edge_label,
labeled, ds_attrs['is_directed'])
if verbose:
iterator = tqdm(pool.imap_unordered(getps_partial, itr, chunksize),
iterator = tqdm(pool.imap_unordered(get_partial, itr, chunksize),
desc='getting canonkeys', file=sys.stdout)
else:
iterator = pool.imap_unordered(getps_partial, itr, chunksize)
iterator = pool.imap_unordered(get_partial, itr, chunksize)
for i, ck in iterator:
canonkeys[i] = ck
pool.close()


+ 0
- 382
pygraph/kernels/unfinished/treeletKernel.py View File

@@ -1,382 +0,0 @@
"""
@author: linlin
@references: Gaüzère B, Brun L, Villemin D. Two new graphs kernels in chemoinformatics. Pattern Recognition Letters. 2012 Nov 1;33(15):2038-47.
"""

import sys
import pathlib
sys.path.insert(0, "../")
import time

from collections import Counter
from itertools import chain

import networkx as nx
import numpy as np


def treeletkernel(*args, node_label = 'atom', edge_label = 'bond_type', labeled = True):
"""Calculate treelet graph kernels between graphs.

Parameters
----------
Gn : List of NetworkX graph
List of graphs between which the kernels are calculated.
/
G1, G2 : NetworkX graphs
2 graphs between which the kernel is calculated.
node_label : string
node attribute used as label. The default node label is atom.
edge_label : string
edge attribute used as label. The default edge label is bond_type.
labeled : boolean
Whether the graphs are labeled. The default is True.

Return
------
Kmatrix/kernel : Numpy matrix/float
Kernel matrix, each element of which is the treelet kernel between 2 praphs. / Treelet kernel between 2 graphs.
"""
if len(args) == 1: # for a list of graphs
Gn = args[0]
Kmatrix = np.zeros((len(Gn), len(Gn)))

start_time = time.time()

# get all canonical keys of all graphs before calculating kernels to save time, but this may cost a lot of memory for large dataset.
canonkeys = [ get_canonkeys(Gn[i], node_label = node_label, edge_label = edge_label, labeled = labeled) \
for i in range(0, len(Gn)) ]

for i in range(0, len(Gn)):
for j in range(i, len(Gn)):
Kmatrix[i][j] = _treeletkernel_do(canonkeys[i], canonkeys[j], node_label = node_label, edge_label = edge_label, labeled = labeled)
Kmatrix[j][i] = Kmatrix[i][j]

run_time = time.time() - start_time
print("\n --- treelet kernel matrix of size %d built in %s seconds ---" % (len(Gn), run_time))

return Kmatrix, run_time
else: # for only 2 graphs
start_time = time.time()
canonkey1 = get_canonkeys(args[0], node_label = node_label, edge_label = edge_label, labeled = labeled)
canonkey2 = get_canonkeys(args[1], node_label = node_label, edge_label = edge_label, labeled = labeled)
kernel = _treeletkernel_do(canonkey1, canonkey2, node_label = node_label, edge_label = edge_label, labeled = labeled)
run_time = time.time() - start_time
print("\n --- treelet kernel built in %s seconds ---" % (run_time))

return kernel, run_time


def _treeletkernel_do(canonkey1, canonkey2, node_label = 'atom', edge_label = 'bond_type', labeled = True):
"""Calculate treelet graph kernel between 2 graphs.
Parameters
----------
canonkey1, canonkey2 : list
List of canonical keys in 2 graphs, where each key is represented by a string.
node_label : string
Node attribute used as label. The default node label is atom.
edge_label : string
Edge attribute used as label. The default edge label is bond_type.
labeled : boolean
Whether the graphs are labeled. The default is True.
Return
------
kernel : float
Treelet Kernel between 2 graphs.
"""
keys = set(canonkey1.keys()) & set(canonkey2.keys()) # find same canonical keys in both graphs
vector1 = np.array([ (canonkey1[key] if (key in canonkey1.keys()) else 0) for key in keys ])
vector2 = np.array([ (canonkey2[key] if (key in canonkey2.keys()) else 0) for key in keys ])
kernel = np.sum(np.exp(- np.square(vector1 - vector2) / 2))

return kernel


def get_canonkeys(G, node_label = 'atom', edge_label = 'bond_type', labeled = True):
"""Generate canonical keys of all treelets in a graph.
Parameters
----------
G : NetworkX graphs
The graph in which keys are generated.
node_label : string
node attribute used as label. The default node label is atom.
edge_label : string
edge attribute used as label. The default edge label is bond_type.
labeled : boolean
Whether the graphs are labeled. The default is True.
Return
------
canonkey/canonkey_l : dict
For unlabeled graphs, canonkey is a dictionary which records amount of every tree pattern. For labeled graphs, canonkey_l is one which keeps track of amount of every treelet.
"""
patterns = {} # a dictionary which consists of lists of patterns for all graphlet.
canonkey = {} # canonical key, a dictionary which records amount of every tree pattern.

### structural analysis ###
### In this section, a list of patterns is generated for each graphlet, where every pattern is represented by nodes ordered by
### Morgan's extended labeling.
# linear patterns
patterns['0'] = G.nodes()
canonkey['0'] = nx.number_of_nodes(G)
for i in range(1, 6): # for i in range(1, 6):
patterns[str(i)] = find_all_paths(G, i)
canonkey[str(i)] = len(patterns[str(i)])

# n-star patterns
patterns['3star'] = [ [node] + [neighbor for neighbor in G[node]] for node in G.nodes() if G.degree(node) == 3 ]
patterns['4star'] = [ [node] + [neighbor for neighbor in G[node]] for node in G.nodes() if G.degree(node) == 4 ]
patterns['5star'] = [ [node] + [neighbor for neighbor in G[node]] for node in G.nodes() if G.degree(node) == 5 ]
# n-star patterns
canonkey['6'] = len(patterns['3star'])
canonkey['8'] = len(patterns['4star'])
canonkey['d'] = len(patterns['5star'])

# pattern 7
patterns['7'] = [] # the 1st line of Table 1 in Ref [1]
for pattern in patterns['3star']:
for i in range(1, len(pattern)): # for each neighbor of node 0
if G.degree(pattern[i]) >= 2:
pattern_t = pattern[:]
pattern_t[i], pattern_t[3] = pattern_t[3], pattern_t[i] # set the node with degree >= 2 as the 4th node
for neighborx in G[pattern[i]]:
if neighborx != pattern[0]:
new_pattern = pattern_t + [ neighborx ]
patterns['7'].append(new_pattern)
canonkey['7'] = len(patterns['7'])

# pattern 11
patterns['11'] = [] # the 4th line of Table 1 in Ref [1]
for pattern in patterns['4star']:
for i in range(1, len(pattern)):
if G.degree(pattern[i]) >= 2:
pattern_t = pattern[:]
pattern_t[i], pattern_t[4] = pattern_t[4], pattern_t[i]
for neighborx in G[pattern[i]]:
if neighborx != pattern[0]:
new_pattern = pattern_t + [ neighborx ]
patterns['11'].append(new_pattern)
canonkey['b'] = len(patterns['11'])

# pattern 12
patterns['12'] = [] # the 5th line of Table 1 in Ref [1]
rootlist = [] # a list of root nodes, whose extended labels are 3
for pattern in patterns['3star']:
if pattern[0] not in rootlist: # prevent to count the same pattern twice from each of the two root nodes
rootlist.append(pattern[0])
for i in range(1, len(pattern)):
if G.degree(pattern[i]) >= 3:
rootlist.append(pattern[i])
pattern_t = pattern[:]
pattern_t[i], pattern_t[3] = pattern_t[3], pattern_t[i]
for neighborx1 in G[pattern[i]]:
if neighborx1 != pattern[0]:
for neighborx2 in G[pattern[i]]:
if neighborx1 > neighborx2 and neighborx2 != pattern[0]:
new_pattern = pattern_t + [neighborx1] + [neighborx2]
# new_patterns = [ pattern + [neighborx1] + [neighborx2] for neighborx1 in G[pattern[i]] if neighborx1 != pattern[0] for neighborx2 in G[pattern[i]] if (neighborx1 > neighborx2 and neighborx2 != pattern[0]) ]
patterns['12'].append(new_pattern)
canonkey['c'] = int(len(patterns['12']) / 2)

# pattern 9
patterns['9'] = [] # the 2nd line of Table 1 in Ref [1]
for pattern in patterns['3star']:
for pairs in [ [neighbor1, neighbor2] for neighbor1 in G[pattern[0]] if G.degree(neighbor1) >= 2 \
for neighbor2 in G[pattern[0]] if G.degree(neighbor2) >= 2 if neighbor1 > neighbor2 ]:
pattern_t = pattern[:]
# move nodes with extended labels 4 to specific position to correspond to their children
pattern_t[pattern_t.index(pairs[0])], pattern_t[2] = pattern_t[2], pattern_t[pattern_t.index(pairs[0])]
pattern_t[pattern_t.index(pairs[1])], pattern_t[3] = pattern_t[3], pattern_t[pattern_t.index(pairs[1])]
for neighborx1 in G[pairs[0]]:
if neighborx1 != pattern[0]:
for neighborx2 in G[pairs[1]]:
if neighborx2 != pattern[0]:
new_pattern = pattern_t + [neighborx1] + [neighborx2]
patterns['9'].append(new_pattern)
canonkey['9'] = len(patterns['9'])

# pattern 10
patterns['10'] = [] # the 3rd line of Table 1 in Ref [1]
for pattern in patterns['3star']:
for i in range(1, len(pattern)):
if G.degree(pattern[i]) >= 2:
for neighborx in G[pattern[i]]:
if neighborx != pattern[0] and G.degree(neighborx) >= 2:
pattern_t = pattern[:]
pattern_t[i], pattern_t[3] = pattern_t[3], pattern_t[i]
new_patterns = [ pattern_t + [neighborx] + [neighborxx] for neighborxx in G[neighborx] if neighborxx != pattern[i] ]
patterns['10'].extend(new_patterns)
canonkey['a'] = len(patterns['10'])

### labeling information ###
### In this section, a list of canonical keys is generated for every pattern obtained in the structural analysis
### section above, which is a string corresponding to a unique treelet. A dictionary is built to keep track of
### the amount of every treelet.
if labeled == True:
canonkey_l = {} # canonical key, a dictionary which keeps track of amount of every treelet.

# linear patterns
canonkey_t = Counter(list(nx.get_node_attributes(G, node_label).values()))
for key in canonkey_t:
canonkey_l['0' + key] = canonkey_t[key]

for i in range(1, 6): # for i in range(1, 6):
treelet = []
for pattern in patterns[str(i)]:
canonlist = list(chain.from_iterable((G.node[node][node_label], \
G[node][pattern[idx+1]][edge_label]) for idx, node in enumerate(pattern[:-1])))
canonlist.append(G.node[pattern[-1]][node_label])
canonkey_t = ''.join(canonlist)
canonkey_t = canonkey_t if canonkey_t < canonkey_t[::-1] else canonkey_t[::-1]
treelet.append(str(i) + canonkey_t)
canonkey_l.update(Counter(treelet))

# n-star patterns
for i in range(3, 6):
treelet = []
for pattern in patterns[str(i) + 'star']:
canonlist = [ G.node[leaf][node_label] + G[leaf][pattern[0]][edge_label] for leaf in pattern[1:] ]
canonlist.sort()
canonkey_t = ('d' if i == 5 else str(i * 2)) + G.node[pattern[0]][node_label] + ''.join(canonlist)
treelet.append(canonkey_t)
canonkey_l.update(Counter(treelet))

# pattern 7
treelet = []
for pattern in patterns['7']:
canonlist = [ G.node[leaf][node_label] + G[leaf][pattern[0]][edge_label] for leaf in pattern[1:3] ]
canonlist.sort()
canonkey_t = '7' + G.node[pattern[0]][node_label] + ''.join(canonlist) \
+ G.node[pattern[3]][node_label] + G[pattern[3]][pattern[0]][edge_label] \
+ G.node[pattern[4]][node_label] + G[pattern[4]][pattern[3]][edge_label]
treelet.append(canonkey_t)
canonkey_l.update(Counter(treelet))

# pattern 11
treelet = []
for pattern in patterns['11']:
canonlist = [ G.node[leaf][node_label] + G[leaf][pattern[0]][edge_label] for leaf in pattern[1:4] ]
canonlist.sort()
canonkey_t = 'b' + G.node[pattern[0]][node_label] + ''.join(canonlist) \
+ G.node[pattern[4]][node_label] + G[pattern[4]][pattern[0]][edge_label] \
+ G.node[pattern[5]][node_label] + G[pattern[5]][pattern[4]][edge_label]
treelet.append(canonkey_t)
canonkey_l.update(Counter(treelet))

# pattern 10
treelet = []
for pattern in patterns['10']:
canonkey4 = G.node[pattern[5]][node_label] + G[pattern[5]][pattern[4]][edge_label]
canonlist = [ G.node[leaf][node_label] + G[leaf][pattern[0]][edge_label] for leaf in pattern[1:3] ]
canonlist.sort()
canonkey0 = ''.join(canonlist)
canonkey_t = 'a' + G.node[pattern[3]][node_label] \
+ G.node[pattern[4]][node_label] + G[pattern[4]][pattern[3]][edge_label] \
+ G.node[pattern[0]][node_label] + G[pattern[0]][pattern[3]][edge_label] \
+ canonkey4 + canonkey0
treelet.append(canonkey_t)
canonkey_l.update(Counter(treelet))

# pattern 12
treelet = []
for pattern in patterns['12']:
canonlist0 = [ G.node[leaf][node_label] + G[leaf][pattern[0]][edge_label] for leaf in pattern[1:3] ]
canonlist0.sort()
canonlist3 = [ G.node[leaf][node_label] + G[leaf][pattern[3]][edge_label] for leaf in pattern[4:6] ]
canonlist3.sort()
# 2 possible key can be generated from 2 nodes with extended label 3, select the one with lower lexicographic order.
canonkey_t1 = 'c' + G.node[pattern[0]][node_label] \
+ ''.join(canonlist0) \
+ G.node[pattern[3]][node_label] + G[pattern[3]][pattern[0]][edge_label] \
+ ''.join(canonlist3)

canonkey_t2 = 'c' + G.node[pattern[3]][node_label] \
+ ''.join(canonlist3) \
+ G.node[pattern[0]][node_label] + G[pattern[0]][pattern[3]][edge_label] \
+ ''.join(canonlist0)

treelet.append(canonkey_t1 if canonkey_t1 < canonkey_t2 else canonkey_t2)
canonkey_l.update(Counter(treelet))

# pattern 9
treelet = []
for pattern in patterns['9']:
canonkey2 = G.node[pattern[4]][node_label] + G[pattern[4]][pattern[2]][edge_label]
canonkey3 = G.node[pattern[5]][node_label] + G[pattern[5]][pattern[3]][edge_label]
prekey2 = G.node[pattern[2]][node_label] + G[pattern[2]][pattern[0]][edge_label]
prekey3 = G.node[pattern[3]][node_label] + G[pattern[3]][pattern[0]][edge_label]
if prekey2 + canonkey2 < prekey3 + canonkey3:
canonkey_t = G.node[pattern[1]][node_label] + G[pattern[1]][pattern[0]][edge_label] \
+ prekey2 + prekey3 + canonkey2 + canonkey3
else:
canonkey_t = G.node[pattern[1]][node_label] + G[pattern[1]][pattern[0]][edge_label] \
+ prekey3 + prekey2 + canonkey3 + canonkey2
treelet.append('9' + G.node[pattern[0]][node_label] + canonkey_t)
canonkey_l.update(Counter(treelet))

return canonkey_l

return canonkey

def find_paths(G, source_node, length):
"""Find all paths with a certain length those start from a source node. A recursive depth first search is applied.
Parameters
----------
G : NetworkX graphs
The graph in which paths are searched.
source_node : integer
The number of the node from where all paths start.
length : integer
The length of paths.
Return
------
path : list of list
List of paths retrieved, where each path is represented by a list of nodes.
"""
if length == 0:
return [[source_node]]
path = [ [source_node] + path for neighbor in G[source_node] \
for path in find_paths(G, neighbor, length - 1) if source_node not in path ]
return path


def find_all_paths(G, length):
"""Find all paths with a certain length in a graph. A recursive depth first search is applied.
Parameters
----------
G : NetworkX graphs
The graph in which paths are searched.
length : integer
The length of paths.
Return
------
path : list of list
List of paths retrieved, where each path is represented by a list of nodes.
"""
all_paths = []
for node in G:
all_paths.extend(find_paths(G, node, length))
all_paths_r = [ path[::-1] for path in all_paths ]
# For each path, two presentation are retrieved from its two extremities. Remove one of them.
for idx, path in enumerate(all_paths[:-1]):
for path2 in all_paths_r[idx+1::]:
if path == path2:
all_paths[idx] = []
break
return list(filter(lambda a: a != [], all_paths))

+ 1
- 0
pygraph/kernels/untilHPathKernel.py View File

@@ -60,6 +60,7 @@ def untilhpathkernel(*args,
# pre-process
depth = int(depth)
Gn = args[0] if len(args) == 1 else [args[0], args[1]]
Gn = [g.copy() for g in Gn]
Kmatrix = np.zeros((len(Gn), len(Gn)))
ds_attrs = get_dataset_attributes(
Gn,


+ 549
- 0
pygraph/kernels/weisfeilerLehmanKernel.py View File

@@ -0,0 +1,549 @@
"""
@author: linlin
@references:
[1] Shervashidze N, Schweitzer P, Leeuwen EJ, Mehlhorn K, Borgwardt KM.
Weisfeiler-lehman graph kernels. Journal of Machine Learning Research.
2011;12(Sep):2539-61.
"""

import sys
from collections import Counter
sys.path.insert(0, "../")
from functools import partial
import time
#from multiprocessing import Pool
from tqdm import tqdm

import networkx as nx
import numpy as np

#from pygraph.kernels.pathKernel import pathkernel
from pygraph.utils.graphdataset import get_dataset_attributes
from pygraph.utils.parallel import parallel_gm

# @todo: support edge kernel, sp kernel, user-defined kernel.
def weisfeilerlehmankernel(*args,
node_label='atom',
edge_label='bond_type',
height=0,
base_kernel='subtree',
parallel=None,
n_jobs=None,
verbose=True):
"""Calculate Weisfeiler-Lehman kernels between graphs.
Parameters
----------
Gn : List of NetworkX graph
List of graphs between which the kernels are calculated.
/
G1, G2 : NetworkX graphs
2 graphs between which the kernel is calculated.
node_label : string
node attribute used as label. The default node label is atom.
edge_label : string
edge attribute used as label. The default edge label is bond_type.
height : int
subtree height
base_kernel : string
base kernel used in each iteration of WL kernel. The default base kernel is subtree kernel. For user-defined kernel, base_kernel is the name of the base kernel function used in each iteration of WL kernel. This function returns a Numpy matrix, each element of which is the user-defined Weisfeiler-Lehman kernel between 2 praphs.

Return
------
Kmatrix : Numpy matrix
Kernel matrix, each element of which is the Weisfeiler-Lehman kernel between 2 praphs.

Notes
-----
This function now supports WL subtree kernel only.
"""
# pre-process
base_kernel = base_kernel.lower()
Gn = args[0] if len(args) == 1 else [args[0], args[1]] # arrange all graphs in a list
Gn = [g.copy() for g in Gn]
ds_attrs = get_dataset_attributes(Gn, attr_names=['node_labeled'],
node_label=node_label)
if not ds_attrs['node_labeled']:
for G in Gn:
nx.set_node_attributes(G, '0', 'atom')

start_time = time.time()

# for WL subtree kernel
if base_kernel == 'subtree':
Kmatrix = _wl_kernel_do(Gn, node_label, edge_label, height, parallel, n_jobs, verbose)

# for WL shortest path kernel
elif base_kernel == 'sp':
Kmatrix = _wl_spkernel_do(Gn, node_label, edge_label, height)

# for WL edge kernel
elif base_kernel == 'edge':
Kmatrix = _wl_edgekernel_do(Gn, node_label, edge_label, height)

# for user defined base kernel
else:
Kmatrix = _wl_userkernel_do(Gn, node_label, edge_label, height, base_kernel)

run_time = time.time() - start_time
if verbose:
print("\n --- Weisfeiler-Lehman %s kernel matrix of size %d built in %s seconds ---"
% (base_kernel, len(args[0]), run_time))

return Kmatrix, run_time


def _wl_kernel_do(Gn, node_label, edge_label, height, parallel, n_jobs, verbose):
"""Calculate Weisfeiler-Lehman kernels between graphs.

Parameters
----------
Gn : List of NetworkX graph
List of graphs between which the kernels are calculated.
node_label : string
node attribute used as label.
edge_label : string
edge attribute used as label.
height : int
wl height.

Return
------
Kmatrix : Numpy matrix
Kernel matrix, each element of which is the Weisfeiler-Lehman kernel between 2 praphs.
"""
height = int(height)
Kmatrix = np.zeros((len(Gn), len(Gn)))

# initial for height = 0
all_num_of_each_label = [] # number of occurence of each label in each graph in this iteration

# for each graph
for G in Gn:
# get the set of original labels
labels_ori = list(nx.get_node_attributes(G, node_label).values())
# number of occurence of each label in G
all_num_of_each_label.append(dict(Counter(labels_ori)))

# calculate subtree kernel with the 0th iteration and add it to the final kernel
compute_kernel_matrix(Kmatrix, all_num_of_each_label, Gn, parallel, n_jobs, False)

# iterate each height
for h in range(1, height + 1):
all_set_compressed = {} # a dictionary mapping original labels to new ones in all graphs in this iteration
num_of_labels_occured = 0 # number of the set of letters that occur before as node labels at least once in all graphs
# all_labels_ori = set() # all unique orignal labels in all graphs in this iteration
all_num_of_each_label = [] # number of occurence of each label in G

# # for each graph
# # ---- use pool.imap_unordered to parallel and track progress. ----
# pool = Pool(n_jobs)
# itr = zip(Gn, range(0, len(Gn)))
# if len(Gn) < 100 * n_jobs:
# chunksize = int(len(Gn) / n_jobs) + 1
# else:
# chunksize = 100
# all_multisets_list = [[] for _ in range(len(Gn))]
## set_unique_list = [[] for _ in range(len(Gn))]
# get_partial = partial(wrapper_wl_iteration, node_label)
## if verbose:
## iterator = tqdm(pool.imap_unordered(get_partial, itr, chunksize),
## desc='wl iteration', file=sys.stdout)
## else:
# iterator = pool.imap_unordered(get_partial, itr, chunksize)
# for i, all_multisets in iterator:
# all_multisets_list[i] = all_multisets
## set_unique_list[i] = set_unique
## all_set_unique = all_set_unique | set(set_unique)
# pool.close()
# pool.join()
# all_set_unique = set()
# for uset in all_multisets_list:
# all_set_unique = all_set_unique | set(uset)
#
# all_set_unique = list(all_set_unique)
## # a dictionary mapping original labels to new ones.
## set_compressed = {}
## for idx, uset in enumerate(all_set_unique):
## set_compressed.update({uset: idx})
#
# for ig, G in enumerate(Gn):
#
## # a dictionary mapping original labels to new ones.
## set_compressed = {}
## # if a label occured before, assign its former compressed label,
## # else assign the number of labels occured + 1 as the compressed label.
## for value in set_unique_list[i]:
## if uset in all_set_unique:
## set_compressed.update({uset: all_set_compressed[value]})
## else:
## set_compressed.update({value: str(num_of_labels_occured + 1)})
## num_of_labels_occured += 1
#
## all_set_compressed.update(set_compressed)
#
# # relabel nodes
# for idx, node in enumerate(G.nodes()):
# G.nodes[node][node_label] = all_set_unique.index(all_multisets_list[ig][idx])
#
# # get the set of compressed labels
# labels_comp = list(nx.get_node_attributes(G, node_label).values())
## all_labels_ori.update(labels_comp)
# all_num_of_each_label[ig] = dict(Counter(labels_comp))

# all_set_unique = list(all_set_unique)
# @todo: parallel this part.
for idx, G in enumerate(Gn):

all_multisets = []
for node, attrs in G.nodes(data=True):
# Multiset-label determination.
multiset = [G.nodes[neighbors][node_label] for neighbors in G[node]]
# sorting each multiset
multiset.sort()
multiset = [attrs[node_label]] + multiset # add the prefix
all_multisets.append(tuple(multiset))

# label compression
set_unique = list(set(all_multisets)) # set of unique multiset labels
# a dictionary mapping original labels to new ones.
set_compressed = {}
# if a label occured before, assign its former compressed label,
# else assign the number of labels occured + 1 as the compressed label.
for value in set_unique:
if value in all_set_compressed.keys():
set_compressed.update({value: all_set_compressed[value]})
else:
set_compressed.update({value: str(num_of_labels_occured + 1)})
num_of_labels_occured += 1

all_set_compressed.update(set_compressed)

# relabel nodes
for idx, node in enumerate(G.nodes()):
G.nodes[node][node_label] = set_compressed[all_multisets[idx]]

# get the set of compressed labels
labels_comp = list(nx.get_node_attributes(G, node_label).values())
# all_labels_ori.update(labels_comp)
all_num_of_each_label.append(dict(Counter(labels_comp)))

# calculate subtree kernel with h iterations and add it to the final kernel
compute_kernel_matrix(Kmatrix, all_num_of_each_label, Gn, parallel, n_jobs, False)

return Kmatrix


def wl_iteration(G, node_label):
all_multisets = []
for node, attrs in G.nodes(data=True):
# Multiset-label determination.
multiset = [G.nodes[neighbors][node_label] for neighbors in G[node]]
# sorting each multiset
multiset.sort()
multiset = [attrs[node_label]] + multiset # add the prefix
all_multisets.append(tuple(multiset))
# # label compression
# set_unique = list(set(all_multisets)) # set of unique multiset labels
return all_multisets
# # a dictionary mapping original labels to new ones.
# set_compressed = {}
# # if a label occured before, assign its former compressed label,
# # else assign the number of labels occured + 1 as the compressed label.
# for value in set_unique:
# if value in all_set_compressed.keys():
# set_compressed.update({value: all_set_compressed[value]})
# else:
# set_compressed.update({value: str(num_of_labels_occured + 1)})
# num_of_labels_occured += 1
#
# all_set_compressed.update(set_compressed)
#
# # relabel nodes
# for idx, node in enumerate(G.nodes()):
# G.nodes[node][node_label] = set_compressed[all_multisets[idx]]
#
# # get the set of compressed labels
# labels_comp = list(nx.get_node_attributes(G, node_label).values())
# all_labels_ori.update(labels_comp)
# all_num_of_each_label.append(dict(Counter(labels_comp)))
# return


def wrapper_wl_iteration(node_label, itr_item):
g = itr_item[0]
i = itr_item[1]
all_multisets = wl_iteration(g, node_label)
return i, all_multisets


def compute_kernel_matrix(Kmatrix, all_num_of_each_label, Gn, parallel, n_jobs, verbose):
"""Compute kernel matrix using the base kernel.
"""
if parallel == 'imap_unordered':
# compute kernels.
def init_worker(alllabels_toshare):
global G_alllabels
G_alllabels = alllabels_toshare
do_partial = partial(wrapper_compute_subtree_kernel, Kmatrix)
parallel_gm(do_partial, Kmatrix, Gn, init_worker=init_worker,
glbv=(all_num_of_each_label,), n_jobs=n_jobs, verbose=verbose)
elif parallel == None:
for i in range(len(Kmatrix)):
for j in range(i, len(Kmatrix)):
Kmatrix[i][j] = compute_subtree_kernel(all_num_of_each_label[i],
all_num_of_each_label[j], Kmatrix[i][j])
Kmatrix[j][i] = Kmatrix[i][j]


def compute_subtree_kernel(num_of_each_label1, num_of_each_label2, kernel):
"""Compute the subtree kernel.
"""
labels = set(list(num_of_each_label1.keys()) + list(num_of_each_label2.keys()))
vector1 = np.array([(num_of_each_label1[label]
if (label in num_of_each_label1.keys()) else 0)
for label in labels])
vector2 = np.array([(num_of_each_label2[label]
if (label in num_of_each_label2.keys()) else 0)
for label in labels])
kernel += np.dot(vector1, vector2)
return kernel


def wrapper_compute_subtree_kernel(Kmatrix, itr):
i = itr[0]
j = itr[1]
return i, j, compute_subtree_kernel(G_alllabels[i], G_alllabels[j], Kmatrix[i][j])

def _wl_spkernel_do(Gn, node_label, edge_label, height):
"""Calculate Weisfeiler-Lehman shortest path kernels between graphs.
Parameters
----------
Gn : List of NetworkX graph
List of graphs between which the kernels are calculated.
node_label : string
node attribute used as label.
edge_label : string
edge attribute used as label.
height : int
subtree height.
Return
------
Kmatrix : Numpy matrix
Kernel matrix, each element of which is the Weisfeiler-Lehman kernel between 2 praphs.
"""
pass
from pygraph.utils.utils import getSPGraph
# init.
height = int(height)
Kmatrix = np.zeros((len(Gn), len(Gn))) # init kernel

Gn = [ getSPGraph(G, edge_weight = edge_label) for G in Gn ] # get shortest path graphs of Gn
# initial for height = 0
for i in range(0, len(Gn)):
for j in range(i, len(Gn)):
for e1 in Gn[i].edges(data = True):
for e2 in Gn[j].edges(data = True):
if e1[2]['cost'] != 0 and e1[2]['cost'] == e2[2]['cost'] and ((e1[0] == e2[0] and e1[1] == e2[1]) or (e1[0] == e2[1] and e1[1] == e2[0])):
Kmatrix[i][j] += 1
Kmatrix[j][i] = Kmatrix[i][j]
# iterate each height
for h in range(1, height + 1):
all_set_compressed = {} # a dictionary mapping original labels to new ones in all graphs in this iteration
num_of_labels_occured = 0 # number of the set of letters that occur before as node labels at least once in all graphs
for G in Gn: # for each graph
set_multisets = []
for node in G.nodes(data = True):
# Multiset-label determination.
multiset = [ G.node[neighbors][node_label] for neighbors in G[node[0]] ]
# sorting each multiset
multiset.sort()
multiset = node[1][node_label] + ''.join(multiset) # concatenate to a string and add the prefix
set_multisets.append(multiset)

# label compression
set_unique = list(set(set_multisets)) # set of unique multiset labels
# a dictionary mapping original labels to new ones.
set_compressed = {}
# if a label occured before, assign its former compressed label, else assign the number of labels occured + 1 as the compressed label
for value in set_unique:
if value in all_set_compressed.keys():
set_compressed.update({ value : all_set_compressed[value] })
else:
set_compressed.update({ value : str(num_of_labels_occured + 1) })
num_of_labels_occured += 1

all_set_compressed.update(set_compressed)
# relabel nodes
for node in G.nodes(data = True):
node[1][node_label] = set_compressed[set_multisets[node[0]]]
# calculate subtree kernel with h iterations and add it to the final kernel
for i in range(0, len(Gn)):
for j in range(i, len(Gn)):
for e1 in Gn[i].edges(data = True):
for e2 in Gn[j].edges(data = True):
if e1[2]['cost'] != 0 and e1[2]['cost'] == e2[2]['cost'] and ((e1[0] == e2[0] and e1[1] == e2[1]) or (e1[0] == e2[1] and e1[1] == e2[0])):
Kmatrix[i][j] += 1
Kmatrix[j][i] = Kmatrix[i][j]
return Kmatrix



def _wl_edgekernel_do(Gn, node_label, edge_label, height):
"""Calculate Weisfeiler-Lehman edge kernels between graphs.
Parameters
----------
Gn : List of NetworkX graph
List of graphs between which the kernels are calculated.
node_label : string
node attribute used as label.
edge_label : string
edge attribute used as label.
height : int
subtree height.
Return
------
Kmatrix : Numpy matrix
Kernel matrix, each element of which is the Weisfeiler-Lehman kernel between 2 praphs.
"""
pass
# init.
height = int(height)
Kmatrix = np.zeros((len(Gn), len(Gn))) # init kernel
# initial for height = 0
for i in range(0, len(Gn)):
for j in range(i, len(Gn)):
for e1 in Gn[i].edges(data = True):
for e2 in Gn[j].edges(data = True):
if e1[2][edge_label] == e2[2][edge_label] and ((e1[0] == e2[0] and e1[1] == e2[1]) or (e1[0] == e2[1] and e1[1] == e2[0])):
Kmatrix[i][j] += 1
Kmatrix[j][i] = Kmatrix[i][j]
# iterate each height
for h in range(1, height + 1):
all_set_compressed = {} # a dictionary mapping original labels to new ones in all graphs in this iteration
num_of_labels_occured = 0 # number of the set of letters that occur before as node labels at least once in all graphs
for G in Gn: # for each graph
set_multisets = []
for node in G.nodes(data = True):
# Multiset-label determination.
multiset = [ G.node[neighbors][node_label] for neighbors in G[node[0]] ]
# sorting each multiset
multiset.sort()
multiset = node[1][node_label] + ''.join(multiset) # concatenate to a string and add the prefix
set_multisets.append(multiset)

# label compression
set_unique = list(set(set_multisets)) # set of unique multiset labels
# a dictionary mapping original labels to new ones.
set_compressed = {}
# if a label occured before, assign its former compressed label, else assign the number of labels occured + 1 as the compressed label
for value in set_unique:
if value in all_set_compressed.keys():
set_compressed.update({ value : all_set_compressed[value] })
else:
set_compressed.update({ value : str(num_of_labels_occured + 1) })
num_of_labels_occured += 1

all_set_compressed.update(set_compressed)
# relabel nodes
for node in G.nodes(data = True):
node[1][node_label] = set_compressed[set_multisets[node[0]]]
# calculate subtree kernel with h iterations and add it to the final kernel
for i in range(0, len(Gn)):
for j in range(i, len(Gn)):
for e1 in Gn[i].edges(data = True):
for e2 in Gn[j].edges(data = True):
if e1[2][edge_label] == e2[2][edge_label] and ((e1[0] == e2[0] and e1[1] == e2[1]) or (e1[0] == e2[1] and e1[1] == e2[0])):
Kmatrix[i][j] += 1
Kmatrix[j][i] = Kmatrix[i][j]
return Kmatrix


def _wl_userkernel_do(Gn, node_label, edge_label, height, base_kernel):
"""Calculate Weisfeiler-Lehman kernels based on user-defined kernel between graphs.
Parameters
----------
Gn : List of NetworkX graph
List of graphs between which the kernels are calculated.
node_label : string
node attribute used as label.
edge_label : string
edge attribute used as label.
height : int
subtree height.
base_kernel : string
Name of the base kernel function used in each iteration of WL kernel. This function returns a Numpy matrix, each element of which is the user-defined Weisfeiler-Lehman kernel between 2 praphs.
Return
------
Kmatrix : Numpy matrix
Kernel matrix, each element of which is the Weisfeiler-Lehman kernel between 2 praphs.
"""
pass
# init.
height = int(height)
Kmatrix = np.zeros((len(Gn), len(Gn))) # init kernel
# initial for height = 0
Kmatrix = base_kernel(Gn, node_label, edge_label)
# iterate each height
for h in range(1, height + 1):
all_set_compressed = {} # a dictionary mapping original labels to new ones in all graphs in this iteration
num_of_labels_occured = 0 # number of the set of letters that occur before as node labels at least once in all graphs
for G in Gn: # for each graph
set_multisets = []
for node in G.nodes(data = True):
# Multiset-label determination.
multiset = [ G.node[neighbors][node_label] for neighbors in G[node[0]] ]
# sorting each multiset
multiset.sort()
multiset = node[1][node_label] + ''.join(multiset) # concatenate to a string and add the prefix
set_multisets.append(multiset)

# label compression
set_unique = list(set(set_multisets)) # set of unique multiset labels
# a dictionary mapping original labels to new ones.
set_compressed = {}
# if a label occured before, assign its former compressed label, else assign the number of labels occured + 1 as the compressed label
for value in set_unique:
if value in all_set_compressed.keys():
set_compressed.update({ value : all_set_compressed[value] })
else:
set_compressed.update({ value : str(num_of_labels_occured + 1) })
num_of_labels_occured += 1

all_set_compressed.update(set_compressed)
# relabel nodes
for node in G.nodes(data = True):
node[1][node_label] = set_compressed[set_multisets[node[0]]]
# calculate kernel with h iterations and add it to the final kernel
Kmatrix += base_kernel(Gn, node_label, edge_label)
return Kmatrix

+ 22
- 1
pygraph/utils/kernels.py View File

@@ -61,7 +61,7 @@ def polynomialkernel(x, y, d=1, c=0):
"""Polynomial kernel.
Compute the polynomial kernel between x and y:

K(x, y) = (x^Ty)^d + c.
K(x, y) = <x, y> ^d + c.

Parameters
----------
@@ -78,6 +78,27 @@ def polynomialkernel(x, y, d=1, c=0):
return np.dot(x, y) ** d + c


def linearkernel(x, y):
"""Polynomial kernel.
Compute the polynomial kernel between x and y:

K(x, y) = <x, y>.

Parameters
----------
x, y : array

d : integer, default 1
c : float, default 0

Returns
-------
kernel : float
"""
return np.dot(x, y)


def kernelsum(k1, k2, d11, d12, d21=None, d22=None, lamda1=1, lamda2=1):
"""Sum of a pair of kernels.



+ 19
- 1
pygraph/utils/utils.py View File

@@ -241,4 +241,22 @@ def graph_isIdentical(G1, G2):
return False
# check graph attributes.
return True
return True


def get_node_labels(Gn, node_label):
"""Get node labels of dataset Gn.
"""
nl = set()
for G in Gn:
nl = nl | set(nx.get_node_attributes(G, node_label).values())
return nl


def get_edge_labels(Gn, edge_label):
"""Get edge labels of dataset Gn.
"""
el = set()
for G in Gn:
el = el | set(nx.get_edge_attributes(G, edge_label).values())
return el

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