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- import sys
- import pathlib
- sys.path.insert(0, "../")
-
-
- import networkx as nx
- import numpy as np
- import time
-
- from pygraph.utils.utils import getSPGraph
-
-
- def spkernel(*args, edge_weight = 'bond_type'):
- """Calculate shortest-path 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.
- edge_weight : string
- edge attribute corresponding to the edge weight. The default edge weight is bond_type.
-
- Return
- ------
- Kmatrix/Kernel : Numpy matrix/int
- Kernel matrix, each element of which is the sp kernel between 2 praphs. / SP Kernel between 2 graphs.
-
- References
- ----------
- [1] Borgwardt KM, Kriegel HP. Shortest-path kernels on graphs. InData Mining, Fifth IEEE International Conference on 2005 Nov 27 (pp. 8-pp). IEEE.
- """
- if len(args) == 1: # for a list of graphs
- Gn = args[0]
-
- Kmatrix = np.zeros((len(Gn), len(Gn)))
-
- Sn = [] # get shortest path graphs of Gn
- for i in range(0, len(Gn)):
- Sn.append(getSPGraph(Gn[i], edge_weight = edge_weight))
-
- start_time = time.time()
- for i in range(0, len(Gn)):
- for j in range(i, len(Gn)):
- for e1 in Sn[i].edges(data = True):
- for e2 in Sn[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] += (0 if i == j else 1)
-
- run_time = time.time() - start_time
- print("--- shortest path kernel matrix of size %d built in %s seconds ---" % (len(Gn), run_time))
-
- return Kmatrix, run_time
-
- else: # for only 2 graphs
- G1 = getSPGraph(args[0], edge_weight = edge_weight)
- G2 = getSPGraph(args[1], edge_weight = edge_weight)
-
- kernel = 0
-
- start_time = time.time()
- for e1 in G1.edges(data = True):
- for e2 in G2.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])):
- kernel += 1
-
- # print("--- shortest path kernel built in %s seconds ---" % (time.time() - start_time))
-
- return kernel
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