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|
""" Functions measuring similarity using graph edit distance.
|
|
|
|
|
|
The graph edit distance is the number of edge/node changes needed
|
|
|
to make two graphs isomorphic.
|
|
|
|
|
|
The default algorithm/implementation is sub-optimal for some graphs.
|
|
|
The problem of finding the exact Graph Edit Distance (GED) is NP-hard
|
|
|
so it is often slow. If the simple interface `graph_edit_distance`
|
|
|
takes too long for your graph, try `optimize_graph_edit_distance`
|
|
|
and/or `optimize_edit_paths`.
|
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|
|
|
|
At the same time, I encourage capable people to investigate
|
|
|
alternative GED algorithms, in order to improve the choices available.
|
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|
"""
|
|
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|
|
|
import math
|
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|
import time
|
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|
import warnings
|
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|
from dataclasses import dataclass
|
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|
from itertools import product
|
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|
import networkx as nx
|
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|
from networkx.utils import np_random_state
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|
__all__ = [
|
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|
"graph_edit_distance",
|
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|
"optimal_edit_paths",
|
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|
"optimize_graph_edit_distance",
|
|
|
"optimize_edit_paths",
|
|
|
"simrank_similarity",
|
|
|
"panther_similarity",
|
|
|
"generate_random_paths",
|
|
|
]
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|
|
def debug_print(*args, **kwargs):
|
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|
print(*args, **kwargs)
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|
@nx._dispatchable(
|
|
|
graphs={"G1": 0, "G2": 1}, preserve_edge_attrs=True, preserve_node_attrs=True
|
|
|
)
|
|
|
def graph_edit_distance(
|
|
|
G1,
|
|
|
G2,
|
|
|
node_match=None,
|
|
|
edge_match=None,
|
|
|
node_subst_cost=None,
|
|
|
node_del_cost=None,
|
|
|
node_ins_cost=None,
|
|
|
edge_subst_cost=None,
|
|
|
edge_del_cost=None,
|
|
|
edge_ins_cost=None,
|
|
|
roots=None,
|
|
|
upper_bound=None,
|
|
|
timeout=None,
|
|
|
):
|
|
|
"""Returns GED (graph edit distance) between graphs G1 and G2.
|
|
|
|
|
|
Graph edit distance is a graph similarity measure analogous to
|
|
|
Levenshtein distance for strings. It is defined as minimum cost
|
|
|
of edit path (sequence of node and edge edit operations)
|
|
|
transforming graph G1 to graph isomorphic to G2.
|
|
|
|
|
|
Parameters
|
|
|
----------
|
|
|
G1, G2: graphs
|
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|
The two graphs G1 and G2 must be of the same type.
|
|
|
|
|
|
node_match : callable
|
|
|
A function that returns True if node n1 in G1 and n2 in G2
|
|
|
should be considered equal during matching.
|
|
|
|
|
|
The function will be called like
|
|
|
|
|
|
node_match(G1.nodes[n1], G2.nodes[n2]).
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|
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|
|
That is, the function will receive the node attribute
|
|
|
dictionaries for n1 and n2 as inputs.
|
|
|
|
|
|
Ignored if node_subst_cost is specified. If neither
|
|
|
node_match nor node_subst_cost are specified then node
|
|
|
attributes are not considered.
|
|
|
|
|
|
edge_match : callable
|
|
|
A function that returns True if the edge attribute dictionaries
|
|
|
for the pair of nodes (u1, v1) in G1 and (u2, v2) in G2 should
|
|
|
be considered equal during matching.
|
|
|
|
|
|
The function will be called like
|
|
|
|
|
|
edge_match(G1[u1][v1], G2[u2][v2]).
|
|
|
|
|
|
That is, the function will receive the edge attribute
|
|
|
dictionaries of the edges under consideration.
|
|
|
|
|
|
Ignored if edge_subst_cost is specified. If neither
|
|
|
edge_match nor edge_subst_cost are specified then edge
|
|
|
attributes are not considered.
|
|
|
|
|
|
node_subst_cost, node_del_cost, node_ins_cost : callable
|
|
|
Functions that return the costs of node substitution, node
|
|
|
deletion, and node insertion, respectively.
|
|
|
|
|
|
The functions will be called like
|
|
|
|
|
|
node_subst_cost(G1.nodes[n1], G2.nodes[n2]),
|
|
|
node_del_cost(G1.nodes[n1]),
|
|
|
node_ins_cost(G2.nodes[n2]).
|
|
|
|
|
|
That is, the functions will receive the node attribute
|
|
|
dictionaries as inputs. The functions are expected to return
|
|
|
positive numeric values.
|
|
|
|
|
|
Function node_subst_cost overrides node_match if specified.
|
|
|
If neither node_match nor node_subst_cost are specified then
|
|
|
default node substitution cost of 0 is used (node attributes
|
|
|
are not considered during matching).
|
|
|
|
|
|
If node_del_cost is not specified then default node deletion
|
|
|
cost of 1 is used. If node_ins_cost is not specified then
|
|
|
default node insertion cost of 1 is used.
|
|
|
|
|
|
edge_subst_cost, edge_del_cost, edge_ins_cost : callable
|
|
|
Functions that return the costs of edge substitution, edge
|
|
|
deletion, and edge insertion, respectively.
|
|
|
|
|
|
The functions will be called like
|
|
|
|
|
|
edge_subst_cost(G1[u1][v1], G2[u2][v2]),
|
|
|
edge_del_cost(G1[u1][v1]),
|
|
|
edge_ins_cost(G2[u2][v2]).
|
|
|
|
|
|
That is, the functions will receive the edge attribute
|
|
|
dictionaries as inputs. The functions are expected to return
|
|
|
positive numeric values.
|
|
|
|
|
|
Function edge_subst_cost overrides edge_match if specified.
|
|
|
If neither edge_match nor edge_subst_cost are specified then
|
|
|
default edge substitution cost of 0 is used (edge attributes
|
|
|
are not considered during matching).
|
|
|
|
|
|
If edge_del_cost is not specified then default edge deletion
|
|
|
cost of 1 is used. If edge_ins_cost is not specified then
|
|
|
default edge insertion cost of 1 is used.
|
|
|
|
|
|
roots : 2-tuple
|
|
|
Tuple where first element is a node in G1 and the second
|
|
|
is a node in G2.
|
|
|
These nodes are forced to be matched in the comparison to
|
|
|
allow comparison between rooted graphs.
|
|
|
|
|
|
upper_bound : numeric
|
|
|
Maximum edit distance to consider. Return None if no edit
|
|
|
distance under or equal to upper_bound exists.
|
|
|
|
|
|
timeout : numeric
|
|
|
Maximum number of seconds to execute.
|
|
|
After timeout is met, the current best GED is returned.
|
|
|
|
|
|
Examples
|
|
|
--------
|
|
|
>>> G1 = nx.cycle_graph(6)
|
|
|
>>> G2 = nx.wheel_graph(7)
|
|
|
>>> nx.graph_edit_distance(G1, G2)
|
|
|
7.0
|
|
|
|
|
|
>>> G1 = nx.star_graph(5)
|
|
|
>>> G2 = nx.star_graph(5)
|
|
|
>>> nx.graph_edit_distance(G1, G2, roots=(0, 0))
|
|
|
0.0
|
|
|
>>> nx.graph_edit_distance(G1, G2, roots=(1, 0))
|
|
|
8.0
|
|
|
|
|
|
See Also
|
|
|
--------
|
|
|
optimal_edit_paths, optimize_graph_edit_distance,
|
|
|
|
|
|
is_isomorphic: test for graph edit distance of 0
|
|
|
|
|
|
References
|
|
|
----------
|
|
|
.. [1] Zeina Abu-Aisheh, Romain Raveaux, Jean-Yves Ramel, Patrick
|
|
|
Martineau. An Exact Graph Edit Distance Algorithm for Solving
|
|
|
Pattern Recognition Problems. 4th International Conference on
|
|
|
Pattern Recognition Applications and Methods 2015, Jan 2015,
|
|
|
Lisbon, Portugal. 2015,
|
|
|
<10.5220/0005209202710278>. <hal-01168816>
|
|
|
https://hal.archives-ouvertes.fr/hal-01168816
|
|
|
|
|
|
"""
|
|
|
bestcost = None
|
|
|
for _, _, cost in optimize_edit_paths(
|
|
|
G1,
|
|
|
G2,
|
|
|
node_match,
|
|
|
edge_match,
|
|
|
node_subst_cost,
|
|
|
node_del_cost,
|
|
|
node_ins_cost,
|
|
|
edge_subst_cost,
|
|
|
edge_del_cost,
|
|
|
edge_ins_cost,
|
|
|
upper_bound,
|
|
|
True,
|
|
|
roots,
|
|
|
timeout,
|
|
|
):
|
|
|
# assert bestcost is None or cost < bestcost
|
|
|
bestcost = cost
|
|
|
return bestcost
|
|
|
|
|
|
|
|
|
@nx._dispatchable(graphs={"G1": 0, "G2": 1})
|
|
|
def optimal_edit_paths(
|
|
|
G1,
|
|
|
G2,
|
|
|
node_match=None,
|
|
|
edge_match=None,
|
|
|
node_subst_cost=None,
|
|
|
node_del_cost=None,
|
|
|
node_ins_cost=None,
|
|
|
edge_subst_cost=None,
|
|
|
edge_del_cost=None,
|
|
|
edge_ins_cost=None,
|
|
|
upper_bound=None,
|
|
|
):
|
|
|
"""Returns all minimum-cost edit paths transforming G1 to G2.
|
|
|
|
|
|
Graph edit path is a sequence of node and edge edit operations
|
|
|
transforming graph G1 to graph isomorphic to G2. Edit operations
|
|
|
include substitutions, deletions, and insertions.
|
|
|
|
|
|
Parameters
|
|
|
----------
|
|
|
G1, G2: graphs
|
|
|
The two graphs G1 and G2 must be of the same type.
|
|
|
|
|
|
node_match : callable
|
|
|
A function that returns True if node n1 in G1 and n2 in G2
|
|
|
should be considered equal during matching.
|
|
|
|
|
|
The function will be called like
|
|
|
|
|
|
node_match(G1.nodes[n1], G2.nodes[n2]).
|
|
|
|
|
|
That is, the function will receive the node attribute
|
|
|
dictionaries for n1 and n2 as inputs.
|
|
|
|
|
|
Ignored if node_subst_cost is specified. If neither
|
|
|
node_match nor node_subst_cost are specified then node
|
|
|
attributes are not considered.
|
|
|
|
|
|
edge_match : callable
|
|
|
A function that returns True if the edge attribute dictionaries
|
|
|
for the pair of nodes (u1, v1) in G1 and (u2, v2) in G2 should
|
|
|
be considered equal during matching.
|
|
|
|
|
|
The function will be called like
|
|
|
|
|
|
edge_match(G1[u1][v1], G2[u2][v2]).
|
|
|
|
|
|
That is, the function will receive the edge attribute
|
|
|
dictionaries of the edges under consideration.
|
|
|
|
|
|
Ignored if edge_subst_cost is specified. If neither
|
|
|
edge_match nor edge_subst_cost are specified then edge
|
|
|
attributes are not considered.
|
|
|
|
|
|
node_subst_cost, node_del_cost, node_ins_cost : callable
|
|
|
Functions that return the costs of node substitution, node
|
|
|
deletion, and node insertion, respectively.
|
|
|
|
|
|
The functions will be called like
|
|
|
|
|
|
node_subst_cost(G1.nodes[n1], G2.nodes[n2]),
|
|
|
node_del_cost(G1.nodes[n1]),
|
|
|
node_ins_cost(G2.nodes[n2]).
|
|
|
|
|
|
That is, the functions will receive the node attribute
|
|
|
dictionaries as inputs. The functions are expected to return
|
|
|
positive numeric values.
|
|
|
|
|
|
Function node_subst_cost overrides node_match if specified.
|
|
|
If neither node_match nor node_subst_cost are specified then
|
|
|
default node substitution cost of 0 is used (node attributes
|
|
|
are not considered during matching).
|
|
|
|
|
|
If node_del_cost is not specified then default node deletion
|
|
|
cost of 1 is used. If node_ins_cost is not specified then
|
|
|
default node insertion cost of 1 is used.
|
|
|
|
|
|
edge_subst_cost, edge_del_cost, edge_ins_cost : callable
|
|
|
Functions that return the costs of edge substitution, edge
|
|
|
deletion, and edge insertion, respectively.
|
|
|
|
|
|
The functions will be called like
|
|
|
|
|
|
edge_subst_cost(G1[u1][v1], G2[u2][v2]),
|
|
|
edge_del_cost(G1[u1][v1]),
|
|
|
edge_ins_cost(G2[u2][v2]).
|
|
|
|
|
|
That is, the functions will receive the edge attribute
|
|
|
dictionaries as inputs. The functions are expected to return
|
|
|
positive numeric values.
|
|
|
|
|
|
Function edge_subst_cost overrides edge_match if specified.
|
|
|
If neither edge_match nor edge_subst_cost are specified then
|
|
|
default edge substitution cost of 0 is used (edge attributes
|
|
|
are not considered during matching).
|
|
|
|
|
|
If edge_del_cost is not specified then default edge deletion
|
|
|
cost of 1 is used. If edge_ins_cost is not specified then
|
|
|
default edge insertion cost of 1 is used.
|
|
|
|
|
|
upper_bound : numeric
|
|
|
Maximum edit distance to consider.
|
|
|
|
|
|
Returns
|
|
|
-------
|
|
|
edit_paths : list of tuples (node_edit_path, edge_edit_path)
|
|
|
node_edit_path : list of tuples (u, v)
|
|
|
edge_edit_path : list of tuples ((u1, v1), (u2, v2))
|
|
|
|
|
|
cost : numeric
|
|
|
Optimal edit path cost (graph edit distance). When the cost
|
|
|
is zero, it indicates that `G1` and `G2` are isomorphic.
|
|
|
|
|
|
Examples
|
|
|
--------
|
|
|
>>> G1 = nx.cycle_graph(4)
|
|
|
>>> G2 = nx.wheel_graph(5)
|
|
|
>>> paths, cost = nx.optimal_edit_paths(G1, G2)
|
|
|
>>> len(paths)
|
|
|
40
|
|
|
>>> cost
|
|
|
5.0
|
|
|
|
|
|
Notes
|
|
|
-----
|
|
|
To transform `G1` into a graph isomorphic to `G2`, apply the node
|
|
|
and edge edits in the returned ``edit_paths``.
|
|
|
In the case of isomorphic graphs, the cost is zero, and the paths
|
|
|
represent different isomorphic mappings (isomorphisms). That is, the
|
|
|
edits involve renaming nodes and edges to match the structure of `G2`.
|
|
|
|
|
|
See Also
|
|
|
--------
|
|
|
graph_edit_distance, optimize_edit_paths
|
|
|
|
|
|
References
|
|
|
----------
|
|
|
.. [1] Zeina Abu-Aisheh, Romain Raveaux, Jean-Yves Ramel, Patrick
|
|
|
Martineau. An Exact Graph Edit Distance Algorithm for Solving
|
|
|
Pattern Recognition Problems. 4th International Conference on
|
|
|
Pattern Recognition Applications and Methods 2015, Jan 2015,
|
|
|
Lisbon, Portugal. 2015,
|
|
|
<10.5220/0005209202710278>. <hal-01168816>
|
|
|
https://hal.archives-ouvertes.fr/hal-01168816
|
|
|
|
|
|
"""
|
|
|
paths = []
|
|
|
bestcost = None
|
|
|
for vertex_path, edge_path, cost in optimize_edit_paths(
|
|
|
G1,
|
|
|
G2,
|
|
|
node_match,
|
|
|
edge_match,
|
|
|
node_subst_cost,
|
|
|
node_del_cost,
|
|
|
node_ins_cost,
|
|
|
edge_subst_cost,
|
|
|
edge_del_cost,
|
|
|
edge_ins_cost,
|
|
|
upper_bound,
|
|
|
False,
|
|
|
):
|
|
|
# assert bestcost is None or cost <= bestcost
|
|
|
if bestcost is not None and cost < bestcost:
|
|
|
paths = []
|
|
|
paths.append((vertex_path, edge_path))
|
|
|
bestcost = cost
|
|
|
return paths, bestcost
|
|
|
|
|
|
|
|
|
@nx._dispatchable(graphs={"G1": 0, "G2": 1})
|
|
|
def optimize_graph_edit_distance(
|
|
|
G1,
|
|
|
G2,
|
|
|
node_match=None,
|
|
|
edge_match=None,
|
|
|
node_subst_cost=None,
|
|
|
node_del_cost=None,
|
|
|
node_ins_cost=None,
|
|
|
edge_subst_cost=None,
|
|
|
edge_del_cost=None,
|
|
|
edge_ins_cost=None,
|
|
|
upper_bound=None,
|
|
|
):
|
|
|
"""Returns consecutive approximations of GED (graph edit distance)
|
|
|
between graphs G1 and G2.
|
|
|
|
|
|
Graph edit distance is a graph similarity measure analogous to
|
|
|
Levenshtein distance for strings. It is defined as minimum cost
|
|
|
of edit path (sequence of node and edge edit operations)
|
|
|
transforming graph G1 to graph isomorphic to G2.
|
|
|
|
|
|
Parameters
|
|
|
----------
|
|
|
G1, G2: graphs
|
|
|
The two graphs G1 and G2 must be of the same type.
|
|
|
|
|
|
node_match : callable
|
|
|
A function that returns True if node n1 in G1 and n2 in G2
|
|
|
should be considered equal during matching.
|
|
|
|
|
|
The function will be called like
|
|
|
|
|
|
node_match(G1.nodes[n1], G2.nodes[n2]).
|
|
|
|
|
|
That is, the function will receive the node attribute
|
|
|
dictionaries for n1 and n2 as inputs.
|
|
|
|
|
|
Ignored if node_subst_cost is specified. If neither
|
|
|
node_match nor node_subst_cost are specified then node
|
|
|
attributes are not considered.
|
|
|
|
|
|
edge_match : callable
|
|
|
A function that returns True if the edge attribute dictionaries
|
|
|
for the pair of nodes (u1, v1) in G1 and (u2, v2) in G2 should
|
|
|
be considered equal during matching.
|
|
|
|
|
|
The function will be called like
|
|
|
|
|
|
edge_match(G1[u1][v1], G2[u2][v2]).
|
|
|
|
|
|
That is, the function will receive the edge attribute
|
|
|
dictionaries of the edges under consideration.
|
|
|
|
|
|
Ignored if edge_subst_cost is specified. If neither
|
|
|
edge_match nor edge_subst_cost are specified then edge
|
|
|
attributes are not considered.
|
|
|
|
|
|
node_subst_cost, node_del_cost, node_ins_cost : callable
|
|
|
Functions that return the costs of node substitution, node
|
|
|
deletion, and node insertion, respectively.
|
|
|
|
|
|
The functions will be called like
|
|
|
|
|
|
node_subst_cost(G1.nodes[n1], G2.nodes[n2]),
|
|
|
node_del_cost(G1.nodes[n1]),
|
|
|
node_ins_cost(G2.nodes[n2]).
|
|
|
|
|
|
That is, the functions will receive the node attribute
|
|
|
dictionaries as inputs. The functions are expected to return
|
|
|
positive numeric values.
|
|
|
|
|
|
Function node_subst_cost overrides node_match if specified.
|
|
|
If neither node_match nor node_subst_cost are specified then
|
|
|
default node substitution cost of 0 is used (node attributes
|
|
|
are not considered during matching).
|
|
|
|
|
|
If node_del_cost is not specified then default node deletion
|
|
|
cost of 1 is used. If node_ins_cost is not specified then
|
|
|
default node insertion cost of 1 is used.
|
|
|
|
|
|
edge_subst_cost, edge_del_cost, edge_ins_cost : callable
|
|
|
Functions that return the costs of edge substitution, edge
|
|
|
deletion, and edge insertion, respectively.
|
|
|
|
|
|
The functions will be called like
|
|
|
|
|
|
edge_subst_cost(G1[u1][v1], G2[u2][v2]),
|
|
|
edge_del_cost(G1[u1][v1]),
|
|
|
edge_ins_cost(G2[u2][v2]).
|
|
|
|
|
|
That is, the functions will receive the edge attribute
|
|
|
dictionaries as inputs. The functions are expected to return
|
|
|
positive numeric values.
|
|
|
|
|
|
Function edge_subst_cost overrides edge_match if specified.
|
|
|
If neither edge_match nor edge_subst_cost are specified then
|
|
|
default edge substitution cost of 0 is used (edge attributes
|
|
|
are not considered during matching).
|
|
|
|
|
|
If edge_del_cost is not specified then default edge deletion
|
|
|
cost of 1 is used. If edge_ins_cost is not specified then
|
|
|
default edge insertion cost of 1 is used.
|
|
|
|
|
|
upper_bound : numeric
|
|
|
Maximum edit distance to consider.
|
|
|
|
|
|
Returns
|
|
|
-------
|
|
|
Generator of consecutive approximations of graph edit distance.
|
|
|
|
|
|
Examples
|
|
|
--------
|
|
|
>>> G1 = nx.cycle_graph(6)
|
|
|
>>> G2 = nx.wheel_graph(7)
|
|
|
>>> for v in nx.optimize_graph_edit_distance(G1, G2):
|
|
|
... minv = v
|
|
|
>>> minv
|
|
|
7.0
|
|
|
|
|
|
See Also
|
|
|
--------
|
|
|
graph_edit_distance, optimize_edit_paths
|
|
|
|
|
|
References
|
|
|
----------
|
|
|
.. [1] Zeina Abu-Aisheh, Romain Raveaux, Jean-Yves Ramel, Patrick
|
|
|
Martineau. An Exact Graph Edit Distance Algorithm for Solving
|
|
|
Pattern Recognition Problems. 4th International Conference on
|
|
|
Pattern Recognition Applications and Methods 2015, Jan 2015,
|
|
|
Lisbon, Portugal. 2015,
|
|
|
<10.5220/0005209202710278>. <hal-01168816>
|
|
|
https://hal.archives-ouvertes.fr/hal-01168816
|
|
|
"""
|
|
|
for _, _, cost in optimize_edit_paths(
|
|
|
G1,
|
|
|
G2,
|
|
|
node_match,
|
|
|
edge_match,
|
|
|
node_subst_cost,
|
|
|
node_del_cost,
|
|
|
node_ins_cost,
|
|
|
edge_subst_cost,
|
|
|
edge_del_cost,
|
|
|
edge_ins_cost,
|
|
|
upper_bound,
|
|
|
True,
|
|
|
):
|
|
|
yield cost
|
|
|
|
|
|
|
|
|
@nx._dispatchable(
|
|
|
graphs={"G1": 0, "G2": 1}, preserve_edge_attrs=True, preserve_node_attrs=True
|
|
|
)
|
|
|
def optimize_edit_paths(
|
|
|
G1,
|
|
|
G2,
|
|
|
node_match=None,
|
|
|
edge_match=None,
|
|
|
node_subst_cost=None,
|
|
|
node_del_cost=None,
|
|
|
node_ins_cost=None,
|
|
|
edge_subst_cost=None,
|
|
|
edge_del_cost=None,
|
|
|
edge_ins_cost=None,
|
|
|
upper_bound=None,
|
|
|
strictly_decreasing=True,
|
|
|
roots=None,
|
|
|
timeout=None,
|
|
|
):
|
|
|
"""GED (graph edit distance) calculation: advanced interface.
|
|
|
|
|
|
Graph edit path is a sequence of node and edge edit operations
|
|
|
transforming graph G1 to graph isomorphic to G2. Edit operations
|
|
|
include substitutions, deletions, and insertions.
|
|
|
|
|
|
Graph edit distance is defined as minimum cost of edit path.
|
|
|
|
|
|
Parameters
|
|
|
----------
|
|
|
G1, G2: graphs
|
|
|
The two graphs G1 and G2 must be of the same type.
|
|
|
|
|
|
node_match : callable
|
|
|
A function that returns True if node n1 in G1 and n2 in G2
|
|
|
should be considered equal during matching.
|
|
|
|
|
|
The function will be called like
|
|
|
|
|
|
node_match(G1.nodes[n1], G2.nodes[n2]).
|
|
|
|
|
|
That is, the function will receive the node attribute
|
|
|
dictionaries for n1 and n2 as inputs.
|
|
|
|
|
|
Ignored if node_subst_cost is specified. If neither
|
|
|
node_match nor node_subst_cost are specified then node
|
|
|
attributes are not considered.
|
|
|
|
|
|
edge_match : callable
|
|
|
A function that returns True if the edge attribute dictionaries
|
|
|
for the pair of nodes (u1, v1) in G1 and (u2, v2) in G2 should
|
|
|
be considered equal during matching.
|
|
|
|
|
|
The function will be called like
|
|
|
|
|
|
edge_match(G1[u1][v1], G2[u2][v2]).
|
|
|
|
|
|
That is, the function will receive the edge attribute
|
|
|
dictionaries of the edges under consideration.
|
|
|
|
|
|
Ignored if edge_subst_cost is specified. If neither
|
|
|
edge_match nor edge_subst_cost are specified then edge
|
|
|
attributes are not considered.
|
|
|
|
|
|
node_subst_cost, node_del_cost, node_ins_cost : callable
|
|
|
Functions that return the costs of node substitution, node
|
|
|
deletion, and node insertion, respectively.
|
|
|
|
|
|
The functions will be called like
|
|
|
|
|
|
node_subst_cost(G1.nodes[n1], G2.nodes[n2]),
|
|
|
node_del_cost(G1.nodes[n1]),
|
|
|
node_ins_cost(G2.nodes[n2]).
|
|
|
|
|
|
That is, the functions will receive the node attribute
|
|
|
dictionaries as inputs. The functions are expected to return
|
|
|
positive numeric values.
|
|
|
|
|
|
Function node_subst_cost overrides node_match if specified.
|
|
|
If neither node_match nor node_subst_cost are specified then
|
|
|
default node substitution cost of 0 is used (node attributes
|
|
|
are not considered during matching).
|
|
|
|
|
|
If node_del_cost is not specified then default node deletion
|
|
|
cost of 1 is used. If node_ins_cost is not specified then
|
|
|
default node insertion cost of 1 is used.
|
|
|
|
|
|
edge_subst_cost, edge_del_cost, edge_ins_cost : callable
|
|
|
Functions that return the costs of edge substitution, edge
|
|
|
deletion, and edge insertion, respectively.
|
|
|
|
|
|
The functions will be called like
|
|
|
|
|
|
edge_subst_cost(G1[u1][v1], G2[u2][v2]),
|
|
|
edge_del_cost(G1[u1][v1]),
|
|
|
edge_ins_cost(G2[u2][v2]).
|
|
|
|
|
|
That is, the functions will receive the edge attribute
|
|
|
dictionaries as inputs. The functions are expected to return
|
|
|
positive numeric values.
|
|
|
|
|
|
Function edge_subst_cost overrides edge_match if specified.
|
|
|
If neither edge_match nor edge_subst_cost are specified then
|
|
|
default edge substitution cost of 0 is used (edge attributes
|
|
|
are not considered during matching).
|
|
|
|
|
|
If edge_del_cost is not specified then default edge deletion
|
|
|
cost of 1 is used. If edge_ins_cost is not specified then
|
|
|
default edge insertion cost of 1 is used.
|
|
|
|
|
|
upper_bound : numeric
|
|
|
Maximum edit distance to consider.
|
|
|
|
|
|
strictly_decreasing : bool
|
|
|
If True, return consecutive approximations of strictly
|
|
|
decreasing cost. Otherwise, return all edit paths of cost
|
|
|
less than or equal to the previous minimum cost.
|
|
|
|
|
|
roots : 2-tuple
|
|
|
Tuple where first element is a node in G1 and the second
|
|
|
is a node in G2.
|
|
|
These nodes are forced to be matched in the comparison to
|
|
|
allow comparison between rooted graphs.
|
|
|
|
|
|
timeout : numeric
|
|
|
Maximum number of seconds to execute.
|
|
|
After timeout is met, the current best GED is returned.
|
|
|
|
|
|
Returns
|
|
|
-------
|
|
|
Generator of tuples (node_edit_path, edge_edit_path, cost)
|
|
|
node_edit_path : list of tuples (u, v)
|
|
|
edge_edit_path : list of tuples ((u1, v1), (u2, v2))
|
|
|
cost : numeric
|
|
|
|
|
|
See Also
|
|
|
--------
|
|
|
graph_edit_distance, optimize_graph_edit_distance, optimal_edit_paths
|
|
|
|
|
|
References
|
|
|
----------
|
|
|
.. [1] Zeina Abu-Aisheh, Romain Raveaux, Jean-Yves Ramel, Patrick
|
|
|
Martineau. An Exact Graph Edit Distance Algorithm for Solving
|
|
|
Pattern Recognition Problems. 4th International Conference on
|
|
|
Pattern Recognition Applications and Methods 2015, Jan 2015,
|
|
|
Lisbon, Portugal. 2015,
|
|
|
<10.5220/0005209202710278>. <hal-01168816>
|
|
|
https://hal.archives-ouvertes.fr/hal-01168816
|
|
|
|
|
|
"""
|
|
|
# TODO: support DiGraph
|
|
|
|
|
|
import numpy as np
|
|
|
import scipy as sp
|
|
|
|
|
|
@dataclass
|
|
|
class CostMatrix:
|
|
|
C: ...
|
|
|
lsa_row_ind: ...
|
|
|
lsa_col_ind: ...
|
|
|
ls: ...
|
|
|
|
|
|
def make_CostMatrix(C, m, n):
|
|
|
# assert(C.shape == (m + n, m + n))
|
|
|
lsa_row_ind, lsa_col_ind = sp.optimize.linear_sum_assignment(C)
|
|
|
|
|
|
# Fixup dummy assignments:
|
|
|
# each substitution i<->j should have dummy assignment m+j<->n+i
|
|
|
# NOTE: fast reduce of Cv relies on it
|
|
|
# assert len(lsa_row_ind) == len(lsa_col_ind)
|
|
|
indexes = zip(range(len(lsa_row_ind)), lsa_row_ind, lsa_col_ind)
|
|
|
subst_ind = [k for k, i, j in indexes if i < m and j < n]
|
|
|
indexes = zip(range(len(lsa_row_ind)), lsa_row_ind, lsa_col_ind)
|
|
|
dummy_ind = [k for k, i, j in indexes if i >= m and j >= n]
|
|
|
# assert len(subst_ind) == len(dummy_ind)
|
|
|
lsa_row_ind[dummy_ind] = lsa_col_ind[subst_ind] + m
|
|
|
lsa_col_ind[dummy_ind] = lsa_row_ind[subst_ind] + n
|
|
|
|
|
|
return CostMatrix(
|
|
|
C, lsa_row_ind, lsa_col_ind, C[lsa_row_ind, lsa_col_ind].sum()
|
|
|
)
|
|
|
|
|
|
def extract_C(C, i, j, m, n):
|
|
|
# assert(C.shape == (m + n, m + n))
|
|
|
row_ind = [k in i or k - m in j for k in range(m + n)]
|
|
|
col_ind = [k in j or k - n in i for k in range(m + n)]
|
|
|
return C[row_ind, :][:, col_ind]
|
|
|
|
|
|
def reduce_C(C, i, j, m, n):
|
|
|
# assert(C.shape == (m + n, m + n))
|
|
|
row_ind = [k not in i and k - m not in j for k in range(m + n)]
|
|
|
col_ind = [k not in j and k - n not in i for k in range(m + n)]
|
|
|
return C[row_ind, :][:, col_ind]
|
|
|
|
|
|
def reduce_ind(ind, i):
|
|
|
# assert set(ind) == set(range(len(ind)))
|
|
|
rind = ind[[k not in i for k in ind]]
|
|
|
for k in set(i):
|
|
|
rind[rind >= k] -= 1
|
|
|
return rind
|
|
|
|
|
|
def match_edges(u, v, pending_g, pending_h, Ce, matched_uv=None):
|
|
|
"""
|
|
|
Parameters:
|
|
|
u, v: matched vertices, u=None or v=None for
|
|
|
deletion/insertion
|
|
|
pending_g, pending_h: lists of edges not yet mapped
|
|
|
Ce: CostMatrix of pending edge mappings
|
|
|
matched_uv: partial vertex edit path
|
|
|
list of tuples (u, v) of previously matched vertex
|
|
|
mappings u<->v, u=None or v=None for
|
|
|
deletion/insertion
|
|
|
|
|
|
Returns:
|
|
|
list of (i, j): indices of edge mappings g<->h
|
|
|
localCe: local CostMatrix of edge mappings
|
|
|
(basically submatrix of Ce at cross of rows i, cols j)
|
|
|
"""
|
|
|
M = len(pending_g)
|
|
|
N = len(pending_h)
|
|
|
# assert Ce.C.shape == (M + N, M + N)
|
|
|
|
|
|
# only attempt to match edges after one node match has been made
|
|
|
# this will stop self-edges on the first node being automatically deleted
|
|
|
# even when a substitution is the better option
|
|
|
if matched_uv is None or len(matched_uv) == 0:
|
|
|
g_ind = []
|
|
|
h_ind = []
|
|
|
else:
|
|
|
g_ind = [
|
|
|
i
|
|
|
for i in range(M)
|
|
|
if pending_g[i][:2] == (u, u)
|
|
|
or any(
|
|
|
pending_g[i][:2] in ((p, u), (u, p), (p, p)) for p, q in matched_uv
|
|
|
)
|
|
|
]
|
|
|
h_ind = [
|
|
|
j
|
|
|
for j in range(N)
|
|
|
if pending_h[j][:2] == (v, v)
|
|
|
or any(
|
|
|
pending_h[j][:2] in ((q, v), (v, q), (q, q)) for p, q in matched_uv
|
|
|
)
|
|
|
]
|
|
|
|
|
|
m = len(g_ind)
|
|
|
n = len(h_ind)
|
|
|
|
|
|
if m or n:
|
|
|
C = extract_C(Ce.C, g_ind, h_ind, M, N)
|
|
|
# assert C.shape == (m + n, m + n)
|
|
|
|
|
|
# Forbid structurally invalid matches
|
|
|
# NOTE: inf remembered from Ce construction
|
|
|
for k, i in enumerate(g_ind):
|
|
|
g = pending_g[i][:2]
|
|
|
for l, j in enumerate(h_ind):
|
|
|
h = pending_h[j][:2]
|
|
|
if nx.is_directed(G1) or nx.is_directed(G2):
|
|
|
if any(
|
|
|
g == (p, u) and h == (q, v) or g == (u, p) and h == (v, q)
|
|
|
for p, q in matched_uv
|
|
|
):
|
|
|
continue
|
|
|
else:
|
|
|
if any(
|
|
|
g in ((p, u), (u, p)) and h in ((q, v), (v, q))
|
|
|
for p, q in matched_uv
|
|
|
):
|
|
|
continue
|
|
|
if g == (u, u) or any(g == (p, p) for p, q in matched_uv):
|
|
|
continue
|
|
|
if h == (v, v) or any(h == (q, q) for p, q in matched_uv):
|
|
|
continue
|
|
|
C[k, l] = inf
|
|
|
|
|
|
localCe = make_CostMatrix(C, m, n)
|
|
|
ij = [
|
|
|
(
|
|
|
g_ind[k] if k < m else M + h_ind[l],
|
|
|
h_ind[l] if l < n else N + g_ind[k],
|
|
|
)
|
|
|
for k, l in zip(localCe.lsa_row_ind, localCe.lsa_col_ind)
|
|
|
if k < m or l < n
|
|
|
]
|
|
|
|
|
|
else:
|
|
|
ij = []
|
|
|
localCe = CostMatrix(np.empty((0, 0)), [], [], 0)
|
|
|
|
|
|
return ij, localCe
|
|
|
|
|
|
def reduce_Ce(Ce, ij, m, n):
|
|
|
if len(ij):
|
|
|
i, j = zip(*ij)
|
|
|
m_i = m - sum(1 for t in i if t < m)
|
|
|
n_j = n - sum(1 for t in j if t < n)
|
|
|
return make_CostMatrix(reduce_C(Ce.C, i, j, m, n), m_i, n_j)
|
|
|
return Ce
|
|
|
|
|
|
def get_edit_ops(
|
|
|
matched_uv, pending_u, pending_v, Cv, pending_g, pending_h, Ce, matched_cost
|
|
|
):
|
|
|
"""
|
|
|
Parameters:
|
|
|
matched_uv: partial vertex edit path
|
|
|
list of tuples (u, v) of vertex mappings u<->v,
|
|
|
u=None or v=None for deletion/insertion
|
|
|
pending_u, pending_v: lists of vertices not yet mapped
|
|
|
Cv: CostMatrix of pending vertex mappings
|
|
|
pending_g, pending_h: lists of edges not yet mapped
|
|
|
Ce: CostMatrix of pending edge mappings
|
|
|
matched_cost: cost of partial edit path
|
|
|
|
|
|
Returns:
|
|
|
sequence of
|
|
|
(i, j): indices of vertex mapping u<->v
|
|
|
Cv_ij: reduced CostMatrix of pending vertex mappings
|
|
|
(basically Cv with row i, col j removed)
|
|
|
list of (x, y): indices of edge mappings g<->h
|
|
|
Ce_xy: reduced CostMatrix of pending edge mappings
|
|
|
(basically Ce with rows x, cols y removed)
|
|
|
cost: total cost of edit operation
|
|
|
NOTE: most promising ops first
|
|
|
"""
|
|
|
m = len(pending_u)
|
|
|
n = len(pending_v)
|
|
|
# assert Cv.C.shape == (m + n, m + n)
|
|
|
|
|
|
# 1) a vertex mapping from optimal linear sum assignment
|
|
|
i, j = min(
|
|
|
(k, l) for k, l in zip(Cv.lsa_row_ind, Cv.lsa_col_ind) if k < m or l < n
|
|
|
)
|
|
|
xy, localCe = match_edges(
|
|
|
pending_u[i] if i < m else None,
|
|
|
pending_v[j] if j < n else None,
|
|
|
pending_g,
|
|
|
pending_h,
|
|
|
Ce,
|
|
|
matched_uv,
|
|
|
)
|
|
|
Ce_xy = reduce_Ce(Ce, xy, len(pending_g), len(pending_h))
|
|
|
# assert Ce.ls <= localCe.ls + Ce_xy.ls
|
|
|
if prune(matched_cost + Cv.ls + localCe.ls + Ce_xy.ls):
|
|
|
pass
|
|
|
else:
|
|
|
# get reduced Cv efficiently
|
|
|
Cv_ij = CostMatrix(
|
|
|
reduce_C(Cv.C, (i,), (j,), m, n),
|
|
|
reduce_ind(Cv.lsa_row_ind, (i, m + j)),
|
|
|
reduce_ind(Cv.lsa_col_ind, (j, n + i)),
|
|
|
Cv.ls - Cv.C[i, j],
|
|
|
)
|
|
|
yield (i, j), Cv_ij, xy, Ce_xy, Cv.C[i, j] + localCe.ls
|
|
|
|
|
|
# 2) other candidates, sorted by lower-bound cost estimate
|
|
|
other = []
|
|
|
fixed_i, fixed_j = i, j
|
|
|
if m <= n:
|
|
|
candidates = (
|
|
|
(t, fixed_j)
|
|
|
for t in range(m + n)
|
|
|
if t != fixed_i and (t < m or t == m + fixed_j)
|
|
|
)
|
|
|
else:
|
|
|
candidates = (
|
|
|
(fixed_i, t)
|
|
|
for t in range(m + n)
|
|
|
if t != fixed_j and (t < n or t == n + fixed_i)
|
|
|
)
|
|
|
for i, j in candidates:
|
|
|
if prune(matched_cost + Cv.C[i, j] + Ce.ls):
|
|
|
continue
|
|
|
Cv_ij = make_CostMatrix(
|
|
|
reduce_C(Cv.C, (i,), (j,), m, n),
|
|
|
m - 1 if i < m else m,
|
|
|
n - 1 if j < n else n,
|
|
|
)
|
|
|
# assert Cv.ls <= Cv.C[i, j] + Cv_ij.ls
|
|
|
if prune(matched_cost + Cv.C[i, j] + Cv_ij.ls + Ce.ls):
|
|
|
continue
|
|
|
xy, localCe = match_edges(
|
|
|
pending_u[i] if i < m else None,
|
|
|
pending_v[j] if j < n else None,
|
|
|
pending_g,
|
|
|
pending_h,
|
|
|
Ce,
|
|
|
matched_uv,
|
|
|
)
|
|
|
if prune(matched_cost + Cv.C[i, j] + Cv_ij.ls + localCe.ls):
|
|
|
continue
|
|
|
Ce_xy = reduce_Ce(Ce, xy, len(pending_g), len(pending_h))
|
|
|
# assert Ce.ls <= localCe.ls + Ce_xy.ls
|
|
|
if prune(matched_cost + Cv.C[i, j] + Cv_ij.ls + localCe.ls + Ce_xy.ls):
|
|
|
continue
|
|
|
other.append(((i, j), Cv_ij, xy, Ce_xy, Cv.C[i, j] + localCe.ls))
|
|
|
|
|
|
yield from sorted(other, key=lambda t: t[4] + t[1].ls + t[3].ls)
|
|
|
|
|
|
def get_edit_paths(
|
|
|
matched_uv,
|
|
|
pending_u,
|
|
|
pending_v,
|
|
|
Cv,
|
|
|
matched_gh,
|
|
|
pending_g,
|
|
|
pending_h,
|
|
|
Ce,
|
|
|
matched_cost,
|
|
|
):
|
|
|
"""
|
|
|
Parameters:
|
|
|
matched_uv: partial vertex edit path
|
|
|
list of tuples (u, v) of vertex mappings u<->v,
|
|
|
u=None or v=None for deletion/insertion
|
|
|
pending_u, pending_v: lists of vertices not yet mapped
|
|
|
Cv: CostMatrix of pending vertex mappings
|
|
|
matched_gh: partial edge edit path
|
|
|
list of tuples (g, h) of edge mappings g<->h,
|
|
|
g=None or h=None for deletion/insertion
|
|
|
pending_g, pending_h: lists of edges not yet mapped
|
|
|
Ce: CostMatrix of pending edge mappings
|
|
|
matched_cost: cost of partial edit path
|
|
|
|
|
|
Returns:
|
|
|
sequence of (vertex_path, edge_path, cost)
|
|
|
vertex_path: complete vertex edit path
|
|
|
list of tuples (u, v) of vertex mappings u<->v,
|
|
|
u=None or v=None for deletion/insertion
|
|
|
edge_path: complete edge edit path
|
|
|
list of tuples (g, h) of edge mappings g<->h,
|
|
|
g=None or h=None for deletion/insertion
|
|
|
cost: total cost of edit path
|
|
|
NOTE: path costs are non-increasing
|
|
|
"""
|
|
|
# debug_print('matched-uv:', matched_uv)
|
|
|
# debug_print('matched-gh:', matched_gh)
|
|
|
# debug_print('matched-cost:', matched_cost)
|
|
|
# debug_print('pending-u:', pending_u)
|
|
|
# debug_print('pending-v:', pending_v)
|
|
|
# debug_print(Cv.C)
|
|
|
# assert list(sorted(G1.nodes)) == list(sorted(list(u for u, v in matched_uv if u is not None) + pending_u))
|
|
|
# assert list(sorted(G2.nodes)) == list(sorted(list(v for u, v in matched_uv if v is not None) + pending_v))
|
|
|
# debug_print('pending-g:', pending_g)
|
|
|
# debug_print('pending-h:', pending_h)
|
|
|
# debug_print(Ce.C)
|
|
|
# assert list(sorted(G1.edges)) == list(sorted(list(g for g, h in matched_gh if g is not None) + pending_g))
|
|
|
# assert list(sorted(G2.edges)) == list(sorted(list(h for g, h in matched_gh if h is not None) + pending_h))
|
|
|
# debug_print()
|
|
|
|
|
|
if prune(matched_cost + Cv.ls + Ce.ls):
|
|
|
return
|
|
|
|
|
|
if not max(len(pending_u), len(pending_v)):
|
|
|
# assert not len(pending_g)
|
|
|
# assert not len(pending_h)
|
|
|
# path completed!
|
|
|
# assert matched_cost <= maxcost_value
|
|
|
nonlocal maxcost_value
|
|
|
maxcost_value = min(maxcost_value, matched_cost)
|
|
|
yield matched_uv, matched_gh, matched_cost
|
|
|
|
|
|
else:
|
|
|
edit_ops = get_edit_ops(
|
|
|
matched_uv,
|
|
|
pending_u,
|
|
|
pending_v,
|
|
|
Cv,
|
|
|
pending_g,
|
|
|
pending_h,
|
|
|
Ce,
|
|
|
matched_cost,
|
|
|
)
|
|
|
for ij, Cv_ij, xy, Ce_xy, edit_cost in edit_ops:
|
|
|
i, j = ij
|
|
|
# assert Cv.C[i, j] + sum(Ce.C[t] for t in xy) == edit_cost
|
|
|
if prune(matched_cost + edit_cost + Cv_ij.ls + Ce_xy.ls):
|
|
|
continue
|
|
|
|
|
|
# dive deeper
|
|
|
u = pending_u.pop(i) if i < len(pending_u) else None
|
|
|
v = pending_v.pop(j) if j < len(pending_v) else None
|
|
|
matched_uv.append((u, v))
|
|
|
for x, y in xy:
|
|
|
len_g = len(pending_g)
|
|
|
len_h = len(pending_h)
|
|
|
matched_gh.append(
|
|
|
(
|
|
|
pending_g[x] if x < len_g else None,
|
|
|
pending_h[y] if y < len_h else None,
|
|
|
)
|
|
|
)
|
|
|
sortedx = sorted(x for x, y in xy)
|
|
|
sortedy = sorted(y for x, y in xy)
|
|
|
G = [
|
|
|
(pending_g.pop(x) if x < len(pending_g) else None)
|
|
|
for x in reversed(sortedx)
|
|
|
]
|
|
|
H = [
|
|
|
(pending_h.pop(y) if y < len(pending_h) else None)
|
|
|
for y in reversed(sortedy)
|
|
|
]
|
|
|
|
|
|
yield from get_edit_paths(
|
|
|
matched_uv,
|
|
|
pending_u,
|
|
|
pending_v,
|
|
|
Cv_ij,
|
|
|
matched_gh,
|
|
|
pending_g,
|
|
|
pending_h,
|
|
|
Ce_xy,
|
|
|
matched_cost + edit_cost,
|
|
|
)
|
|
|
|
|
|
# backtrack
|
|
|
if u is not None:
|
|
|
pending_u.insert(i, u)
|
|
|
if v is not None:
|
|
|
pending_v.insert(j, v)
|
|
|
matched_uv.pop()
|
|
|
for x, g in zip(sortedx, reversed(G)):
|
|
|
if g is not None:
|
|
|
pending_g.insert(x, g)
|
|
|
for y, h in zip(sortedy, reversed(H)):
|
|
|
if h is not None:
|
|
|
pending_h.insert(y, h)
|
|
|
for _ in xy:
|
|
|
matched_gh.pop()
|
|
|
|
|
|
# Initialization
|
|
|
|
|
|
pending_u = list(G1.nodes)
|
|
|
pending_v = list(G2.nodes)
|
|
|
|
|
|
initial_cost = 0
|
|
|
if roots:
|
|
|
root_u, root_v = roots
|
|
|
if root_u not in pending_u or root_v not in pending_v:
|
|
|
raise nx.NodeNotFound("Root node not in graph.")
|
|
|
|
|
|
# remove roots from pending
|
|
|
pending_u.remove(root_u)
|
|
|
pending_v.remove(root_v)
|
|
|
|
|
|
# cost matrix of vertex mappings
|
|
|
m = len(pending_u)
|
|
|
n = len(pending_v)
|
|
|
C = np.zeros((m + n, m + n))
|
|
|
if node_subst_cost:
|
|
|
C[0:m, 0:n] = np.array(
|
|
|
[
|
|
|
node_subst_cost(G1.nodes[u], G2.nodes[v])
|
|
|
for u in pending_u
|
|
|
for v in pending_v
|
|
|
]
|
|
|
).reshape(m, n)
|
|
|
if roots:
|
|
|
initial_cost = node_subst_cost(G1.nodes[root_u], G2.nodes[root_v])
|
|
|
elif node_match:
|
|
|
C[0:m, 0:n] = np.array(
|
|
|
[
|
|
|
1 - int(node_match(G1.nodes[u], G2.nodes[v]))
|
|
|
for u in pending_u
|
|
|
for v in pending_v
|
|
|
]
|
|
|
).reshape(m, n)
|
|
|
if roots:
|
|
|
initial_cost = 1 - node_match(G1.nodes[root_u], G2.nodes[root_v])
|
|
|
else:
|
|
|
# all zeroes
|
|
|
pass
|
|
|
# assert not min(m, n) or C[0:m, 0:n].min() >= 0
|
|
|
if node_del_cost:
|
|
|
del_costs = [node_del_cost(G1.nodes[u]) for u in pending_u]
|
|
|
else:
|
|
|
del_costs = [1] * len(pending_u)
|
|
|
# assert not m or min(del_costs) >= 0
|
|
|
if node_ins_cost:
|
|
|
ins_costs = [node_ins_cost(G2.nodes[v]) for v in pending_v]
|
|
|
else:
|
|
|
ins_costs = [1] * len(pending_v)
|
|
|
# assert not n or min(ins_costs) >= 0
|
|
|
inf = C[0:m, 0:n].sum() + sum(del_costs) + sum(ins_costs) + 1
|
|
|
C[0:m, n : n + m] = np.array(
|
|
|
[del_costs[i] if i == j else inf for i in range(m) for j in range(m)]
|
|
|
).reshape(m, m)
|
|
|
C[m : m + n, 0:n] = np.array(
|
|
|
[ins_costs[i] if i == j else inf for i in range(n) for j in range(n)]
|
|
|
).reshape(n, n)
|
|
|
Cv = make_CostMatrix(C, m, n)
|
|
|
# debug_print(f"Cv: {m} x {n}")
|
|
|
# debug_print(Cv.C)
|
|
|
|
|
|
pending_g = list(G1.edges)
|
|
|
pending_h = list(G2.edges)
|
|
|
|
|
|
# cost matrix of edge mappings
|
|
|
m = len(pending_g)
|
|
|
n = len(pending_h)
|
|
|
C = np.zeros((m + n, m + n))
|
|
|
if edge_subst_cost:
|
|
|
C[0:m, 0:n] = np.array(
|
|
|
[
|
|
|
edge_subst_cost(G1.edges[g], G2.edges[h])
|
|
|
for g in pending_g
|
|
|
for h in pending_h
|
|
|
]
|
|
|
).reshape(m, n)
|
|
|
elif edge_match:
|
|
|
C[0:m, 0:n] = np.array(
|
|
|
[
|
|
|
1 - int(edge_match(G1.edges[g], G2.edges[h]))
|
|
|
for g in pending_g
|
|
|
for h in pending_h
|
|
|
]
|
|
|
).reshape(m, n)
|
|
|
else:
|
|
|
# all zeroes
|
|
|
pass
|
|
|
# assert not min(m, n) or C[0:m, 0:n].min() >= 0
|
|
|
if edge_del_cost:
|
|
|
del_costs = [edge_del_cost(G1.edges[g]) for g in pending_g]
|
|
|
else:
|
|
|
del_costs = [1] * len(pending_g)
|
|
|
# assert not m or min(del_costs) >= 0
|
|
|
if edge_ins_cost:
|
|
|
ins_costs = [edge_ins_cost(G2.edges[h]) for h in pending_h]
|
|
|
else:
|
|
|
ins_costs = [1] * len(pending_h)
|
|
|
# assert not n or min(ins_costs) >= 0
|
|
|
inf = C[0:m, 0:n].sum() + sum(del_costs) + sum(ins_costs) + 1
|
|
|
C[0:m, n : n + m] = np.array(
|
|
|
[del_costs[i] if i == j else inf for i in range(m) for j in range(m)]
|
|
|
).reshape(m, m)
|
|
|
C[m : m + n, 0:n] = np.array(
|
|
|
[ins_costs[i] if i == j else inf for i in range(n) for j in range(n)]
|
|
|
).reshape(n, n)
|
|
|
Ce = make_CostMatrix(C, m, n)
|
|
|
# debug_print(f'Ce: {m} x {n}')
|
|
|
# debug_print(Ce.C)
|
|
|
# debug_print()
|
|
|
|
|
|
maxcost_value = Cv.C.sum() + Ce.C.sum() + 1
|
|
|
|
|
|
if timeout is not None:
|
|
|
if timeout <= 0:
|
|
|
raise nx.NetworkXError("Timeout value must be greater than 0")
|
|
|
start = time.perf_counter()
|
|
|
|
|
|
def prune(cost):
|
|
|
if timeout is not None:
|
|
|
if time.perf_counter() - start > timeout:
|
|
|
return True
|
|
|
if upper_bound is not None:
|
|
|
if cost > upper_bound:
|
|
|
return True
|
|
|
if cost > maxcost_value:
|
|
|
return True
|
|
|
if strictly_decreasing and cost >= maxcost_value:
|
|
|
return True
|
|
|
return False
|
|
|
|
|
|
# Now go!
|
|
|
|
|
|
done_uv = [] if roots is None else [roots]
|
|
|
|
|
|
for vertex_path, edge_path, cost in get_edit_paths(
|
|
|
done_uv, pending_u, pending_v, Cv, [], pending_g, pending_h, Ce, initial_cost
|
|
|
):
|
|
|
# assert sorted(G1.nodes) == sorted(u for u, v in vertex_path if u is not None)
|
|
|
# assert sorted(G2.nodes) == sorted(v for u, v in vertex_path if v is not None)
|
|
|
# assert sorted(G1.edges) == sorted(g for g, h in edge_path if g is not None)
|
|
|
# assert sorted(G2.edges) == sorted(h for g, h in edge_path if h is not None)
|
|
|
# print(vertex_path, edge_path, cost, file = sys.stderr)
|
|
|
# assert cost == maxcost_value
|
|
|
yield list(vertex_path), list(edge_path), float(cost)
|
|
|
|
|
|
|
|
|
@nx._dispatchable
|
|
|
def simrank_similarity(
|
|
|
G,
|
|
|
source=None,
|
|
|
target=None,
|
|
|
importance_factor=0.9,
|
|
|
max_iterations=1000,
|
|
|
tolerance=1e-4,
|
|
|
):
|
|
|
"""Returns the SimRank similarity of nodes in the graph ``G``.
|
|
|
|
|
|
SimRank is a similarity metric that says "two objects are considered
|
|
|
to be similar if they are referenced by similar objects." [1]_.
|
|
|
|
|
|
The pseudo-code definition from the paper is::
|
|
|
|
|
|
def simrank(G, u, v):
|
|
|
in_neighbors_u = G.predecessors(u)
|
|
|
in_neighbors_v = G.predecessors(v)
|
|
|
scale = C / (len(in_neighbors_u) * len(in_neighbors_v))
|
|
|
return scale * sum(
|
|
|
simrank(G, w, x) for w, x in product(in_neighbors_u, in_neighbors_v)
|
|
|
)
|
|
|
|
|
|
where ``G`` is the graph, ``u`` is the source, ``v`` is the target,
|
|
|
and ``C`` is a float decay or importance factor between 0 and 1.
|
|
|
|
|
|
The SimRank algorithm for determining node similarity is defined in
|
|
|
[2]_.
|
|
|
|
|
|
Parameters
|
|
|
----------
|
|
|
G : NetworkX graph
|
|
|
A NetworkX graph
|
|
|
|
|
|
source : node
|
|
|
If this is specified, the returned dictionary maps each node
|
|
|
``v`` in the graph to the similarity between ``source`` and
|
|
|
``v``.
|
|
|
|
|
|
target : node
|
|
|
If both ``source`` and ``target`` are specified, the similarity
|
|
|
value between ``source`` and ``target`` is returned. If
|
|
|
``target`` is specified but ``source`` is not, this argument is
|
|
|
ignored.
|
|
|
|
|
|
importance_factor : float
|
|
|
The relative importance of indirect neighbors with respect to
|
|
|
direct neighbors.
|
|
|
|
|
|
max_iterations : integer
|
|
|
Maximum number of iterations.
|
|
|
|
|
|
tolerance : float
|
|
|
Error tolerance used to check convergence. When an iteration of
|
|
|
the algorithm finds that no similarity value changes more than
|
|
|
this amount, the algorithm halts.
|
|
|
|
|
|
Returns
|
|
|
-------
|
|
|
similarity : dictionary or float
|
|
|
If ``source`` and ``target`` are both ``None``, this returns a
|
|
|
dictionary of dictionaries, where keys are node pairs and value
|
|
|
are similarity of the pair of nodes.
|
|
|
|
|
|
If ``source`` is not ``None`` but ``target`` is, this returns a
|
|
|
dictionary mapping node to the similarity of ``source`` and that
|
|
|
node.
|
|
|
|
|
|
If neither ``source`` nor ``target`` is ``None``, this returns
|
|
|
the similarity value for the given pair of nodes.
|
|
|
|
|
|
Raises
|
|
|
------
|
|
|
ExceededMaxIterations
|
|
|
If the algorithm does not converge within ``max_iterations``.
|
|
|
|
|
|
NodeNotFound
|
|
|
If either ``source`` or ``target`` is not in `G`.
|
|
|
|
|
|
Examples
|
|
|
--------
|
|
|
>>> G = nx.cycle_graph(2)
|
|
|
>>> nx.simrank_similarity(G)
|
|
|
{0: {0: 1.0, 1: 0.0}, 1: {0: 0.0, 1: 1.0}}
|
|
|
>>> nx.simrank_similarity(G, source=0)
|
|
|
{0: 1.0, 1: 0.0}
|
|
|
>>> nx.simrank_similarity(G, source=0, target=0)
|
|
|
1.0
|
|
|
|
|
|
The result of this function can be converted to a numpy array
|
|
|
representing the SimRank matrix by using the node order of the
|
|
|
graph to determine which row and column represent each node.
|
|
|
Other ordering of nodes is also possible.
|
|
|
|
|
|
>>> import numpy as np
|
|
|
>>> sim = nx.simrank_similarity(G)
|
|
|
>>> np.array([[sim[u][v] for v in G] for u in G])
|
|
|
array([[1., 0.],
|
|
|
[0., 1.]])
|
|
|
>>> sim_1d = nx.simrank_similarity(G, source=0)
|
|
|
>>> np.array([sim[0][v] for v in G])
|
|
|
array([1., 0.])
|
|
|
|
|
|
References
|
|
|
----------
|
|
|
.. [1] https://en.wikipedia.org/wiki/SimRank
|
|
|
.. [2] G. Jeh and J. Widom.
|
|
|
"SimRank: a measure of structural-context similarity",
|
|
|
In KDD'02: Proceedings of the Eighth ACM SIGKDD
|
|
|
International Conference on Knowledge Discovery and Data Mining,
|
|
|
pp. 538--543. ACM Press, 2002.
|
|
|
"""
|
|
|
import numpy as np
|
|
|
|
|
|
nodelist = list(G)
|
|
|
if source is not None:
|
|
|
if source not in nodelist:
|
|
|
raise nx.NodeNotFound(f"Source node {source} not in G")
|
|
|
else:
|
|
|
s_indx = nodelist.index(source)
|
|
|
else:
|
|
|
s_indx = None
|
|
|
|
|
|
if target is not None:
|
|
|
if target not in nodelist:
|
|
|
raise nx.NodeNotFound(f"Target node {target} not in G")
|
|
|
else:
|
|
|
t_indx = nodelist.index(target)
|
|
|
else:
|
|
|
t_indx = None
|
|
|
|
|
|
x = _simrank_similarity_numpy(
|
|
|
G, s_indx, t_indx, importance_factor, max_iterations, tolerance
|
|
|
)
|
|
|
|
|
|
if isinstance(x, np.ndarray):
|
|
|
if x.ndim == 1:
|
|
|
return dict(zip(G, x.tolist()))
|
|
|
# else x.ndim == 2
|
|
|
return {u: dict(zip(G, row)) for u, row in zip(G, x.tolist())}
|
|
|
return float(x)
|
|
|
|
|
|
|
|
|
def _simrank_similarity_python(
|
|
|
G,
|
|
|
source=None,
|
|
|
target=None,
|
|
|
importance_factor=0.9,
|
|
|
max_iterations=1000,
|
|
|
tolerance=1e-4,
|
|
|
):
|
|
|
"""Returns the SimRank similarity of nodes in the graph ``G``.
|
|
|
|
|
|
This pure Python version is provided for pedagogical purposes.
|
|
|
|
|
|
Examples
|
|
|
--------
|
|
|
>>> G = nx.cycle_graph(2)
|
|
|
>>> nx.similarity._simrank_similarity_python(G)
|
|
|
{0: {0: 1, 1: 0.0}, 1: {0: 0.0, 1: 1}}
|
|
|
>>> nx.similarity._simrank_similarity_python(G, source=0)
|
|
|
{0: 1, 1: 0.0}
|
|
|
>>> nx.similarity._simrank_similarity_python(G, source=0, target=0)
|
|
|
1
|
|
|
"""
|
|
|
# build up our similarity adjacency dictionary output
|
|
|
newsim = {u: {v: 1 if u == v else 0 for v in G} for u in G}
|
|
|
|
|
|
# These functions compute the update to the similarity value of the nodes
|
|
|
# `u` and `v` with respect to the previous similarity values.
|
|
|
def avg_sim(s):
|
|
|
return sum(newsim[w][x] for (w, x) in s) / len(s) if s else 0.0
|
|
|
|
|
|
Gadj = G.pred if G.is_directed() else G.adj
|
|
|
|
|
|
def sim(u, v):
|
|
|
return importance_factor * avg_sim(list(product(Gadj[u], Gadj[v])))
|
|
|
|
|
|
for its in range(max_iterations):
|
|
|
oldsim = newsim
|
|
|
newsim = {u: {v: sim(u, v) if u != v else 1 for v in G} for u in G}
|
|
|
is_close = all(
|
|
|
all(
|
|
|
abs(newsim[u][v] - old) <= tolerance * (1 + abs(old))
|
|
|
for v, old in nbrs.items()
|
|
|
)
|
|
|
for u, nbrs in oldsim.items()
|
|
|
)
|
|
|
if is_close:
|
|
|
break
|
|
|
|
|
|
if its + 1 == max_iterations:
|
|
|
raise nx.ExceededMaxIterations(
|
|
|
f"simrank did not converge after {max_iterations} iterations."
|
|
|
)
|
|
|
|
|
|
if source is not None and target is not None:
|
|
|
return newsim[source][target]
|
|
|
if source is not None:
|
|
|
return newsim[source]
|
|
|
return newsim
|
|
|
|
|
|
|
|
|
def _simrank_similarity_numpy(
|
|
|
G,
|
|
|
source=None,
|
|
|
target=None,
|
|
|
importance_factor=0.9,
|
|
|
max_iterations=1000,
|
|
|
tolerance=1e-4,
|
|
|
):
|
|
|
"""Calculate SimRank of nodes in ``G`` using matrices with ``numpy``.
|
|
|
|
|
|
The SimRank algorithm for determining node similarity is defined in
|
|
|
[1]_.
|
|
|
|
|
|
Parameters
|
|
|
----------
|
|
|
G : NetworkX graph
|
|
|
A NetworkX graph
|
|
|
|
|
|
source : node
|
|
|
If this is specified, the returned dictionary maps each node
|
|
|
``v`` in the graph to the similarity between ``source`` and
|
|
|
``v``.
|
|
|
|
|
|
target : node
|
|
|
If both ``source`` and ``target`` are specified, the similarity
|
|
|
value between ``source`` and ``target`` is returned. If
|
|
|
``target`` is specified but ``source`` is not, this argument is
|
|
|
ignored.
|
|
|
|
|
|
importance_factor : float
|
|
|
The relative importance of indirect neighbors with respect to
|
|
|
direct neighbors.
|
|
|
|
|
|
max_iterations : integer
|
|
|
Maximum number of iterations.
|
|
|
|
|
|
tolerance : float
|
|
|
Error tolerance used to check convergence. When an iteration of
|
|
|
the algorithm finds that no similarity value changes more than
|
|
|
this amount, the algorithm halts.
|
|
|
|
|
|
Returns
|
|
|
-------
|
|
|
similarity : numpy array or float
|
|
|
If ``source`` and ``target`` are both ``None``, this returns a
|
|
|
2D array containing SimRank scores of the nodes.
|
|
|
|
|
|
If ``source`` is not ``None`` but ``target`` is, this returns an
|
|
|
1D array containing SimRank scores of ``source`` and that
|
|
|
node.
|
|
|
|
|
|
If neither ``source`` nor ``target`` is ``None``, this returns
|
|
|
the similarity value for the given pair of nodes.
|
|
|
|
|
|
Examples
|
|
|
--------
|
|
|
>>> G = nx.cycle_graph(2)
|
|
|
>>> nx.similarity._simrank_similarity_numpy(G)
|
|
|
array([[1., 0.],
|
|
|
[0., 1.]])
|
|
|
>>> nx.similarity._simrank_similarity_numpy(G, source=0)
|
|
|
array([1., 0.])
|
|
|
>>> nx.similarity._simrank_similarity_numpy(G, source=0, target=0)
|
|
|
1.0
|
|
|
|
|
|
References
|
|
|
----------
|
|
|
.. [1] G. Jeh and J. Widom.
|
|
|
"SimRank: a measure of structural-context similarity",
|
|
|
In KDD'02: Proceedings of the Eighth ACM SIGKDD
|
|
|
International Conference on Knowledge Discovery and Data Mining,
|
|
|
pp. 538--543. ACM Press, 2002.
|
|
|
"""
|
|
|
# This algorithm follows roughly
|
|
|
#
|
|
|
# S = max{C * (A.T * S * A), I}
|
|
|
#
|
|
|
# where C is the importance factor, A is the column normalized
|
|
|
# adjacency matrix, and I is the identity matrix.
|
|
|
import numpy as np
|
|
|
|
|
|
adjacency_matrix = nx.to_numpy_array(G)
|
|
|
|
|
|
# column-normalize the ``adjacency_matrix``
|
|
|
s = np.array(adjacency_matrix.sum(axis=0))
|
|
|
s[s == 0] = 1
|
|
|
adjacency_matrix /= s # adjacency_matrix.sum(axis=0)
|
|
|
|
|
|
newsim = np.eye(len(G), dtype=np.float64)
|
|
|
for its in range(max_iterations):
|
|
|
prevsim = newsim.copy()
|
|
|
newsim = importance_factor * ((adjacency_matrix.T @ prevsim) @ adjacency_matrix)
|
|
|
np.fill_diagonal(newsim, 1.0)
|
|
|
|
|
|
if np.allclose(prevsim, newsim, atol=tolerance):
|
|
|
break
|
|
|
|
|
|
if its + 1 == max_iterations:
|
|
|
raise nx.ExceededMaxIterations(
|
|
|
f"simrank did not converge after {max_iterations} iterations."
|
|
|
)
|
|
|
|
|
|
if source is not None and target is not None:
|
|
|
return float(newsim[source, target])
|
|
|
if source is not None:
|
|
|
return newsim[source]
|
|
|
return newsim
|
|
|
|
|
|
|
|
|
@nx._dispatchable(edge_attrs="weight")
|
|
|
def panther_similarity(
|
|
|
G, source, k=5, path_length=5, c=0.5, delta=0.1, eps=None, weight="weight"
|
|
|
):
|
|
|
r"""Returns the Panther similarity of nodes in the graph `G` to node ``v``.
|
|
|
|
|
|
Panther is a similarity metric that says "two objects are considered
|
|
|
to be similar if they frequently appear on the same paths." [1]_.
|
|
|
|
|
|
Parameters
|
|
|
----------
|
|
|
G : NetworkX graph
|
|
|
A NetworkX graph
|
|
|
source : node
|
|
|
Source node for which to find the top `k` similar other nodes
|
|
|
k : int (default = 5)
|
|
|
The number of most similar nodes to return.
|
|
|
path_length : int (default = 5)
|
|
|
How long the randomly generated paths should be (``T`` in [1]_)
|
|
|
c : float (default = 0.5)
|
|
|
A universal positive constant used to scale the number
|
|
|
of sample random paths to generate.
|
|
|
delta : float (default = 0.1)
|
|
|
The probability that the similarity $S$ is not an epsilon-approximation to (R, phi),
|
|
|
where $R$ is the number of random paths and $\phi$ is the probability
|
|
|
that an element sampled from a set $A \subseteq D$, where $D$ is the domain.
|
|
|
eps : float or None (default = None)
|
|
|
The error bound. Per [1]_, a good value is ``sqrt(1/|E|)``. Therefore,
|
|
|
if no value is provided, the recommended computed value will be used.
|
|
|
weight : string or None, optional (default="weight")
|
|
|
The name of an edge attribute that holds the numerical value
|
|
|
used as a weight. If None then each edge has weight 1.
|
|
|
|
|
|
Returns
|
|
|
-------
|
|
|
similarity : dictionary
|
|
|
Dictionary of nodes to similarity scores (as floats). Note:
|
|
|
the self-similarity (i.e., ``v``) will not be included in
|
|
|
the returned dictionary. So, for ``k = 5``, a dictionary of
|
|
|
top 4 nodes and their similarity scores will be returned.
|
|
|
|
|
|
Raises
|
|
|
------
|
|
|
NetworkXUnfeasible
|
|
|
If `source` is an isolated node.
|
|
|
|
|
|
NodeNotFound
|
|
|
If `source` is not in `G`.
|
|
|
|
|
|
Notes
|
|
|
-----
|
|
|
The isolated nodes in `G` are ignored.
|
|
|
|
|
|
Examples
|
|
|
--------
|
|
|
>>> G = nx.star_graph(10)
|
|
|
>>> sim = nx.panther_similarity(G, 0)
|
|
|
|
|
|
References
|
|
|
----------
|
|
|
.. [1] Zhang, J., Tang, J., Ma, C., Tong, H., Jing, Y., & Li, J.
|
|
|
Panther: Fast top-k similarity search on large networks.
|
|
|
In Proceedings of the ACM SIGKDD International Conference
|
|
|
on Knowledge Discovery and Data Mining (Vol. 2015-August, pp. 1445–1454).
|
|
|
Association for Computing Machinery. https://doi.org/10.1145/2783258.2783267.
|
|
|
"""
|
|
|
import numpy as np
|
|
|
|
|
|
if source not in G:
|
|
|
raise nx.NodeNotFound(f"Source node {source} not in G")
|
|
|
|
|
|
isolates = set(nx.isolates(G))
|
|
|
|
|
|
if source in isolates:
|
|
|
raise nx.NetworkXUnfeasible(
|
|
|
f"Panther similarity is not defined for the isolated source node {source}."
|
|
|
)
|
|
|
|
|
|
G = G.subgraph([node for node in G.nodes if node not in isolates]).copy()
|
|
|
|
|
|
num_nodes = G.number_of_nodes()
|
|
|
if num_nodes < k:
|
|
|
warnings.warn(
|
|
|
f"Number of nodes is {num_nodes}, but requested k is {k}. "
|
|
|
"Setting k to number of nodes."
|
|
|
)
|
|
|
k = num_nodes
|
|
|
# According to [1], they empirically determined
|
|
|
# a good value for ``eps`` to be sqrt( 1 / |E| )
|
|
|
if eps is None:
|
|
|
eps = np.sqrt(1.0 / G.number_of_edges())
|
|
|
|
|
|
inv_node_map = {name: index for index, name in enumerate(G.nodes)}
|
|
|
node_map = np.array(G)
|
|
|
|
|
|
# Calculate the sample size ``R`` for how many paths
|
|
|
# to randomly generate
|
|
|
t_choose_2 = math.comb(path_length, 2)
|
|
|
sample_size = int((c / eps**2) * (np.log2(t_choose_2) + 1 + np.log(1 / delta)))
|
|
|
index_map = {}
|
|
|
_ = list(
|
|
|
generate_random_paths(
|
|
|
G, sample_size, path_length=path_length, index_map=index_map, weight=weight
|
|
|
)
|
|
|
)
|
|
|
S = np.zeros(num_nodes)
|
|
|
|
|
|
inv_sample_size = 1 / sample_size
|
|
|
|
|
|
source_paths = set(index_map[source])
|
|
|
|
|
|
# Calculate the path similarities
|
|
|
# between ``source`` (v) and ``node`` (v_j)
|
|
|
# using our inverted index mapping of
|
|
|
# vertices to paths
|
|
|
for node, paths in index_map.items():
|
|
|
# Only consider paths where both
|
|
|
# ``node`` and ``source`` are present
|
|
|
common_paths = source_paths.intersection(paths)
|
|
|
S[inv_node_map[node]] = len(common_paths) * inv_sample_size
|
|
|
|
|
|
# Retrieve top ``k`` similar
|
|
|
# Note: the below performed anywhere from 4-10x faster
|
|
|
# (depending on input sizes) vs the equivalent ``np.argsort(S)[::-1]``
|
|
|
top_k_unsorted = np.argpartition(S, -k)[-k:]
|
|
|
top_k_sorted = top_k_unsorted[np.argsort(S[top_k_unsorted])][::-1]
|
|
|
|
|
|
# Add back the similarity scores
|
|
|
top_k_with_val = dict(
|
|
|
zip(node_map[top_k_sorted].tolist(), S[top_k_sorted].tolist())
|
|
|
)
|
|
|
|
|
|
# Remove the self-similarity
|
|
|
top_k_with_val.pop(source, None)
|
|
|
return top_k_with_val
|
|
|
|
|
|
|
|
|
@np_random_state(5)
|
|
|
@nx._dispatchable(edge_attrs="weight")
|
|
|
def generate_random_paths(
|
|
|
G, sample_size, path_length=5, index_map=None, weight="weight", seed=None
|
|
|
):
|
|
|
"""Randomly generate `sample_size` paths of length `path_length`.
|
|
|
|
|
|
Parameters
|
|
|
----------
|
|
|
G : NetworkX graph
|
|
|
A NetworkX graph
|
|
|
sample_size : integer
|
|
|
The number of paths to generate. This is ``R`` in [1]_.
|
|
|
path_length : integer (default = 5)
|
|
|
The maximum size of the path to randomly generate.
|
|
|
This is ``T`` in [1]_. According to the paper, ``T >= 5`` is
|
|
|
recommended.
|
|
|
index_map : dictionary, optional
|
|
|
If provided, this will be populated with the inverted
|
|
|
index of nodes mapped to the set of generated random path
|
|
|
indices within ``paths``.
|
|
|
weight : string or None, optional (default="weight")
|
|
|
The name of an edge attribute that holds the numerical value
|
|
|
used as a weight. If None then each edge has weight 1.
|
|
|
seed : integer, random_state, or None (default)
|
|
|
Indicator of random number generation state.
|
|
|
See :ref:`Randomness<randomness>`.
|
|
|
|
|
|
Returns
|
|
|
-------
|
|
|
paths : generator of lists
|
|
|
Generator of `sample_size` paths each with length `path_length`.
|
|
|
|
|
|
Examples
|
|
|
--------
|
|
|
Note that the return value is the list of paths:
|
|
|
|
|
|
>>> G = nx.star_graph(3)
|
|
|
>>> random_path = nx.generate_random_paths(G, 2)
|
|
|
|
|
|
By passing a dictionary into `index_map`, it will build an
|
|
|
inverted index mapping of nodes to the paths in which that node is present:
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>>> G = nx.star_graph(3)
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>>> index_map = {}
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>>> random_path = nx.generate_random_paths(G, 3, index_map=index_map)
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>>> paths_containing_node_0 = [
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... random_path[path_idx] for path_idx in index_map.get(0, [])
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... ]
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References
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----------
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.. [1] Zhang, J., Tang, J., Ma, C., Tong, H., Jing, Y., & Li, J.
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Panther: Fast top-k similarity search on large networks.
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In Proceedings of the ACM SIGKDD International Conference
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on Knowledge Discovery and Data Mining (Vol. 2015-August, pp. 1445–1454).
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Association for Computing Machinery. https://doi.org/10.1145/2783258.2783267.
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"""
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import numpy as np
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randint_fn = (
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seed.integers if isinstance(seed, np.random.Generator) else seed.randint
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)
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# Calculate transition probabilities between
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# every pair of vertices according to Eq. (3)
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adj_mat = nx.to_numpy_array(G, weight=weight)
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inv_row_sums = np.reciprocal(adj_mat.sum(axis=1)).reshape(-1, 1)
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transition_probabilities = adj_mat * inv_row_sums
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node_map = list(G)
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num_nodes = G.number_of_nodes()
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for path_index in range(sample_size):
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# Sample current vertex v = v_i uniformly at random
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node_index = randint_fn(num_nodes)
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node = node_map[node_index]
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# Add v into p_r and add p_r into the path set
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# of v, i.e., P_v
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path = [node]
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# Build the inverted index (P_v) of vertices to paths
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if index_map is not None:
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if node in index_map:
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index_map[node].add(path_index)
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else:
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index_map[node] = {path_index}
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starting_index = node_index
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for _ in range(path_length):
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# Randomly sample a neighbor (v_j) according
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# to transition probabilities from ``node`` (v) to its neighbors
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nbr_index = seed.choice(
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num_nodes, p=transition_probabilities[starting_index]
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)
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# Set current vertex (v = v_j)
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starting_index = nbr_index
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# Add v into p_r
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nbr_node = node_map[nbr_index]
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path.append(nbr_node)
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# Add p_r into P_v
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if index_map is not None:
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if nbr_node in index_map:
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index_map[nbr_node].add(path_index)
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else:
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index_map[nbr_node] = {path_index}
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yield path
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