# Source code for netrd.distance.netsimile

```
"""
netsimile.py
--------------
Graph distance based on:
Berlingerio, M., Koutra, D., Eliassi-Rad, T. & Faloutsos, C. NetSimile: A Scalable Approach to Size-Independent Network Similarity. arXiv (2012)
author: Alex Gates
email: ajgates42@gmail.com (optional)
Submitted as part of the 2019 NetSI Collabathon.
"""
import networkx as nx
import numpy as np
from scipy.spatial.distance import canberra
from scipy.stats import skew, kurtosis
from .base import BaseDistance
from ..utilities import undirected, unweighted
[docs]class NetSimile(BaseDistance):
"""Compares node signature distributions."""
[docs] @undirected
@unweighted
def dist(self, G1, G2):
"""A scalable approach to network similarity.
A network similarity measure based on node signature distributions.
The results dictionary includes the underlying feature matrices in
`'feature_matrices'` and the underlying signature vectors in
`'signature_vectors'`.
Parameters
----------
G1, G2 (nx.Graph)
two undirected networkx graphs to be compared.
Returns
-------
dist (float)
the distance between `G1` and `G2`.
References
----------
.. [1] Michele Berlingerio, Danai Koutra, Tina Eliassi-Rad,
Christos Faloutsos: NetSimile: A Scalable Approach to
Size-Independent Network Similarity. CoRR abs/1209.2684
(2012)
"""
# find the graph node feature matrices
G1_node_features = feature_extraction(G1)
G2_node_features = feature_extraction(G2)
# get the graph signature vectors
G1_signature = graph_signature(G1_node_features)
G2_signature = graph_signature(G2_node_features)
# the final distance is the absolute canberra distance
dist = abs(canberra(G1_signature, G2_signature))
self.results['feature_matrices'] = G1_node_features, G2_node_features
self.results['signature_vectors'] = G1_signature, G2_signature
self.results['dist'] = dist
return dist
def feature_extraction(G):
"""Node feature extraction.
Parameters
----------
G (nx.Graph): a networkx graph.
Returns
-------
node_features (float): the Nx7 matrix of node features."""
# necessary data structures
node_features = np.zeros(shape=(G.number_of_nodes(), 7))
node_list = sorted(G.nodes())
node_degree_dict = dict(G.degree())
node_clustering_dict = dict(nx.clustering(G))
egonets = [nx.ego_graph(G, n) for n in node_list]
# node degrees
degs = [node_degree_dict[n] for n in node_list]
# clustering coefficient
clusts = [node_clustering_dict[n] for n in node_list]
# average degree of neighborhood
neighbor_degs = [
np.mean([node_degree_dict[m] for m in egonets[n].nodes if m != n])
if node_degree_dict[n] > 0
else 0
for n in node_list
]
# average clustering coefficient of neighborhood
neighbor_clusts = [
np.mean([node_clustering_dict[m] for m in egonets[n].nodes if m != n])
if node_degree_dict[n] > 0
else 0
for n in node_list
]
# number of edges in the neighborhood
neighbor_edges = [
egonets[n].number_of_edges() if node_degree_dict[n] > 0 else 0
for n in node_list
]
# number of outgoing edges from the neighborhood
# the sum of neighborhood degrees = 2*(internal edges) + external edges
# node_features[:,5] = node_features[:,0] * node_features[:,2] - 2*node_features[:,4]
neighbor_outgoing_edges = [
len(
[
edge
for edge in set.union(*[set(G.edges(j)) for j in egonets[i].nodes])
if not egonets[i].has_edge(*edge)
]
)
for i in node_list
]
# number of neighbors of neighbors (not in neighborhood)
neighbors_of_neighbors = [
len(
set([p for m in G.neighbors(n) for p in G.neighbors(m)])
- set(G.neighbors(n))
- set([n])
)
if node_degree_dict[n] > 0
else 0
for n in node_list
]
# assembling the features
node_features[:, 0] = degs
node_features[:, 1] = clusts
node_features[:, 2] = neighbor_degs
node_features[:, 3] = neighbor_clusts
node_features[:, 4] = neighbor_edges
node_features[:, 5] = neighbor_outgoing_edges
node_features[:, 6] = neighbors_of_neighbors
return np.nan_to_num(node_features)
def graph_signature(node_features):
signature_vec = np.zeros(7 * 5)
# for each of the 7 features
for k in range(7):
# find the mean
signature_vec[k * 5] = node_features[:, k].mean()
# find the median
signature_vec[k * 5 + 1] = np.median(node_features[:, k])
# find the std
signature_vec[k * 5 + 2] = node_features[:, k].std()
# find the skew
signature_vec[k * 5 + 3] = skew(node_features[:, k])
# find the kurtosis
signature_vec[k * 5 + 4] = kurtosis(node_features[:, k])
return signature_vec
"""
# sample usage
>>>from netrd.distance import NetSimile
>>>G1 = nx.karate_club_graph()
>>>G2 = nx.krackhardt_kite_graph()
>>>test = NetSimile()
>>>print(test.dist(G1, G2))
20.180783067167326
"""
```