import scipy
import numpy as np
import networkx as nx
from karateclub.estimator import Estimator
from sklearn.decomposition import TruncatedSVD
class FeatherNode(Estimator):
r"""An implementation of `"FEATHER-N" <https://arxiv.org/abs/2005.07959>`_
from the paper "Characteristic Functions on Graphs: Birds of a Feather,
from Statistical Descriptors to Parametric Models". The procedure
uses characteristic functions of node features with random walk weights to describe
node neighborhoods.
Args:
reduction_dimensions (int): SVD reduction dimensions. Default is 64.
svd_iterations (int): SVD iteration count. Default is 20.
theta_max (float): Maximal evaluation point. Default is 2.5.
eval_points (int): Number of characteristic function evaluation points. Default is 25.
order (int): Scale - number of adjacency matrix powers. Default is 5.
seed (int): Random seed value. Default is 42.
"""
def __init__(self, reduction_dimensions=64, svd_iterations=20,
theta_max=2.5, eval_points=25, order=5, seed=42):
self.reduction_dimensions = reduction_dimensions
self.svd_iterations = svd_iterations
self.seed = seed
self.theta_max = theta_max
self.eval_points = eval_points
self.order = order
self.seed = seed
def _create_D_inverse(self, graph):
"""
Creating a sparse inverse degree matrix.
Arg types:
* **graph** *(NetworkX graph)* - The graph to be embedded.
Return types:
* **D_inverse** *(Scipy array)* - Diagonal inverse degree matrix.
"""
index = np.arange(graph.number_of_nodes())
values = np.array([1.0/graph.degree[node] for node in range(graph.number_of_nodes())])
shape = (graph.number_of_nodes(), graph.number_of_nodes())
D_inverse = scipy.sparse.coo_matrix((values, (index, index)), shape=shape)
return D_inverse
def _create_A_tilde(self, graph):
"""
Creating a sparse normalized adjacency matrix.
Arg types:
* **graph** *(NetworkX graph)* - The graph to be embedded.
Return types:
* **A_tilde** *(Scipy array)* - The normalized adjacency matrix.
"""
A = nx.adjacency_matrix(graph, nodelist=range(graph.number_of_nodes()))
D_inverse = self._create_D_inverse(graph)
A_tilde = D_inverse.dot(A)
return A_tilde
def _reduce_dimensions(self, X):
"""
Using Truncated SVD.
Arg types:
* **X** *(Scipy COO or Numpy array)* - The wide feature matrix.
Return types:
* **X** *(Numpy array)* - The reduced feature matrix of nodes.
"""
svd = TruncatedSVD(n_components=self.reduction_dimensions,
n_iter=self.svd_iterations,
random_state=self.seed)
svd.fit(X)
X = svd.transform(X)
return X
def _create_reduced_features(self, X):
"""
Creating a dense reduced node feature matrix.
Arg types:
* **X** *(Scipy COO or Numpy array)* - The wide feature matrix.
Return types:
* **X** *(Numpy array)* - The reduced feature matrix of nodes.
"""
if scipy.sparse.issparse(X):
X = self._reduce_dimensions(X)
elif (type(X) is np.ndarray) and (X.shape[1] > self.reduction_dimensions):
X = self._reduce_dimensions(X)
else:
X = X
return X
def fit(self, graph, X):
"""
Fitting a FEATHER-N model.
Arg types:
* **graph** *(NetworkX graph)* - The graph to be embedded.
* **X** *(Scipy COO or Numpy array)* - The matrix of node features.
"""
self._set_seed()
self._check_graph(graph)
X = self._create_reduced_features(X)
A_tilde = self._create_A_tilde(graph)
theta = np.linspace(0.01, self.theta_max, self.eval_points)
X = np.outer(X, theta)
X = X.reshape(graph.number_of_nodes(), -1)
X = np.concatenate([np.cos(X), np.sin(X)], axis=1)
self._feature_blocks = []
for _ in range(self.order):
X = A_tilde.dot(X)
self._feature_blocks.append(X)
self._feature_blocks = np.concatenate(self._feature_blocks, axis=1)
def get_embedding(self):
r"""Getting the node embedding.
Return types:
* **embedding** *(Numpy array)* - The embedding of nodes.
"""
return self._feature_blocks
