Source code for grakel.kernels.neighborhood_subgraph_pairwise_distance
"""Neighborhood subgraph pairwise distance kernel :cite:`costa2010fast`."""
# Author: Ioannis Siglidis <y.siglidis@gmail.com>
# License: BSD 3 clause
import collections
import warnings
import numpy as np
from scipy.sparse import csr_matrix
from sklearn.exceptions import NotFittedError
from sklearn.utils.validation import check_is_fitted
from grakel.kernels import Kernel
from grakel.graph import Graph
from grakel.kernels._c_functions import APHash
# Python 2/3 cross-compatibility import
from six import iteritems
from six.moves import filterfalse
from builtins import range
[docs]class NeighborhoodSubgraphPairwiseDistance(Kernel):
"""The Neighborhood subgraph pairwise distance kernel.
See :cite:`costa2010fast`.
Parameters
----------
r : int, default=3
The maximum considered radius between vertices.
d : int, default=4
Neighborhood depth.
Attributes
----------
_ngx : int
The number of graphs upon fit.
_ngy : int
The number of graphs upon transform.
_fit_keys : dict
A dictionary with keys from `0` to `_d+1`, constructed upon fit
holding an enumeration of all the found (in the fit dataset)
tuples of two hashes and a radius in this certain level.
_X_level_norm_factor : dict
A dictionary with keys from `0` to `_d+1`, that holds the self
calculated kernel `[krg(X_i, X_i) for i=1:ngraphs_X]` for all levels.
"""
_graph_format = "dictionary"
[docs] def __init__(self, n_jobs=None, normalize=False, verbose=False, r=3, d=4):
"""Initialize an NSPD kernel."""
# setup valid parameters and initialise from parent
super(NeighborhoodSubgraphPairwiseDistance, self).__init__(
n_jobs=n_jobs,
normalize=normalize,
verbose=verbose)
self.r = r
self.d = d
self._initialized.update({"r": False, "d": False})
[docs] def initialize(self):
"""Initialize all transformer arguments, needing initialization."""
if not self._initialized["n_jobs"]:
if self.n_jobs is not None:
warnings.warn('no implemented parallelization for NeighborhoodSubgraphPairwiseDistance')
self._initialized["n_jobs"] = True
if not self._initialized["r"]:
if type(self.r) is not int or self.r < 0:
raise ValueError('r must be a positive integer')
self._initialized["r"] = True
if not self._initialized["d"]:
if type(self.d) is not int or self.d < 0:
raise ValueError('d must be a positive integer')
self._initialized["d"] = True
[docs] def parse_input(self, X):
"""Parse and create features for the NSPD kernel.
Parameters
----------
X : iterable
For the input to pass the test, we must have:
Each element must be an iterable with at most three features and at
least one. The first that is obligatory is a valid graph structure
(adjacency matrix or edge_dictionary) while the second is
node_labels and the third edge_labels (that correspond to the given
graph format). A valid input also consists of graph type objects.
Returns
-------
M : dict
A dictionary with keys all the distances from 0 to self.d
and values the the np.arrays with rows corresponding to the
non-null input graphs and columns to the enumerations of tuples
consisting of pairs of hash values and radius, from all the given
graphs of the input (plus the fitted one's on transform).
"""
if not isinstance(X, collections.Iterable):
raise TypeError('input must be an iterable\n')
else:
# Hold the number of graphs
ng = 0
# Holds all the data for combinations of r, d
data = collections.defaultdict(dict)
# Index all keys for combinations of r, d
all_keys = collections.defaultdict(dict)
for (idx, x) in enumerate(iter(X)):
is_iter = False
if isinstance(x, collections.Iterable):
is_iter, x = True, list(x)
if is_iter and len(x) in [0, 3]:
if len(x) == 0:
warnings.warn('Ignoring empty element' +
' on index: '+str(idx))
continue
else:
g = Graph(x[0], x[1], x[2])
g.change_format("adjacency")
elif type(x) is Graph:
g = Graph(x.get_adjacency_matrix(),
x.get_labels(purpose="adjacency", label_type="vertex"),
x.get_labels(purpose="adjacency", label_type="edge"))
else:
raise TypeError('each element of X must have either ' +
'a graph with labels for node and edge ' +
'or 3 elements consisting of a graph ' +
'type object, labels for vertices and ' +
'labels for edges.')
# Bring to the desired format
g.change_format(self._graph_format)
# Take the vertices
vertices = set(g.get_vertices(purpose=self._graph_format))
# Extract the dicitionary
ed = g.get_edge_dictionary()
# Convert edges to tuples
edges = {(j, k) for j in ed.keys() for k in ed[j].keys()}
# Extract labels for nodes
Lv = g.get_labels(purpose=self._graph_format)
# and for edges
Le = g.get_labels(purpose=self._graph_format, label_type="edge")
# Produce all the neighborhoods and the distance pairs
# up to the desired radius and maximum distance
N, D, D_pair = g.produce_neighborhoods(self.r, purpose="dictionary",
with_distances=True, d=self.d)
# Hash all the neighborhoods
H = self._hash_neighborhoods(vertices, edges, Lv, Le, N, D_pair)
if self._method_calling == 1:
for d in filterfalse(lambda x: x not in D,
range(self.d+1)):
for (A, B) in D[d]:
for r in range(self.r+1):
key = (H[r, A], H[r, B])
keys = all_keys[r, d]
idx = keys.get(key, None)
if idx is None:
idx = len(keys)
keys[key] = idx
data[r, d][ng, idx] = data[r, d].get((ng, idx), 0) + 1
elif self._method_calling == 3:
for d in filterfalse(lambda x: x not in D,
range(self.d+1)):
for (A, B) in D[d]:
# Based on the edges of the bidirected graph
for r in range(self.r+1):
keys = all_keys[r, d]
fit_keys = self._fit_keys[r, d]
key = (H[r, A], H[r, B])
idx = fit_keys.get(key, None)
if idx is None:
idx = keys.get(key, None)
if idx is None:
idx = len(keys) + len(fit_keys)
keys[key] = idx
data[r, d][ng, idx] = data[r, d].get((ng, idx), 0) + 1
ng += 1
if ng == 0:
raise ValueError('parsed input is empty')
if self._method_calling == 1:
# A feature matrix for all levels
M = dict()
for (key, d) in filterfalse(lambda a: len(a[1]) == 0,
iteritems(data)):
indexes, data = zip(*iteritems(d))
rows, cols = zip(*indexes)
M[key] = csr_matrix((data, (rows, cols)), shape=(ng, len(all_keys[key])),
dtype=np.int64)
self._fit_keys = all_keys
self._ngx = ng
elif self._method_calling == 3:
# A feature matrix for all levels
M = dict()
for (key, d) in filterfalse(lambda a: len(a[1]) == 0,
iteritems(data)):
indexes, data = zip(*iteritems(d))
rows, cols = zip(*indexes)
M[key] = csr_matrix((data, (rows, cols)),
shape=(ng, len(all_keys[key]) + len(self._fit_keys[key])),
dtype=np.int64)
self._ngy = ng
return M
[docs] def transform(self, X, y=None):
"""Calculate the kernel matrix, between given and fitted dataset.
Parameters
----------
X : iterable
Each element must be an iterable with at most three features and at
least one. The first that is obligatory is a valid graph structure
(adjacency matrix or edge_dictionary) while the second is
node_labels and the third edge_labels (that fitting the given graph
format).
y : Object, default=None
Ignored argument, added for the pipeline.
Returns
-------
K : numpy array, shape = [n_targets, n_input_graphs]
corresponding to the kernel matrix, a calculation between
all pairs of graphs between target an features
"""
self._method_calling = 3
# Check is fit had been called
check_is_fitted(self, ['X'])
# Input validation and parsing
if X is None:
raise ValueError('transform input cannot be None')
else:
Y = self.parse_input(X)
try:
check_is_fitted(self, ['_X_level_norm_factor'])
except NotFittedError:
self._X_level_norm_factor = \
{key: np.array(M.power(2).sum(-1))
for (key, M) in iteritems(self.X)}
N = self._X_level_norm_factor
S = np.zeros(shape=(self._ngy, self._ngx))
for (key, Mp) in filterfalse(lambda x: x[0] not in self.X,
iteritems(Y)):
M = self.X[key]
K = M.dot(Mp.T[:M.shape[1]]).toarray().T
S += np.nan_to_num(K / np.sqrt(np.outer(np.array(Mp.power(2).sum(-1)), N[key])))
self._Y = Y
self._is_transformed = True
if self.normalize:
S /= np.sqrt(np.outer(*self.diagonal()))
return S
[docs] def fit_transform(self, X):
"""Fit and transform, on the same dataset.
Parameters
----------
X : iterable
Each element must be an iterable with at most three features and at
least one. The first that is obligatory is a valid graph structure
(adjacency matrix or edge_dictionary) while the second is
node_labels and the third edge_labels (that fitting the given graph
format). If None the kernel matrix is calculated upon fit data.
The test samples.
Returns
-------
K : numpy array, shape = [n_input_graphs, n_input_graphs]
corresponding to the kernel matrix, a calculation between
all pairs of graphs between target an features
"""
self._method_calling = 2
self.fit(X)
S, N = np.zeros(shape=(self._ngx, self._ngx)), dict()
for (key, M) in iteritems(self.X):
K = M.dot(M.T).toarray()
K_diag = K.diagonal()
N[key] = K_diag
S += np.nan_to_num(K / np.sqrt(np.outer(K_diag, K_diag)))
self._X_level_norm_factor = N
if self.normalize:
return S / len(self.X)
else:
return S
[docs] def diagonal(self):
"""Calculate the kernel matrix diagonal of the fitted data.
Static. Added for completeness.
Parameters
----------
None.
Returns
-------
X_diag : int
Always equal with r*d.
Y_diag : int
Always equal with r*d.
"""
# constant based on normalization of krd
check_is_fitted(self, ['X'])
try:
check_is_fitted(self, ['_X_diag'])
except NotFittedError:
# Calculate diagonal of X
self._X_diag = len(self.X)
try:
check_is_fitted(self, ['_Y'])
return self._X_diag, len(self._Y)
except NotFittedError:
return self._X_diag
def _hash_neighborhoods(self, vertices, edges, Lv, Le, N, D_pair):
"""Hash all neighborhoods and all root nodes.
Parameters
----------
vertices : set
The graph vertices.
edges : set
The set of edges
N : dict
Neighborhoods that map levels (int) to dictionaries of root node
symbols (keys) to list of vertex symbols, which correspond to the
neighbors, that belong to this neighborhood.
D_pairs : dict
A dictionary that maps edges (tuple pairs of vertex symbols) to
element distances (int - as produced from a BFS traversal).
Returns
-------
H : dict
The hashed neighborhoods as a 2-level dict from radious,
vertex to the hashed values.
"""
H, sel = dict(), sorted(list(edges))
for v in vertices:
re, lv, le = sel, Lv, Le
for radius in range(self.r, -1, -1):
sub_vertices = sorted(N[radius][v])
re = {(i, j) for (i, j) in re
if i in sub_vertices and j in sub_vertices}
lv = {v: lv[v] for v in sub_vertices}
le = {e: le[e] for e in edges}
H[radius, v] = hash_graph(D_pair, sub_vertices, re, lv, le)
return H
def hash_graph(D, vertices, edges, glv, gle):
"""Make labels for hashing according to the proposed method.
Produces the graph hash needed for fast comparison.
Parameters
----------
D_pairs : dict
A dictionary that maps edges (tuple pairs of vertex symbols) to
element distances (int - as produced from a BFS traversal).
vertices : set
A set of vertices.
edges : set
A set of edges.
glv : dict
Labels for vertices of the graph.
gle : dict
Labels for edges of the graph.
Returns
-------
hash : int.
The hash value for the given graph.
"""
encoding = ""
# Make labels for vertices
Lv = dict()
for i in vertices:
label = "|".join(sorted([str(D[(i, j)]) + ',' + str(glv[j])
for j in vertices if (i, j) in D]))
encoding += label + "."
Lv[i] = label
encoding = encoding[:-1]+":"
# Expand to labels for edges
for (i, j) in edges:
encoding += Lv[i] + ',' + Lv[j] + ',' + str(gle[(i, j)]) + "_"
# Arash Partov hashing, as in the original
# implementation of NSPK.
return APHash(encoding)