def fit(self, graph):
"""
Fitting a Walklets model.
Arg types:
* **graph** *(NetworkX graph)* - The graph to be embedded.
"""
walker = RandomWalker(self.walk_number, self.walk_length)
walker.do_walks(graph)
num_of_nodes = graph.number_of_nodes()
self._embedding = []
for power in range(1, self.window_size + 1):
walklets = self._select_walklets(walker.walks, power)
model = Word2Vec(walklets,
hs=0,
alpha=self.learning_rate,
iter=self.epochs,
size=self.dimensions,
window=1,
min_count=self.min_count,
workers=self.workers)
embedding = np.array([model[str(n)] for n in range(num_of_nodes)])
self._embedding.append(embedding)
def fit(self, graph: nx.classes.graph.Graph, X: Union[np.array,
coo_matrix]):
"""
Fitting a SINE model.
Arg types:
* **graph** *(NetworkX graph)* - The graph to be embedded.
* **X** *(Scipy COO array)* - The matrix of node features.
"""
self._set_seed()
self._check_graph(graph)
self._walker = RandomWalker(self.walk_length, self.walk_number)
self._walker.do_walks(graph)
self._features = self._feature_transform(graph, X)
self._select_walklets()
model = Word2Vec(self._walklets,
hs=0,
alpha=self.learning_rate,
size=self.dimensions,
window=1,
min_count=self.min_count,
workers=self.workers,
seed=self.seed,
iter=self.epochs)
self.embedding = np.array(
[model[str(n)] for n in range(graph.number_of_nodes())])
def fit(self, graph: nx.classes.graph.Graph):
"""
Fitting a DeepWalk model.
Arg types:
* **graph** *(NetworkX graph)* - The graph to be embedded.
"""
self._set_seed()
graph = self._check_graph(graph)
walker = RandomWalker(self.walk_length, self.walk_number)
walker.do_walks(graph)
model = Word2Vec(
walker.walks,
hs=1,
alpha=self.learning_rate,
epochs=self.epochs,
vector_size=self.dimensions,
window=self.window_size,
min_count=self.min_count,
workers=self.workers,
seed=self.seed,
)
num_of_nodes = graph.number_of_nodes()
self._embedding = [model.wv[str(n)] for n in range(num_of_nodes)]
def fit(self, graph: nx.classes.graph.Graph):
"""
Fitting a Role2vec model.
Arg types:
* **graph** *(NetworkX graph)* - The graph to be embedded.
"""
self._set_seed()
self._check_graph(graph)
walker = RandomWalker(self.walk_length, self.walk_number)
walker.do_walks(graph)
hasher = WeisfeilerLehmanHashing(
graph=graph,
wl_iterations=self.wl_iterations,
attributed=False,
erase_base_features=self.erase_base_features)
node_features = hasher.get_node_features()
documents = self._create_documents(walker.walks, node_features)
model = Doc2Vec(documents,
vector_size=self.dimensions,
window=0,
min_count=self.min_count,
dm=0,
workers=self.workers,
sample=self.down_sampling,
iter=self.epochs,
alpha=self.learning_rate,
seed=self.seed)
self._embedding = [
model.docvecs[str(i)] for i, _ in enumerate(documents)
]
def fit(self, graph):
"""
Fitting a DeepWalk model.
Arg types:
* **graph** *(NetworkX graph)* - The graph to be embedded.
"""
if not self.check_if_walk_exists():
self._check_graph(graph)
# This creates the sentences and keeps it in memory
walker = RandomWalker(self.walk_length, self.walk_number)
walker.do_walks(graph)
sentences = walker.walks
else:
# This returns a iterator
sentences = self.load_prewalk()
self.model = Word2Vec(sentences,
hs=1,
alpha=self.learning_rate,
iter=self.epochs,
size=self.dimensions,
window=self.window_size,
min_count=self.min_count,
workers=self.workers)
def fit(self, graph):
"""
Fitting a GEMSEC model.
Arg types:
* **graph** *(NetworkX graph)* - The graph to be embedded.
"""
self._check_graph(graph)
self._setup_sampling_weights(graph)
self.walker = RandomWalker(self.walk_length, self.walk_number)
self.walker.do_walks(graph)
self._initialize_node_embeddings(graph)
self._initialize_cluster_centers(graph)
self._do_gradient_descent()
def fit(self, graph, X):
"""
Fitting a MUSAE model.
Arg types:
* **graph** *(NetworkX graph)* - The graph to be embedded.
* **X** *(Scipy COO array)* - The binary matrix of node features.
"""
self.graph = graph
self.walker = RandomWalker(self.walk_length, self.walk_number)
self.walker.do_walks(graph)
self.features = self._feature_transform(graph, X)
self.base_docs = self._create_base_docs()
self.embeddings = [self._create_single_embedding(self.base_docs)]
self._learn_musae_embedding()
def fit(self, graph: nx.classes.graph.Graph, X: Union[np.array, coo_matrix]):
"""
Fitting an AE model.
Arg types:
* **graph** *(NetworkX graph)* - The graph to be embedded.
* **X** *(Scipy COO array)* - The binary matrix of node features.
"""
self._set_seed()
self._check_graph(graph)
self.graph = graph
self._walker = RandomWalker(self.walk_length, self.walk_number)
self._walker.do_walks(graph)
self.features = self._feature_transform(graph, X)
self._base_docs = self._create_base_docs()
self._embeddings = [self._create_single_embedding(self._base_docs)]
self._learn_ae_embedding()
def fit(self, graph):
"""
Fitting a DeepWalk model.
Arg types:
* **graph** *(NetworkX graph)* - The graph to be embedded.
"""
walker = RandomWalker(self.walk_number, self.walk_length)
walker.do_walks(graph)
model = Word2Vec(walker.walks,
hs=1,
alpha=self.learning_rate,
iter=self.epochs,
size=self.dimensions,
window=self.window_size,
min_count=self.min_count,
workers=self.workers)
num_of_nodes = graph.number_of_nodes()
self._embedding = [model[str(n)] for n in range(num_of_nodes)]
class MUSAE(Estimator):
r"""An implementation of `"MUSAE" <https://arxiv.org/abs/1909.13021>`_
from the Arxiv '19 paper "MUSAE: Multi-Scale Attributed Node Embedding". The
procedure does attributed random walks to approximate the adjacency matrix power
node feature matrix products. The matrices are decomposed implicitly by a Skip-Gram
style optimizer. The individual embeddings are concatenated together to form a
multi-scale attributed node embedding. This way the feature distributions at different scales
are separable.
Args:
walk_number (int): Number of random walks. Default is 10.
walk_length (int): Length of random walks. Default is 80.
dimensions (int): Dimensionality of embedding. Default is 32.
workers (int): Number of cores. Default is 4.
window_size (int): Matrix power order. Default is 3.
epochs (int): Number of epochs. Default is 1.
learning_rate (float): HogWild! learning rate. Default is 0.05.
down_sampling (float): Down sampling rate in the corpus. Default is 0.0001.
min_count (int): Minimal count of node occurences. Default is 1.
"""
def __init__(self,
walk_number=5,
walk_length=80,
dimensions=32,
workers=4,
window_size=3,
epochs=5,
learning_rate=0.05,
down_sampling=0.0001,
min_count=1):
self.walk_number = walk_number
self.walk_length = walk_length
self.dimensions = dimensions
self.workers = workers
self.window_size = window_size
self.epochs = epochs
self.learning_rate = learning_rate
self.down_sampling = down_sampling
self.min_count = min_count
def _feature_transform(self, graph, X):
features = {str(node): [] for node in graph.nodes()}
nodes = X.row
for i, node in enumerate(nodes):
features[str(node)].append("feature_" + str(X.col[i]))
return features
def _create_single_embedding(self, document_collections):
model = Doc2Vec(document_collections,
vector_size=self.dimensions,
window=0,
min_count=self.min_count,
alpha=self.learning_rate,
dm=0,
sample=self.down_sampling,
workers=self.workers,
epochs=self.epochs)
emb = np.array([
model.docvecs[str(n)] for n in range(self.graph.number_of_nodes())
])
return emb
def _create_documents(self, features):
features_out = [
TaggedDocument(words=[
str(feat) for feat_elems in feature_set for feat in feat_elems
],
tags=[str(node)])
for node, feature_set in features.items()
]
return features_out
def _setup_musae_features(self, approximation):
features = {str(node): [] for node in self.graph.nodes()}
for walk in self.walker.walks:
for i in range(len(walk) - approximation):
source = walk[i]
target = walk[i + approximation]
features[str(source)].append(self.features[str(target)] +
[str(target)])
features[str(target)].append(self.features[str(source)] +
[str(source)])
return self._create_documents(features)
def _learn_musae_embedding(self):
for approximation in range(self.window_size):
features = self._setup_musae_features(approximation + 1)
embedding = self._create_single_embedding(features)
self.embeddings.append(embedding)
def _create_base_docs(self):
features_out = [
TaggedDocument(words=[str(feature) for feature in features],
tags=[str(node)])
for node, features in self.features.items()
]
return features_out
def fit(self, graph, X):
"""
Fitting a MUSAE model.
Arg types:
* **graph** *(NetworkX graph)* - The graph to be embedded.
* **X** *(Scipy COO array)* - The binary matrix of node features.
"""
self._check_graph(graph)
self.graph = graph
self.walker = RandomWalker(self.walk_length, self.walk_number)
self.walker.do_walks(graph)
self.features = self._feature_transform(graph, X)
self.base_docs = self._create_base_docs()
self.embeddings = [self._create_single_embedding(self.base_docs)]
self._learn_musae_embedding()
def get_embedding(self):
r"""Getting the node embedding.
Return types:
* **embedding** *(Numpy array)* - The embedding of nodes.
"""
embedding = np.concatenate(self.embeddings, axis=1)
return embedding
class SINE(Estimator):
r"""An implementation of `"SINE" <https://arxiv.org/pdf/1810.06768.pdf>`_
from the ICDM '18 paper "SINE: Scalable Incomplete Network Embedding". The
procedure implicitly factorizes a joint adjacency matrix power and feature matrix.
The decomposition happens on truncated random walks and the adjacency matrix powers
are pooled together.
Args:
walk_number (int): Number of random walks. Default is 10.
walk_length (int): Length of random walks. Default is 80.
dimensions (int): Dimensionality of embedding. Default is 128.
workers (int): Number of cores. Default is 4.
window_size (int): Matrix power order. Default is 5.
epochs (int): Number of epochs. Default is 1.
learning_rate (float): HogWild! learning rate. Default is 0.05.
min_count (int): Minimal count of node occurrences. Default is 1.
seed (int): Random seed value. Default is 42.
"""
def __init__(self,
walk_number: int = 10,
walk_length: int = 80,
dimensions: int = 128,
workers: int = 4,
window_size: int = 5,
epochs: int = 1,
learning_rate: float = 0.05,
min_count: int = 1,
seed: int = 42):
self.walk_number = walk_number
self.walk_length = walk_length
self.dimensions = dimensions
self.workers = workers
self.window_size = window_size
self.epochs = epochs
self.learning_rate = learning_rate
self.min_count = min_count
self.seed = seed
def _feature_transform(self, graph, X):
features = {str(node): [] for node in graph.nodes()}
nodes = X.row
for i, node in enumerate(nodes):
features[str(node)].append("feature_" + str(X.col[i]))
return features
def _select_walklets(self):
self._walklets = []
for walk in self._walker.walks:
for power in range(1, self.window_size + 1):
for step in range(power + 1):
neighbors = [
n for i, n in enumerate(walk[step:]) if i % power == 0
]
neighbors = [n for n in neighbors for _ in range(0, 3)]
neighbors = [
random.choice(self._features[val])
if i % 3 == 1 and self._features[val] else val
for i, val in enumerate(neighbors)
]
self._walklets.append(neighbors)
del self._walker
def fit(self, graph: nx.classes.graph.Graph, X: Union[np.array,
coo_matrix]):
"""
Fitting a SINE model.
Arg types:
* **graph** *(NetworkX graph)* - The graph to be embedded.
* **X** *(Scipy COO array)* - The matrix of node features.
"""
self._set_seed()
self._check_graph(graph)
self._walker = RandomWalker(self.walk_length, self.walk_number)
self._walker.do_walks(graph)
self._features = self._feature_transform(graph, X)
self._select_walklets()
model = Word2Vec(self._walklets,
hs=0,
alpha=self.learning_rate,
size=self.dimensions,
window=1,
min_count=self.min_count,
workers=self.workers,
seed=self.seed,
iter=self.epochs)
self.embedding = np.array(
[model[str(n)] for n in range(graph.number_of_nodes())])
def get_embedding(self) -> np.array:
r"""Getting the node embedding.
Return types:
* **embedding** *(Numpy array)* - The embedding of nodes.
"""
embedding = self.embedding
return embedding
class GEMSEC(Estimator):
r"""An implementation of `"GEMSEC" <https://arxiv.org/abs/1802.03997>`_
from the ASONAM '19 paper "GEMSEC: Graph Embedding with Self Clustering".
The procedure uses random walks to approximate the pointwise mutual information
matrix obtained by pooling normalized adjacency matrix powers. This matrix
is decomposed by an approximate factorization technique which is combined
with a k-means like clustering cost. A node embedding and clustering are
learned jointly.
Args:
walk_number (int): Number of random walks. Default is 5.
walk_length (int): Length of random walks. Default is 80.
dimensions (int): Dimensionality of embedding. Default is 32.
negative_samples (int): Number of negative samples. Default is 5.
window_size (int): Matrix power order. Default is 5.
learning_rate (float): Gradient descent learning rate. Default is 0.1.
clusters (int): Number of cluster centers. Default is 10.
gamma (float): Clustering cost weight coefficient. Default is 0.1.
seed (int): Random seed value. Default is 42.
"""
def __init__(self,
walk_number: int = 5,
walk_length: int = 80,
dimensions: int = 32,
negative_samples: int = 5,
window_size: int = 5,
learning_rate: float = 0.1,
clusters: int = 10,
gamma: float = 0.1,
seed: int = 42):
self.walk_number = walk_number
self.walk_length = walk_length
self.dimensions = dimensions
self.negative_samples = negative_samples
self.window_size = window_size
self.learning_rate = learning_rate
self.clusters = clusters
self.gamma = gamma
self.seed = seed
def _setup_sampling_weights(self, graph):
"""
Creating a negative sampling table.
Arg types:
* **graph** *(NetworkX graph)* - The graph for negative sampling.
"""
self._sampler = {}
index = 0
for node in graph.nodes():
for _ in range(graph.degree(node)):
self._sampler[index] = node
index = index + 1
self._global_index = index - 1
def _initialize_node_embeddings(self, graph):
"""
Creating a node embedding array.
Arg types:
* **graph** *(NetworkX graph)* - The graph for negative sampling.
"""
shape = (graph.number_of_nodes(), self.dimensions)
self._base_embedding = np.random.normal(0, 1.0 / self.dimensions,
shape)
def _initialize_cluster_centers(self, graph):
"""
Creating a cluster center array.
Arg types:
* **graph** *(NetworkX graph)* - The graph for negative sampling.
"""
shape = (self.dimensions, self.clusters)
self._cluster_centers = np.random.normal(0, 1.0 / self.dimensions,
shape)
def _sample_negative_samples(self):
"""
Sampling a batch of nodes as negative samples.
Return types:
* **negative_samples** *(list)*: List of negative sampled nodes.
"""
negative_samples = [
self._sampler[random.randint(0, self._global_index)]
for _ in range(self.negative_samples)
]
return negative_samples
def _calculcate_noise_vector(self, negative_samples, source_node):
"""
Getting the noise vector for the weight update.
Arg types:
* **negative_samples** *(list)*: List of negative sampled nodes.
* **source_node** *(int)* - Source node in the walk.
Return types:
* **noise_vector** *(NumPy array) - Noise update vector.
"""
noise_vectors = self._base_embedding[negative_samples, :]
source_vector = self._base_embedding[int(source_node), :]
raw_scores = noise_vectors.dot(source_vector.T)
raw_scores = np.exp(np.clip(raw_scores, -15, 15))
scores = raw_scores / np.sum(raw_scores)
scores = scores.reshape(-1, 1)
noise_vector = np.sum(scores * noise_vectors, axis=0)
return noise_vector
def _calculate_cluster_vector(self, source_node):
"""
Getting the cluster vector for the weight update.
Arg types:
* **source_node** *(int)* - Source node in the walk.
Return types:
* **cluster_vector** *(NumPy array) - Cluster update vector.
* **cluster_index** *(int)*: Node cluster membership index.
"""
distances = self._base_embedding[int(source_node), :].reshape(
-1, 1) - self._cluster_centers
scores = np.power(np.sum(np.power(distances, 2), axis=0), 0.5)
cluster_index = np.argmin(scores)
cluster_vector = distances[:, cluster_index] / scores[cluster_index]
return cluster_vector, cluster_index
def _do_descent_for_pair(self, negative_samples, source_node, target_node):
"""
Updating the cluster center and the node embedding.
Arg types:
* **negative_samples** *(list)* - Negative samples.
* **source_node** *(int)* - Source node in the walk.
* **target_node** *(int)* - Target node in the walk.
"""
noise_vector = self._calculcate_noise_vector(negative_samples,
source_node)
target_vector = self._base_embedding[int(target_node), :]
cluster_vector, cluster_index = self._calculate_cluster_vector(
source_node)
node_gradient = noise_vector - target_vector + self.gamma * cluster_vector
node_gradient = node_gradient / np.linalg.norm(node_gradient)
self._base_embedding[
int(source_node), :] += -self.learning_rate * node_gradient
self._cluster_centers[:,
cluster_index] += self.learning_rate * self.gamma * cluster_vector
def _update_a_weight(self, source_node, target_node):
"""
Updating the weights for a pair of nodes.
Arg types:
* **source_node** *(int)* - Source node in the walk.
* **target_node** *(int)* - Target node in the walk.
"""
negative_samples = self._sample_negative_samples()
self._do_descent_for_pair(negative_samples, source_node, target_node)
self._do_descent_for_pair(negative_samples, target_node, source_node)
def _do_gradient_descent(self):
"""
Updating the embedding weights and cluster centers with gradient descent.
"""
random.shuffle(self._walker.walks)
for walk in self._walker.walks:
for i, source_node in enumerate(walk[:self.walk_length -
self.window_size]):
for step in range(1, self.window_size + 1):
target_node = walk[i + step]
self._update_a_weight(source_node, target_node)
def fit(self, graph: nx.classes.graph.Graph):
"""
Fitting a GEMSEC model.
Arg types:
* **graph** *(NetworkX graph)* - The graph to be embedded.
"""
self._set_seed()
self._check_graph(graph)
self._setup_sampling_weights(graph)
self._walker = RandomWalker(self.walk_length, self.walk_number)
self._walker.do_walks(graph)
self._initialize_node_embeddings(graph)
self._initialize_cluster_centers(graph)
self._do_gradient_descent()
def get_embedding(self) -> np.array:
r"""Getting the node embedding.
Return types:
* **embedding** *(Numpy array)*: The embedding of nodes.
"""
return np.array(self._base_embedding)
def _get_membership(self, node):
"""Getting the cluster membership of a node.
Arg types:
* **node** *(int)* - The graph to be clustered.
Return types:
* **cluster_index** *(int)*: Node cluster membership index.
"""
distances = self._base_embedding[node, :].reshape(
-1, 1) - self._cluster_centers
scores = np.power(np.sum(np.power(distances, 2), axis=0), 0.5)
cluster_index = np.argmin(scores)
return cluster_index
def get_memberships(self) -> Dict[int, int]:
r"""Getting the cluster membership of nodes.
Return types:
* **memberships** *(dict)*: Node cluster memberships.
"""
memberships = {
node: self._get_membership(node)
for node in range(self._base_embedding.shape[0])
}
return memberships