""" This module provides the functions for node classification problem.
The functions in this module are not imported
into the top level `networkx` namespace.
You can access these functions by importing
the `networkx.algorithms.node_classification` modules,
then accessing the functions as attributes of `node_classification`.
For example:
>>> from networkx.algorithms import node_classification
>>> G = nx.path_graph(4)
>>> G.edges()
EdgeView([(0, 1), (1, 2), (2, 3)])
>>> G.nodes[0]["label"] = "A"
>>> G.nodes[3]["label"] = "B"
>>> node_classification.harmonic_function(G)
['A', 'A', 'B', 'B']
References
----------
Zhu, X., Ghahramani, Z., & Lafferty, J. (2003, August).
Semi-supervised learning using gaussian fields and harmonic functions.
In ICML (Vol. 3, pp. 912-919).
"""
import networkx as nx
__all__ = ["harmonic_function", "local_and_global_consistency"]
[docs]
@nx.utils.not_implemented_for("directed")
@nx._dispatchable(node_attrs="label_name")
def harmonic_function(G, max_iter=30, label_name="label"):
"""Node classification by Harmonic function
Function for computing Harmonic function algorithm by Zhu et al.
Parameters
----------
G : NetworkX Graph
max_iter : int
maximum number of iterations allowed
label_name : string
name of target labels to predict
Returns
-------
predicted : list
List of length ``len(G)`` with the predicted labels for each node.
Raises
------
NetworkXError
If no nodes in `G` have attribute `label_name`.
Examples
--------
>>> from networkx.algorithms import node_classification
>>> G = nx.path_graph(4)
>>> G.nodes[0]["label"] = "A"
>>> G.nodes[3]["label"] = "B"
>>> G.nodes(data=True)
NodeDataView({0: {'label': 'A'}, 1: {}, 2: {}, 3: {'label': 'B'}})
>>> G.edges()
EdgeView([(0, 1), (1, 2), (2, 3)])
>>> predicted = node_classification.harmonic_function(G)
>>> predicted
['A', 'A', 'B', 'B']
References
----------
Zhu, X., Ghahramani, Z., & Lafferty, J. (2003, August).
Semi-supervised learning using gaussian fields and harmonic functions.
In ICML (Vol. 3, pp. 912-919).
"""
import numpy as np
import scipy as sp
X = nx.to_scipy_sparse_array(G) # adjacency matrix
labels, label_dict = _get_label_info(G, label_name)
if labels.shape[0] == 0:
raise nx.NetworkXError(
f"No node on the input graph is labeled by '{label_name}'."
)
n_samples = X.shape[0]
n_classes = label_dict.shape[0]
F = np.zeros((n_samples, n_classes))
# Build propagation matrix
degrees = X.sum(axis=0)
degrees[degrees == 0] = 1 # Avoid division by 0
# TODO: csr_array
D = sp.sparse.csr_array(sp.sparse.diags((1.0 / degrees), offsets=0))
P = (D @ X).tolil()
P[labels[:, 0]] = 0 # labels[:, 0] indicates IDs of labeled nodes
# Build base matrix
B = np.zeros((n_samples, n_classes))
B[labels[:, 0], labels[:, 1]] = 1
for _ in range(max_iter):
F = (P @ F) + B
return label_dict[np.argmax(F, axis=1)].tolist()
[docs]
@nx.utils.not_implemented_for("directed")
@nx._dispatchable(node_attrs="label_name")
def local_and_global_consistency(G, alpha=0.99, max_iter=30, label_name="label"):
"""Node classification by Local and Global Consistency
Function for computing Local and global consistency algorithm by Zhou et al.
Parameters
----------
G : NetworkX Graph
alpha : float
Clamping factor
max_iter : int
Maximum number of iterations allowed
label_name : string
Name of target labels to predict
Returns
-------
predicted : list
List of length ``len(G)`` with the predicted labels for each node.
Raises
------
NetworkXError
If no nodes in `G` have attribute `label_name`.
Examples
--------
>>> from networkx.algorithms import node_classification
>>> G = nx.path_graph(4)
>>> G.nodes[0]["label"] = "A"
>>> G.nodes[3]["label"] = "B"
>>> G.nodes(data=True)
NodeDataView({0: {'label': 'A'}, 1: {}, 2: {}, 3: {'label': 'B'}})
>>> G.edges()
EdgeView([(0, 1), (1, 2), (2, 3)])
>>> predicted = node_classification.local_and_global_consistency(G)
>>> predicted
['A', 'A', 'B', 'B']
References
----------
Zhou, D., Bousquet, O., Lal, T. N., Weston, J., & Schölkopf, B. (2004).
Learning with local and global consistency.
Advances in neural information processing systems, 16(16), 321-328.
"""
import numpy as np
import scipy as sp
X = nx.to_scipy_sparse_array(G) # adjacency matrix
labels, label_dict = _get_label_info(G, label_name)
if labels.shape[0] == 0:
raise nx.NetworkXError(
f"No node on the input graph is labeled by '{label_name}'."
)
n_samples = X.shape[0]
n_classes = label_dict.shape[0]
F = np.zeros((n_samples, n_classes))
# Build propagation matrix
degrees = X.sum(axis=0)
degrees[degrees == 0] = 1 # Avoid division by 0
# TODO: csr_array
D2 = np.sqrt(sp.sparse.csr_array(sp.sparse.diags((1.0 / degrees), offsets=0)))
P = alpha * ((D2 @ X) @ D2)
# Build base matrix
B = np.zeros((n_samples, n_classes))
B[labels[:, 0], labels[:, 1]] = 1 - alpha
for _ in range(max_iter):
F = (P @ F) + B
return label_dict[np.argmax(F, axis=1)].tolist()
def _get_label_info(G, label_name):
"""Get and return information of labels from the input graph
Parameters
----------
G : Network X graph
label_name : string
Name of the target label
Returns
-------
labels : numpy array, shape = [n_labeled_samples, 2]
Array of pairs of labeled node ID and label ID
label_dict : numpy array, shape = [n_classes]
Array of labels
i-th element contains the label corresponding label ID `i`
"""
import numpy as np
labels = []
label_to_id = {}
lid = 0
for i, n in enumerate(G.nodes(data=True)):
if label_name in n[1]:
label = n[1][label_name]
if label not in label_to_id:
label_to_id[label] = lid
lid += 1
labels.append([i, label_to_id[label]])
labels = np.array(labels)
label_dict = np.array(
[label for label, _ in sorted(label_to_id.items(), key=lambda x: x[1])]
)
return (labels, label_dict)
