scikit-network 0.31.0__cp311-cp311-macosx_11_0_arm64.whl → 0.33.0__cp311-cp311-macosx_11_0_arm64.whl

{scikit_network-0.31.0.dist-info → scikit_network-0.33.0.dist-info}/AUTHORS.rst

@@ -13,7 +13,6 @@ Development Lead
 * Simon Delarue <simon.delarue@telecom-paris.fr>
 * Marc Jeanmougin <marc.jeanmougin@telecom-paris.fr>
 
-
 Former lead
 -----------
 
@@ -39,3 +38,6 @@ Contributors
 * Flávio Juvenal
 * Wenzhuo Zhao
 * Henry Carscadden
+* Yiwen Peng
+* Ahmed Zaiou
+* Laurène David

{scikit_network-0.31.0.dist-info → scikit_network-0.33.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scikit-network
-Version: 0.31.0
+Version: 0.33.0
 Summary: Graph algorithms
 Home-page: https://github.com/sknetwork-team/scikit-network
 Author: Scikit-network team
@@ -15,16 +15,16 @@ Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Natural Language :: English
 Classifier: Programming Language :: Cython
-Classifier: Programming Language :: Python :: 3.8
 Classifier: Programming Language :: Python :: 3.9
 Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
-Requires-Python: >=3.8
+Classifier: Programming Language :: Python :: 3.12
+Requires-Python: >=3.9
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 License-File: AUTHORS.rst
-Requires-Dist: numpy (>=1.22.4)
-Requires-Dist: scipy (>=1.7.3)
+Requires-Dist: numpy >=1.22.4
+Requires-Dist: scipy >=1.7.3
 
 .. image:: https://perso.telecom-paristech.fr/bonald/logo_sknetwork.png
     :align: right
@@ -118,6 +118,28 @@ the `Journal of Machine Learning Research <https://jmlr.org>`_:
 History
 =======
 
+0.33.0 (2024-07-16)
+-------------------
+
+* Add Python 3.12
+* Drop Python 3.8
+
+0.32.1 (2024-04-02)
+-------------------
+
+* Fix documentation
+* Fix wheel upload
+
+0.32.0 (2024-03-29)
+-------------------
+
+* Add Leiden clustering algorithm
+* Add k-center clustering algorithm
+* Add functions to detect and break cycles
+* Add damping factor in diffusion
+* Fix F1 scores
+* Remove hierarchical Louvain embedding
+* Get clustering coefficient for directed graphs
 
 0.31.0 (2023-05-22)
 -------------------

scikit_network-0.33.0.dist-info/RECORD

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+scikit_network-0.33.0.dist-info/LICENSE,sha256=zKbJMpbSKgGEUaNr_fKgvJrvw_3W4gnJs5XdLCK5Sxo,1622
+scikit_network-0.33.0.dist-info/WHEEL,sha256=ANsQuXN11eSX1PFSD4UW7vUcpdaOm9VfCH5CSYqUC20,109
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{scikit_network-0.31.0.dist-info → scikit_network-0.33.0.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.38.4)
+Generator: setuptools (70.3.0)
 Root-Is-Purelib: false
 Tag: cp311-cp311-macosx_11_0_arm64
 

sknetwork/__init__.py

@@ -4,7 +4,7 @@
 
 __author__ = """scikit-network team"""
 __email__ = "thomas.bonald@telecom-paris.fr"
-__version__ = '0.31.0'
+__version__ = '0.33.0'
 
 import sknetwork.topology
 import sknetwork.path

sknetwork/classification/base.py

@@ -38,7 +38,7 @@ class BaseClassifier(Algorithm, ABC):
         self.probs_row_ = None
         self.probs_col_ = None
 
-    def predict(self, columns=False) -> np.ndarray:
+    def predict(self, columns: bool = False) -> np.ndarray:
         """Return the labels predicted by the algorithm.
 
         Parameters

sknetwork/classification/base_rank.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
-Created on March 2020
+Created in March 2020
 @author: Nathan de Lara <nathan.delara@polytechnique.org>
 """
 from functools import partial
@@ -12,7 +12,7 @@ import numpy as np
 from scipy import sparse
 
 from sknetwork.classification.base import BaseClassifier
-from sknetwork.linalg.normalization import normalize
+from sknetwork.linalg.normalizer import normalize
 from sknetwork.ranking.base import BaseRanking
 from sknetwork.utils.check import check_labels, check_n_jobs
 from sknetwork.utils.format import get_adjacency_values
@@ -114,7 +114,7 @@ class RankClassifier(BaseClassifier):
         seeds_labels = seeds_labels.astype(int)
         labels_unique, n_classes = check_labels(seeds_labels)
         seeds_all = self._process_labels(seeds_labels)
-        local_function = partial(self.algorithm.fit_transform, adjacency)
+        local_function = partial(self.algorithm.fit_predict, adjacency)
         with Pool(self.n_jobs) as pool:
             scores = np.array(pool.map(local_function, seeds_all))
         scores = scores.T

sknetwork/classification/diffusion.py

@@ -11,7 +11,7 @@ from scipy import sparse
 
 from sknetwork.classification.base import BaseClassifier
 from sknetwork.path.distances import get_distances
-from sknetwork.linalg.normalization import normalize
+from sknetwork.linalg.normalizer import normalize
 from sknetwork.utils.format import get_adjacency_values
 from sknetwork.utils.membership import get_membership
 from sknetwork.utils.neighbors import get_degrees
@@ -38,11 +38,14 @@ class DiffusionClassifier(BaseClassifier):
         Labels of nodes.
     probs_ : sparse.csr_matrix, shape (n_row, n_labels)
         Probability distribution over labels.
-    labels_row_, labels_col_ : np.ndarray
-        Labels of rows and columns, for bipartite graphs.
-    probs_row_, probs_col_ : sparse.csr_matrix, shape (n_row, n_labels)
-        Probability distributions over labels for rows and columns (for bipartite graphs).
-
+    labels_row_ : np.ndarray
+        Labels of rows, for bipartite graphs.
+    labels_col_ : np.ndarray
+        Labels of columns, for bipartite graphs.
+    probs_row_ : sparse.csr_matrix, shape (n_row, n_labels)
+        Probability distributions over labels of rows, for bipartite graphs.
+    probs_col_ : sparse.csr_matrix, shape (n_col, n_labels)
+        Probability distributions over labels of columns, for bipartite graphs.
     Example
     -------
     >>> from sknetwork.data import karate_club
@@ -52,7 +55,7 @@ class DiffusionClassifier(BaseClassifier):
     >>> labels_true = graph.labels
     >>> labels = {0: labels_true[0], 33: labels_true[33]}
     >>> labels_pred = diffusion.fit_predict(adjacency, labels)
-    >>> np.round(np.mean(labels_pred == labels_true), 2)
+    >>> round(np.mean(labels_pred == labels_true), 2)
     0.97
 
     References
@@ -71,20 +74,23 @@ class DiffusionClassifier(BaseClassifier):
         self.scale = scale
 
     def fit(self, input_matrix: Union[sparse.csr_matrix, np.ndarray],
-            labels: Optional[Union[dict, np.ndarray]] = None, labels_row: Optional[Union[dict, np.ndarray]] = None,
-            labels_col: Optional[Union[dict, np.ndarray]] = None, force_bipartite: bool = False) \
+            labels: Optional[Union[dict, list, np.ndarray]] = None,
+            labels_row: Optional[Union[dict, list, np.ndarray]] = None,
+            labels_col: Optional[Union[dict, list, np.ndarray]] = None, force_bipartite: bool = False) \
             -> 'DiffusionClassifier':
         """Compute the solution to the Dirichlet problem (temperatures at equilibrium).
 
         Parameters
         ----------
-        input_matrix :
+        input_matrix : sparse.csr_matrix, np.ndarray
             Adjacency matrix or biadjacency matrix of the graph.
-        labels :
+        labels : dict, np.ndarray
             Known labels (dictionary or vector of int). Negative values ignored.
-        labels_row, labels_col :
-            Labels of rows and columns for bipartite graphs. Negative values ignored.
-        force_bipartite :
+        labels_row : dict, np.ndarray
+            Labels of rows for bipartite graphs. Negative values ignored.
+        labels_col : dict, np.ndarray
+            Labels of columns for bipartite graphs. Negative values ignored.
+        force_bipartite : bool
             If ``True``, consider the input matrix as a biadjacency matrix (default = ``False``).
 
         Returns
@@ -98,7 +104,10 @@ class DiffusionClassifier(BaseClassifier):
         labels = values.astype(int)
         if (labels < 0).all():
             raise ValueError('At least one node must be given a non-negative label.')
-        temperatures = get_membership(labels).toarray()
+        labels_reindex = labels.copy()
+        labels_unique, inverse = np.unique(labels[labels >= 0], return_inverse=True)
+        labels_reindex[labels >= 0] = inverse
+        temperatures = get_membership(labels_reindex).toarray()
         temperatures_seeds = temperatures[labels >= 0]
         temperatures[labels < 0] = 0.5
         diffusion = normalize(adjacency)
@@ -107,7 +116,7 @@ class DiffusionClassifier(BaseClassifier):
             temperatures[labels >= 0] = temperatures_seeds
         if self.centering:
             temperatures -= temperatures.mean(axis=0)
-        labels_ = temperatures.argmax(axis=1)
+        labels_ = labels_unique[temperatures.argmax(axis=1)]
 
         # softmax
         if self.centering:

sknetwork/classification/knn.py

@@ -12,7 +12,7 @@ from scipy import sparse
 
 from sknetwork.classification.base import BaseClassifier
 from sknetwork.embedding.base import BaseEmbedding
-from sknetwork.linalg.normalization import get_norms, normalize
+from sknetwork.linalg.normalizer import get_norms, normalize
 from sknetwork.utils.check import check_n_neighbors
 from sknetwork.utils.format import get_adjacency_values
 
@@ -22,12 +22,12 @@ class NNClassifier(BaseClassifier):
 
     Parameters
     ----------
-    n_neighbors :
+    n_neighbors : int
         Number of nearest neighbors .
-    embedding_method :
+    embedding_method : :class:`BaseEmbedding`
         Embedding method used to represent nodes in vector space.
         If ``None`` (default), use identity.
-    normalize :
+    normalize : bool
         If ``True``, apply normalization so that all vectors have norm 1 in the embedding space.
 
     Attributes
@@ -36,10 +36,14 @@ class NNClassifier(BaseClassifier):
         Labels of nodes.
     probs_ : sparse.csr_matrix, shape (n_row, n_labels)
         Probability distribution over labels.
-    labels_row_, labels_col_ : np.ndarray
-        Labels of rows and columns, for bipartite graphs.
-    probs_row_, probs_col_ : sparse.csr_matrix, shape (n_row, n_labels)
-        Probability distributions over labels for rows and columns (for bipartite graphs).
+    labels_row_ : np.ndarray
+        Labels of rows, for bipartite graphs.
+    labels_col_ : np.ndarray
+        Labels of columns, for bipartite graphs.
+    probs_row_ : sparse.csr_matrix, shape (n_row, n_labels)
+        Probability distributions over labels of rows, for bipartite graphs.
+    probs_col_ : sparse.csr_matrix, shape (n_col, n_labels)
+        Probability distributions over labels of columns, for bipartite graphs.
 
     Example
     -------
@@ -51,7 +55,7 @@ class NNClassifier(BaseClassifier):
     >>> labels_true = graph.labels
     >>> labels = {0: labels_true[0], 33: labels_true[33]}
     >>> labels_pred = classifier.fit_predict(adjacency, labels)
-    >>> np.round(np.mean(labels_pred == labels_true), 2)
+    >>> round(np.mean(labels_pred == labels_true), 2)
     0.82
     """
     def __init__(self, n_neighbors: int = 3, embedding_method: Optional[BaseEmbedding] = None, normalize: bool = True):
@@ -93,18 +97,21 @@ class NNClassifier(BaseClassifier):
 
         return probs, labels
 
-    def fit(self, input_matrix: Union[sparse.csr_matrix, np.ndarray], labels: Union[np.ndarray, dict] = None,
-            labels_row: Union[np.ndarray, dict] = None, labels_col: Union[np.ndarray, dict] = None) -> 'NNClassifier':
+    def fit(self, input_matrix: Union[sparse.csr_matrix, np.ndarray], labels: Union[np.ndarray, list, dict] = None,
+            labels_row: Union[np.ndarray, list, dict] = None,
+            labels_col: Union[np.ndarray, list, dict] = None) -> 'NNClassifier':
         """Node classification by k-nearest neighbors in the embedding space.
 
         Parameters
         ----------
-        input_matrix :
+        input_matrix : sparse.csr_matrix, np.ndarray
             Adjacency matrix or biadjacency matrix of the graph.
-        labels :
-            Known labels (dictionary or array). Negative values ignored.
-        labels_row, labels_col :
-            Known labels of rows and columns (for bipartite graphs).
+        labels : np.ndarray, dict
+            Known labels. Negative values ignored.
+        labels_row : np.ndarray, dict
+            Known labels of rows, for bipartite graphs.
+        labels_col : np.ndarray, dict
+            Known labels of columns, for bipartite graphs.
 
         Returns
         -------

sknetwork/classification/metrics.py

@@ -34,7 +34,7 @@ def get_accuracy_score(labels_true: np.ndarray, labels_pred: np.ndarray) -> floa
     >>> import numpy as np
     >>> labels_true = np.array([0, 0, 1, 1])
     >>> labels_pred = np.array([0, 0, 0, 1])
-    >>> get_accuracy_score(labels_true, labels_pred)
+    >>> round(get_accuracy_score(labels_true, labels_pred), 2)
     0.75
     """
     check_vector_format(labels_true, labels_pred)
@@ -105,7 +105,7 @@ def get_f1_score(labels_true: np.ndarray, labels_pred: np.ndarray, return_precis
     >>> import numpy as np
     >>> labels_true = np.array([0, 0, 1, 1])
     >>> labels_pred = np.array([0, 0, 0, 1])
-    >>> np.round(get_f1_score(labels_true, labels_pred), 2)
+    >>> round(get_f1_score(labels_true, labels_pred), 2)
     0.67
     """
     values = set(labels_true[labels_true >= 0]) | set(labels_pred[labels_pred >= 0])
@@ -158,7 +158,7 @@ def get_f1_scores(labels_true: np.ndarray, labels_pred: np.ndarray, return_preci
     mask = counts_pred > 0
     precisions[mask] = counts_correct[mask] / counts_pred[mask]
     f1_scores = np.zeros(n_labels)
-    mask = (counts_true > 0) & (counts_pred > 0)
+    mask = (precisions > 0) & (recalls > 0)
     f1_scores[mask] = 2 / (1 / precisions[mask] + 1 / recalls[mask])
     if return_precision_recall:
         return f1_scores, precisions, recalls
@@ -188,7 +188,7 @@ def get_average_f1_score(labels_true: np.ndarray, labels_pred: np.ndarray, avera
     >>> import numpy as np
     >>> labels_true = np.array([0, 0, 1, 1])
     >>> labels_pred = np.array([0, 0, 0, 1])
-    >>> np.round(get_average_f1_score(labels_true, labels_pred), 2)
+    >>> round(get_average_f1_score(labels_true, labels_pred), 2)
     0.73
     """
     if average == 'micro':

sknetwork/classification/pagerank.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python3
 # -*- coding: utf-8 -*-
 """
-Created on March 2020
+Created in March 2020
 @author: Nathan de Lara <nathan.delara@polytechnique.org>
 """
 from typing import Optional
@@ -17,9 +17,9 @@ class PageRankClassifier(RankClassifier):
 
     Parameters
     ----------
-    damping_factor:
+    damping_factor: float
         Probability to continue the random walk.
-    solver : :obj:`str`
+    solver : str
         Which solver to use: 'piteration', 'diteration', 'bicgstab', 'lanczos'.
     n_iter : int
         Number of iterations for some solvers such as ``'piteration'`` or ``'diteration'``.
@@ -29,13 +29,17 @@ class PageRankClassifier(RankClassifier):
     Attributes
     ----------
     labels_ : np.ndarray, shape (n_labels,)
-        Label of each node.
+        Labels of nodes.
     probs_ : sparse.csr_matrix, shape (n_row, n_labels)
         Probability distribution over labels.
-    labels_row_, labels_col_ : np.ndarray
-        Labels of rows and columns, for bipartite graphs.
-    probs_row_, probs_col_ : sparse.csr_matrix, shape (n_row, n_labels)
-        Probability distributions over labels for rows and columns (for bipartite graphs).
+    labels_row_ : np.ndarray
+        Labels of rows, for bipartite graphs.
+    labels_col_ : np.ndarray
+        Labels of columns, for bipartite graphs.
+    probs_row_ : sparse.csr_matrix, shape (n_row, n_labels)
+        Probability distributions over labels of rows, for bipartite graphs.
+    probs_col_ : sparse.csr_matrix, shape (n_col, n_labels)
+        Probability distributions over labels of columns, for bipartite graphs.
 
     Example
     -------