scikit-network 0.31.0__cp311-cp311-win_amd64.whl → 0.32.1__cp311-cp311-win_amd64.whl

{scikit_network-0.31.0.dist-info → scikit_network-0.32.1.dist-info}/AUTHORS.rst

@@ -39,3 +39,6 @@ Contributors
 * Flávio Juvenal
 * Wenzhuo Zhao
 * Henry Carscadden
+* Yiwen Peng
+* Ahmed Zaiou
+* Laurène David

{scikit_network-0.31.0.dist-info → scikit_network-0.32.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scikit-network
-Version: 0.31.0
+Version: 0.32.1
 Summary: Graph algorithms
 Home-page: https://github.com/sknetwork-team/scikit-network
 Author: Scikit-network team
@@ -23,8 +23,8 @@ Requires-Python: >=3.8
 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 +118,22 @@ the `Journal of Machine Learning Research <https://jmlr.org>`_:
 History
 =======
 
+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-0.31.0.dist-info → scikit_network-0.32.1.dist-info}/RECORD

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+sknetwork/topology/tests/test_structure.py,sha256=BIJuO39ROQRA-xipUfk8PajHQ0Uk9EY6C-c3JYkmBSg,4033
 sknetwork/topology/tests/test_triangles.py,sha256=5AYxNQ8DkKTvpShWEWV-v1r7WZx1DuylChcEmVF0yTk,1313
 sknetwork/topology/tests/test_wl.py,sha256=vesYcnlJHPphk2RJLzKJH9N6aYpPeKLFJko1E8kBdtc,2290
 sknetwork/utils/__init__.py,sha256=ceT5UU4JRxCqpDlPj84gPBaKMRsI6b_YfaBzkK67Qo4,336
 sknetwork/utils/check.py,sha256=LWUkHwDzr9Z9IyT7AIsrQyDrRAMjO2bzWyFsv_P9Ask,13295
-sknetwork/utils/format.py,sha256=5gKHLLBuGboIqmtNKiwzrC_qbh-sPi_mejhJ_8teaLs,8974
-sknetwork/utils/membership.py,sha256=claXsrZd6BVT4WuuI0P00tqapbczvAxtLAWMWNQ78KE,2234
+sknetwork/utils/format.py,sha256=g_cfUlETJp7AppCiVKG2VZPexH-H9rVNGF4hXh2rshM,8987
+sknetwork/utils/membership.py,sha256=kan9WuytJCyBAZi0CfM0SJEf527XB4WAYMkIctD5D9w,2244
 sknetwork/utils/neighbors.py,sha256=-EwBXigM3mn2qvVTi_aPmG0XifDMojZgsMQ9_A8cLkk,3466
 sknetwork/utils/tfidf.py,sha256=vvISEaZJa7RZrNNgQEAHgMH2rJToARuNWcVjnA8u7po,993
 sknetwork/utils/values.py,sha256=aUc2fuI56J78_6P-S2mT4NhHgiiIZp6D2feNKcsQmG4,2584
@@ -206,16 +213,16 @@ sknetwork/utils/tests/test_membership.py,sha256=d_TobwpRl2K3qCcFBDQV1bGCSmF7Ls3r
 sknetwork/utils/tests/test_neighbors.py,sha256=Q7-Y23CcF4vn5lcyEqjaojEAk7-pG03Mf59O1Rz3IUs,1467
 sknetwork/utils/tests/test_tfidf.py,sha256=KYz_LSxi625kKL-v5-uA1-YQOliIfgXCmNXTAZtgpmw,463
 sknetwork/utils/tests/test_values.py,sha256=K3ctTXpSy9fwiHnpFVlHX5KeTd2wNF4kbFiTXe_gQq8,2334
-sknetwork/visualization/__init__.py,sha256=0gVE7r4oXW6IPlNzq2EXwvr_oRDwCjtuhBh0FN-4I4Y,162
+sknetwork/visualization/__init__.py,sha256=Ww8O1hby1xf_mtRgFftc9srMzvbFgWOzj_khKkqq9Mg,220
 sknetwork/visualization/colors.py,sha256=NhyMQeetfH16khnJD2gD_uZJkBD3JQDV0K3Jzacamqw,2543
-sknetwork/visualization/dendrograms.py,sha256=-U-WVuO-uFpqPrXuWJmhpkIUyeYX-GLemRmChdtbWhY,8280
-sknetwork/visualization/graphs.py,sha256=vx2PC_IilHNW9G6GgNq3muFCM7Hc3Mz0lHMrOmH8Qu8,32806
+sknetwork/visualization/dendrograms.py,sha256=HtubynuGsJ5b7bD5I8dIKL5UqhqynmqOhw_wJt6VGUA,10178
+sknetwork/visualization/graphs.py,sha256=SJDta3IUolBDI69kFdF7WGmjcLsfqkQNw5ixvJwoNuk,42214
 sknetwork/visualization/tests/__init__.py,sha256=hrso2pNVzMWn4D2pRyWA_xAMib-xacKjm-rf91MyGGk,31
-sknetwork/visualization/tests/test_dendrograms.py,sha256=4BEdDonrQZsylKgwDpxwTdUZTnqbMKokpugTYbcAp5o,2455
-sknetwork/visualization/tests/test_graphs.py,sha256=FkzWHYx0KHr0sxP7Go-KZICjoiGXK1EoF8nzIMUiFBc,8968
-scikit_network-0.31.0.dist-info/AUTHORS.rst,sha256=SSAG2WortFtGW_lEWFDX15zhkIvoEOwc60q2yVTRN7Q,921
-scikit_network-0.31.0.dist-info/LICENSE,sha256=BJ1Hth1QjBmjIfHcp1sVxlkEqHYM58Vn5bcpYcggMZE,1656
-scikit_network-0.31.0.dist-info/METADATA,sha256=wXSb_IbBBsuXwnQq37r8hav6vMIyz0PDv3mSRNSayRY,14521
-scikit_network-0.31.0.dist-info/WHEEL,sha256=wklNeoByNLhdCl-oEQTdaHIeDl4q9zaQVqAlPxUEgLU,102
-scikit_network-0.31.0.dist-info/top_level.txt,sha256=fkwspWQ9B3csqb5ENEOoVciRY6XftnMuz4MvTDQeSsg,10
-scikit_network-0.31.0.dist-info/RECORD,,
+sknetwork/visualization/tests/test_dendrograms.py,sha256=e0u3qL9SlWlrQiVAeCVXxq7P6-mU0GaCz3FBu6cm_HA,2519
+sknetwork/visualization/tests/test_graphs.py,sha256=FPZcgGj9asTjOvtkXpENYjeE8xtwh1ES4XYWcYe56Jo,9597
+scikit_network-0.32.1.dist-info/AUTHORS.rst,sha256=t2CJQFYm_OvWod1zQx4Tw-BeKLVlpQjQ0APBIOnYRPE,968
+scikit_network-0.32.1.dist-info/LICENSE,sha256=BJ1Hth1QjBmjIfHcp1sVxlkEqHYM58Vn5bcpYcggMZE,1656
+scikit_network-0.32.1.dist-info/METADATA,sha256=cmHp6cheSqpUDU3TEOHmo-VKw-6fBXvAw2U5SewlIFQ,14907
+scikit_network-0.32.1.dist-info/WHEEL,sha256=ircjsfhzblqgSzO8ow7-0pXK-RVqDqNRGQ8F650AUNM,102
+scikit_network-0.32.1.dist-info/top_level.txt,sha256=fkwspWQ9B3csqb5ENEOoVciRY6XftnMuz4MvTDQeSsg,10
+scikit_network-0.32.1.dist-info/RECORD,,

{scikit_network-0.31.0.dist-info → scikit_network-0.32.1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.38.4)
+Generator: bdist_wheel (0.42.0)
 Root-Is-Purelib: false
 Tag: cp311-cp311-win_amd64
 

sknetwork/__init__.py

@@ -4,7 +4,7 @@
 
 __author__ = """scikit-network team"""
 __email__ = "thomas.bonald@telecom-paris.fr"
-__version__ = '0.31.0'
+__version__ = '0.32.1'
 
 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
@@ -78,13 +81,15 @@ class DiffusionClassifier(BaseClassifier):
 
         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 +103,10 @@ 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 +115,7 @@ 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
     -------
@@ -99,12 +103,14 @@ class NNClassifier(BaseClassifier):
 
         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

@@ -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