scikit-network 0.30.0__cp39-cp39-win_amd64.whl → 0.32.1__cp39-cp39-win_amd64.whl

{scikit_network-0.30.0.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-0.30.0.dist-info → scikit_network-0.32.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: scikit-network
-Version: 0.30.0
+Version: 0.32.1
 Summary: Graph algorithms
 Home-page: https://github.com/sknetwork-team/scikit-network
 Author: Scikit-network team
@@ -18,12 +18,13 @@ 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
 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
@@ -117,6 +118,33 @@ 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)
+-------------------
+
+* Add Python 3.11
+* Add set_param / get_param to algorithms, suggested by Franz Kiraly (#557)
+* Compute shortest paths by matrix-vector multiplications
+* Make tools on topology (cliques, code-decomposition, etc.) as functions
+* Rename parameter membership -> probs for soft classification / clustering
+* Add softmax to classification by diffusion
+
 0.30.0 (2023-04-12)
 -------------------
 

scikit_network-0.32.1.dist-info/RECORD

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+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=GZFS91_ufm4WrNPBaFVPB9MvOXR6bMZQhPcZRRTN5YM,100
+scikit_network-0.32.1.dist-info/top_level.txt,sha256=fkwspWQ9B3csqb5ENEOoVciRY6XftnMuz4MvTDQeSsg,10
+scikit_network-0.32.1.dist-info/RECORD,,

{scikit_network-0.30.0.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: cp39-cp39-win_amd64
 

sknetwork/__init__.py

@@ -4,7 +4,7 @@
 
 __author__ = """scikit-network team"""
 __email__ = "thomas.bonald@telecom-paris.fr"
-__version__ = '0.30.0'
+__version__ = '0.32.1'
 
 import sknetwork.topology
 import sknetwork.path

sknetwork/base.py

@@ -0,0 +1,67 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created in June 2019
+@author: Quentin Lutz <qlutz@enst.fr>
+"""
+import inspect
+
+
+class Algorithm:
+    """Base class for all algorithms.
+    """
+    def get_params(self):
+        """Get parameters as dictionary.
+
+        Returns
+        -------
+        params : dict
+            Parameters of the algorithm.
+        """
+        signature = inspect.signature(self.__class__.__init__)
+        params_exclude = ['self', 'random_state', 'verbose']
+        params = dict()
+        for param in signature.parameters.values():
+            name = param.name
+            if name not in params_exclude:
+                try:
+                    value = self.__dict__[name]
+                except KeyError:
+                    continue
+                params[name] = value
+        return params
+
+    def set_params(self, params: dict) -> 'Algorithm':
+        """Set parameters of the algorithm.
+
+        Parameters
+        ----------
+        params : dict
+            Parameters of the algorithm.
+
+        Returns
+        -------
+        self : :class:`Algorithm`
+        """
+        valid_params = self.get_params()
+        if type(params) is not dict:
+            raise ValueError('The parameters must be given as a dictionary.')
+        for name, value in params.items():
+            if name not in valid_params:
+                raise ValueError(f'Invalid parameter: {name}.')
+            setattr(self, name, value)
+        return self
+
+    def __repr__(self):
+        params_string = []
+        for name, value in self.get_params().items():
+            if type(value) == str:
+                value = "'" + value + "'"
+            else:
+                value = str(value)
+            params_string.append(name + '=' + value)
+        return self.__class__.__name__ + '(' + ', '.join(params_string) + ')'
+
+    def fit(self, *args, **kwargs):
+        """Fit algorithm to data."""
+        raise NotImplementedError

sknetwork/classification/base.py

@@ -9,7 +9,7 @@ from abc import ABC
 import numpy as np
 from scipy import sparse
 
-from sknetwork.utils.base import Algorithm
+from sknetwork.base import Algorithm
 
 
 class BaseClassifier(Algorithm, ABC):
@@ -20,25 +20,25 @@ class BaseClassifier(Algorithm, ABC):
     bipartite : bool
         If ``True``, the fitted graph is bipartite.
     labels_ : np.ndarray, shape (n_labels,)
-        Label of each node.
-    membership_ : sparse.csr_matrix, shape (n_row, n_labels)
-        Membership matrix (soft classification).
+        Labels of nodes.
+    probs_ : sparse.csr_matrix, shape (n_row, n_labels)
+        Probability distribution over labels (soft classification).
     labels_row_ , labels_col_ : np.ndarray
-        Label of rows and columns (for bipartite graphs).
-    membership_row_, membership_col_ : sparse.csr_matrix, shapes (n_row, n_labels) and (n_col, n_labels)
-        Membership matrices of rows and columns (for bipartite graphs).
+        Labels of rows and columns (for bipartite graphs).
+    probs_row_, probs_col_ : sparse.csr_matrix, shapes (n_row, n_labels) and (n_col, n_labels)
+        Probability distributions over labels for rows and columns (for bipartite graphs).
     """
 
     def __init__(self):
         self.bipartite = None
         self.labels_ = None
-        self.membership_ = None
+        self.probs_ = None
         self.labels_row_ = None
         self.labels_col_ = None
-        self.membership_row_ = None
-        self.membership_col_ = None
+        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
@@ -80,8 +80,8 @@ class BaseClassifier(Algorithm, ABC):
             Probability distribution over labels.
         """
         if columns:
-            return self.membership_col_.toarray()
-        return self.membership_.toarray()
+            return self.probs_col_.toarray()
+        return self.probs_.toarray()
 
     def fit_predict_proba(self, *args, **kwargs) -> np.ndarray:
         """Fit algorithm to the data and return the probability distribution over labels.
@@ -105,12 +105,12 @@ class BaseClassifier(Algorithm, ABC):
 
         Returns
         -------
-        membership : sparse.csr_matrix
-            Probability distribution over labels (aka membership matrix).
+        probs : sparse.csr_matrix
+            Probability distribution over labels.
         """
         if columns:
-            return self.membership_col_
-        return self.membership_
+            return self.probs_col_
+        return self.probs_
 
     def fit_transform(self, *args, **kwargs) -> sparse.csr_matrix:
         """Fit algorithm to the data and return the probability distribution over labels in sparse format.
@@ -118,8 +118,8 @@ class BaseClassifier(Algorithm, ABC):
 
         Returns
         -------
-        membership : sparse.csr_matrix
-            Probability of each label.
+        probs : sparse.csr_matrix
+            Probability distribution over labels.
         """
         self.fit(*args, **kwargs)
         return self.transform()
@@ -131,12 +131,12 @@ class BaseClassifier(Algorithm, ABC):
             self.labels_row_ = self.labels_[:n_row]
             self.labels_col_ = self.labels_[n_row:]
             self.labels_ = self.labels_row_
-            self.membership_row_ = self.membership_[:n_row]
-            self.membership_col_ = self.membership_[n_row:]
-            self.membership_ = self.membership_row_
+            self.probs_row_ = self.probs_[:n_row]
+            self.probs_col_ = self.probs_[n_row:]
+            self.probs_ = self.probs_row_
         else:
             self.labels_row_ = self.labels_
             self.labels_col_ = self.labels_
-            self.membership_row_ = self.membership_
-            self.membership_col_ = self.membership_
+            self.probs_row_ = self.probs_
+            self.probs_col_ = self.probs_
         return self

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
@@ -12,14 +12,13 @@ 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
-from sknetwork.utils.verbose import VerboseMixin
 
 
-class RankClassifier(BaseClassifier, VerboseMixin):
+class RankClassifier(BaseClassifier):
     """Generic class for ranking based classifiers.
 
     Parameters
@@ -29,27 +28,20 @@ class RankClassifier(BaseClassifier, VerboseMixin):
     n_jobs :
         If positive, number of parallel jobs allowed (-1 means maximum number).
         If ``None``, no parallel computations are made.
-    verbose :
-        Verbose mode.
 
     Attributes
     ----------
     labels_ : np.ndarray, shape (n_labels,)
         Label of each node.
-    membership_ : sparse.csr_matrix, shape (n_row, n_labels)
-        Membership matrix.
-    labels_row_ : np.ndarray
-        Labels of rows, for bipartite graphs.
-    labels_col_ : np.ndarray
-        Labels of columns, for bipartite graphs.
-    membership_row_ : sparse.csr_matrix, shape (n_row, n_labels)
-        Membership matrix of rows, for bipartite graphs.
-    membership_col_ : sparse.csr_matrix, shape (n_col, n_labels)
-        Membership matrix of columns, for bipartite graphs.
+    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).
     """
     def __init__(self, algorithm: BaseRanking, n_jobs: Optional[int] = None, verbose: bool = False):
         super(RankClassifier, self).__init__()
-        VerboseMixin.__init__(self, verbose)
 
         self.algorithm = algorithm
         self.n_jobs = check_n_jobs(n_jobs)
@@ -78,7 +70,7 @@ class RankClassifier(BaseClassifier, VerboseMixin):
 
     @staticmethod
     def _process_scores(scores: np.ndarray) -> np.ndarray:
-        """Post-processing of the membership matrix.
+        """Post-processing of the scores.
 
         Parameters
         ----------
@@ -97,9 +89,9 @@ class RankClassifier(BaseClassifier, VerboseMixin):
         self.labels_row_ = self.labels_[:n_row]
         self.labels_col_ = self.labels_[n_row:]
         self.labels_ = self.labels_row_
-        self.membership_row_ = self.membership_[:n_row]
-        self.membership_col_ = self.membership_[n_row:]
-        self.membership_ = self.membership_row_
+        self.probs_row_ = self.probs_[:n_row]
+        self.probs_col_ = self.probs_[n_row:]
+        self.probs_ = self.probs_row_
 
     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) -> 'RankClassifier':
@@ -122,7 +114,7 @@ class RankClassifier(BaseClassifier, VerboseMixin):
         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
@@ -130,12 +122,12 @@ class RankClassifier(BaseClassifier, VerboseMixin):
         scores = self._process_scores(scores)
         scores = normalize(scores)
 
-        membership = sparse.coo_matrix(scores)
-        membership.col = labels_unique[membership.col]
+        probs = sparse.coo_matrix(scores)
+        probs.col = labels_unique[probs.col]
 
         labels = np.argmax(scores, axis=1)
         self.labels_ = labels_unique[labels]
-        self.membership_ = sparse.csr_matrix(membership, shape=(adjacency.shape[0], np.max(seeds_labels) + 1))
+        self.probs_ = sparse.csr_matrix(probs, shape=(adjacency.shape[0], np.max(seeds_labels) + 1))
         self._split_vars(input_matrix.shape)
 
         return self