scikit-network 0.33.3__cp313-cp313-win_amd64.whl

sknetwork/data/toy_graphs.py

@@ -0,0 +1,611 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+Created on Nov 29, 2018
+@author: Quentin Lutz <qlutz@enst.fr>
+@author: Nathan de Lara <nathan.delara@polytechnique.org>
+@author: Thomas Bonald <tbonald@enst.fr>
+"""
+from typing import Union
+
+import numpy as np
+from scipy import sparse
+
+from sknetwork.data.base import Dataset
+
+
+def house(metadata: bool = False) -> Union[sparse.csr_matrix, Dataset]:
+    """House graph.
+
+    * Undirected graph
+    * 5 nodes, 6 edges
+
+    Parameters
+    ----------
+    metadata :
+        If ``True``, return a `Dataset` object with metadata.
+
+    Returns
+    -------
+    adjacency or graph : Union[sparse.csr_matrix, Dataset]
+        Adjacency matrix or graph with metadata (positions).
+
+    Example
+    -------
+    >>> from sknetwork.data import house
+    >>> adjacency = house()
+    >>> adjacency.shape
+    (5, 5)
+
+    """
+    row = np.array([0, 0, 1, 1, 2, 3])
+    col = np.array([1, 4, 2, 4, 3, 4])
+    adjacency = sparse.csr_matrix((np.ones(len(row), dtype=int), (row, col)), shape=(5, 5))
+    adjacency = (adjacency + adjacency.T).astype(bool)
+
+    if metadata:
+        x = np.array([0, -1, -1, 1, 1])
+        y = np.array([2, 1, -1, -1, 1])
+        graph = Dataset()
+        graph.adjacency = adjacency
+        graph.position = np.vstack((x, y)).T
+        graph.name = 'house'
+        return graph
+    else:
+        return adjacency
+
+
+def bow_tie(metadata: bool = False) -> Union[sparse.csr_matrix, Dataset]:
+    """Bow tie graph.
+
+    * Undirected graph
+    * 5 nodes, 6 edges
+
+    Parameters
+    ----------
+    metadata :
+        If ``True``, return a `Dataset` object with metadata.
+
+    Returns
+    -------
+    adjacency or graph : Union[sparse.csr_matrix, Dataset]
+        Adjacency matrix or graph with metadata (positions).
+
+    Example
+    -------
+    >>> from sknetwork.data import bow_tie
+    >>> adjacency = bow_tie()
+    >>> adjacency.shape
+    (5, 5)
+    """
+    row = np.array([0, 0, 0, 0, 1, 3])
+    col = np.array([1, 2, 3, 4, 2, 4])
+    adjacency = sparse.csr_matrix((np.ones(len(row), dtype=int), (row, col)), shape=(5, 5))
+    adjacency = (adjacency + adjacency.T).astype(bool)
+
+    if metadata:
+        x = np.array([0, -1, 1, -1, 1])
+        y = np.array([0, 1, 1, -1, -1])
+        graph = Dataset()
+        graph.adjacency = adjacency
+        graph.position = np.vstack((x, y)).T
+        graph.name = 'bow_tie'
+        return graph
+    else:
+        return adjacency
+
+
+def karate_club(metadata: bool = False) -> Union[sparse.csr_matrix, Dataset]:
+    """Karate club graph.
+
+    * Undirected graph
+    * 34 nodes, 78 edges
+    * 2 labels
+
+    Parameters
+    ----------
+    metadata :
+        If ``True``, return a `Dataset` object with metadata.
+
+    Returns
+    -------
+    adjacency or graph : Union[sparse.csr_matrix, Dataset]
+        Adjacency matrix or graph with metadata (labels, positions).
+
+    Example
+    -------
+    >>> from sknetwork.data import karate_club
+    >>> adjacency = karate_club()
+    >>> adjacency.shape
+    (34, 34)
+
+    References
+    ----------
+    Zachary's karate club graph
+    https://en.wikipedia.org/wiki/Zachary%27s_karate_club
+    """
+    row = np.array(
+        [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1,
+         1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 3, 3,
+         3, 4, 4, 5, 5, 5, 6, 8, 8, 8, 9, 13, 14, 14, 15, 15, 18,
+         18, 19, 20, 20, 22, 22, 23, 23, 23, 23, 23, 24, 24, 24, 25, 26, 26,
+         27, 28, 28, 29, 29, 30, 30, 31, 31, 32])
+    col = np.array(
+        [1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 17, 19, 21, 31, 2,
+         3, 7, 13, 17, 19, 21, 30, 3, 7, 8, 9, 13, 27, 28, 32, 7, 12,
+         13, 6, 10, 6, 10, 16, 16, 30, 32, 33, 33, 33, 32, 33, 32, 33, 32,
+         33, 33, 32, 33, 32, 33, 25, 27, 29, 32, 33, 25, 27, 31, 31, 29, 33,
+         33, 31, 33, 32, 33, 32, 33, 32, 33, 33])
+    adjacency = sparse.csr_matrix((np.ones(len(row), dtype=bool), (row, col)), shape=(34, 34))
+    adjacency = sparse.csr_matrix(adjacency + adjacency.T, dtype=bool)
+
+    if metadata:
+        labels = np.array(
+            [1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 1, 1, 1, 0, 0, 1, 1, 0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
+        x = np.array(
+            [0.04,  0.24,  0.01,  0.13,  0.02, -0.08,  0.04,  0.21,  0.08, -0.11, -0.13, -0.28,  0.2,  0.08,
+             0.23,  0.06, -0.06,  0.32, 0.15,  0.19,  0.27,  0.39, -0.04, -0.26, -0.51, -0.49, -0.19, -0.28,
+             -0.11, -0.17,  0.22, -0.21,  0.03, 0])
+        y = np.array(
+            [-0.33, -0.15, -0.01, -0.28, -0.64, -0.75, -0.76, -0.25,  0.09, 0.23, -0.62, -0.4, -0.53, -0.07,
+             0.55,  0.64, -1., -0.42, 0.6, -0.01,  0.45, -0.34,  0.61,  0.41,  0.14,  0.28,  0.68, 0.21,
+             0.12,  0.54,  0.19,  0.09,  0.38,  0.33])
+        graph = Dataset()
+        graph.adjacency = adjacency
+        graph.labels = labels
+        graph.position = np.vstack((x, y)).T
+        graph.name = 'karate_club'
+        return graph
+    else:
+        return adjacency
+
+
+def miserables(metadata: bool = False) -> Union[sparse.csr_matrix, Dataset]:
+    """Co-occurrence graph of the characters in the novel Les miserables by Victor Hugo.
+
+    * Undirected graph
+    * 77 nodes, 508 edges
+    * Names of characters
+
+    Parameters
+    ----------
+    metadata :
+        If ``True``, return a `Dataset` object with metadata.
+
+    Returns
+    -------
+    adjacency or graph : Union[sparse.csr_matrix, Dataset]
+        Adjacency matrix or graph with metadata (names, positions).
+
+    Example
+    -------
+    >>> from sknetwork.data import miserables
+    >>> adjacency = miserables()
+    >>> adjacency.shape
+    (77, 77)
+    """
+    row = np.array(
+        [0,  0,  0,  0,  0,  0,  0,  0,  0,  0,  2,  2,  3, 10, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11,
+         11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 11, 12,
+         16, 16, 16, 16, 16, 16, 16, 16, 16, 17, 17, 17, 17, 17, 17, 18, 18, 18, 18, 18, 19, 19, 19, 19,
+         20, 20, 20, 21, 21, 22, 23, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24, 24, 25, 25, 25,
+         25, 25, 25, 25, 25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 27, 27, 27, 27, 27, 27, 27,
+         27, 27, 27, 27, 27, 28, 28, 29, 29, 29, 29, 29, 30, 34, 34, 34, 34, 35, 35, 35, 36, 36, 37, 39,
+         39, 41, 41, 41, 41, 41, 41, 41, 41, 41, 46, 47, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48,
+         48, 48, 48, 48, 48, 48, 49, 49, 49, 49, 49, 51, 51, 51, 51, 54, 55, 55, 55, 55, 55, 55, 55, 55,
+         55, 57, 57, 57, 57, 57, 57, 57, 57, 58, 58, 58, 58, 58, 58, 58, 58, 58, 58, 59, 59, 59, 59, 59,
+         59, 59, 60, 60, 60, 60, 60, 60, 61, 61, 61, 61, 61, 62, 62, 62, 62, 62, 63, 63, 63, 63, 64, 64,
+         64, 65, 65, 66, 68, 68, 68, 68, 69, 69, 69, 70, 70, 71, 73])
+    col = np.array(
+        [1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 3, 11, 11, 11, 12, 13, 14,
+         15, 23, 24, 25, 26, 27, 28, 29, 31, 32, 33, 34, 35, 36, 37, 38, 43,
+         44, 48, 49, 51, 55, 58, 64, 68, 69, 70, 71, 72, 23, 17, 18, 19, 20,
+         21, 22, 23, 26, 55, 18, 19, 20, 21, 22, 23, 19, 20, 21, 22, 23, 20,
+         21, 22, 23, 21, 22, 23, 22, 23, 23, 24, 25, 27, 29, 30, 31, 25, 26,
+         27, 41, 42, 50, 68, 69, 70, 26, 27, 39, 40, 41, 42, 48, 55, 68, 69,
+         70, 71, 75, 27, 43, 49, 51, 54, 55, 72, 28, 29, 31, 33, 43, 48, 58,
+         68, 69, 70, 71, 72, 44, 45, 34, 35, 36, 37, 38, 31, 35, 36, 37, 38,
+         36, 37, 38, 37, 38, 38, 52, 55, 42, 55, 57, 62, 68, 69, 70, 71, 75,
+         47, 48, 55, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 68, 69, 71, 73,
+         74, 75, 76, 50, 51, 54, 55, 56, 52, 53, 54, 55, 55, 56, 57, 58, 59,
+         61, 62, 63, 64, 65, 58, 59, 61, 62, 63, 64, 65, 67, 59, 60, 61, 62,
+         63, 64, 65, 66, 70, 76, 60, 61, 62, 63, 64, 65, 66, 61, 62, 63, 64,
+         65, 66, 62, 63, 64, 65, 66, 63, 64, 65, 66, 76, 64, 65, 66, 76, 65,
+         66, 76, 66, 76, 76, 69, 70, 71, 75, 70, 71, 75, 71, 75, 75, 74])
+    data = np.array(
+        [1, 8, 10, 1, 1, 1, 1, 2, 1, 5, 6, 3, 3, 1, 1, 1, 1,
+         1, 9, 7, 12, 31, 17, 8, 2, 3, 1, 2, 3, 3, 2, 2, 2, 3,
+         1, 1, 2, 2, 19, 4, 1, 1, 1, 1, 1, 1, 2, 4, 4, 4, 3,
+         3, 3, 3, 1, 1, 4, 4, 3, 3, 3, 3, 4, 3, 3, 3, 3, 4,
+         3, 3, 3, 5, 4, 4, 4, 4, 4, 2, 1, 5, 1, 1, 2, 13, 4,
+         1, 2, 1, 1, 1, 1, 1, 1, 5, 1, 1, 3, 2, 1, 2, 5, 6,
+         4, 1, 3, 1, 1, 3, 2, 1, 21, 2, 1, 1, 1, 1, 1, 1, 6,
+         1, 2, 1, 1, 1, 3, 2, 2, 2, 1, 1, 1, 2, 3, 2, 2, 2,
+         2, 2, 2, 2, 2, 2, 1, 1, 2, 5, 1, 1, 1, 1, 1, 1, 1,
+         1, 2, 4, 1, 7, 6, 1, 2, 7, 5, 5, 3, 1, 1, 1, 1, 2,
+         2, 1, 1, 1, 9, 1, 12, 1, 1, 1, 2, 6, 1, 1, 1, 7, 5,
+         1, 9, 1, 5, 2, 1, 2, 1, 2, 2, 1, 1, 3, 15, 4, 6, 17,
+         4, 10, 5, 3, 1, 1, 2, 5, 13, 5, 9, 5, 1, 2, 3, 2, 2,
+         2, 1, 6, 3, 6, 5, 1, 6, 12, 5, 2, 1, 4, 5, 1, 1, 7,
+         3, 1, 2, 1, 1, 6, 4, 2, 3, 4, 2, 3, 2, 1, 1, 3])
+    adjacency = sparse.csr_matrix((data, (row, col)), shape=(77, 77))
+    adjacency = adjacency + adjacency.T
+
+    if metadata:
+        names = ['Myriel', 'Napoleon', 'Mlle Baptistine', 'Mme Magloire', 'Countess de Lo', 'Geborand',
+                 'Champtercier', 'Cravatte', 'Count', 'Old man', 'Labarre', 'Valjean', 'Marguerite', 'Mme Der',
+                 'Isabeau', 'Gervais', 'Tholomyes', 'Listolier', 'Fameuil', 'Blacheville', 'Favourite', 'Dahlia',
+                 'Zephine', 'Fantine', 'Mme Thenardier', 'Thenardier', 'Cosette', 'Javert', 'Fauchelevent',
+                 'Bamatabois', 'Perpetue', 'Simplice', 'Scaufflaire', 'Woman1', 'Judge', 'Champmathieu', 'Brevet',
+                 'Chenildieu', 'Cochepaille', 'Pontmercy', 'Boulatruelle', 'Eponine', 'Anzelma', 'Woman2',
+                 'Mother Innocent', 'Gribier', 'Jondrette', 'Mme Burgon', 'Gavroche', 'Gillenormand', 'Magnon',
+                 'Mlle Gillenormand', 'Mme Pontmercy', 'Mlle Vaubois', 'Lt Gillenormand', 'Marius', 'Baroness',
+                 'Mabeuf', 'Enjolras', 'Combeferre', 'Prouvaire', 'Feuilly', 'Courfeyrac', 'Bahorel', 'Bossuet',
+                 'Joly', 'Grantaire', 'MotherPlutarch', 'Gueulemer', 'Babet', 'Claquesous', 'Montparnasse',
+                 'Toussaint', 'Child1', 'Child2', 'Brujon', 'Mme Hucheloup']
+        x = np.array(
+            [0.53,  0.98,  0.41,  0.4,  1.,  0.92,  0.84,  0.74,  0.78, 1.,  0.51,  0.09, -0.,  0.29,  0.37,
+             0.41, -0.35, -0.46, -0.42, -0.46, -0.41, -0.37, -0.36, -0.2, -0.06, -0.04, -0.01, -0.02,  0.33,
+             0.17, -0.29, -0.1,  0.58,  0.29,  0.29,  0.26, 0.29,  0.37,  0.35,  0.04, -0.01, -0.18, -0.09,
+             0.2,  0.51, 0.7, -0.95, -0.7, -0.37, -0.08, -0.18, -0.05,  0.04, -0.12, -0.06, -0.13, -0.24, -0.48,
+             -0.25, -0.33, -0.43, -0.39, -0.33, -0.42, -0.31, -0.38, -0.48, -0.74, -0.08, -0.1, -0.02, -0.1,
+             0.14, -0.76, -0.75, -0.18, -0.58])
+        y = np.array(
+            [-0.23, -0.42, -0.14, -0.18, -0.31, -0.52, -0.6, -0.65, -0.38, -0.19,  0.39,  0.03,  0.44, -0.44,
+             0.51, -0.36,  0.27,  0.37, 0.4,  0.32,  0.32,  0.36,  0.4,  0.2,  0.07,  0.14, -0.05, 0.06,  0.06,
+             0.24, -0.26, -0.1,  0.24, -0.04,  0.17,  0.23, 0.31,  0.21,  0.27, -0.36,  0.69,  0.11,  0.38, -0.09,
+             0.05, 0.12,  0.82,  0.44,  0.06, -0.2, -0.4, -0.28, -0.68, -0.79, -0.4, -0.07, -0.51, -0.17, -0.03,
+             -0.09, -0.14, -0.04, -0.04, -0.07, -0.06, -0.11, -0.06, -0.35,  0.24,  0.19,  0.22,  0.29, -0.2,
+             0.06,  0.14,  0.3, -0.1])
+        graph = Dataset()
+        graph.adjacency = adjacency
+        graph.names = np.array(names)
+        graph.position = np.vstack((x, y)).T
+        graph.name = 'miserables'
+        return graph
+    else:
+        return adjacency
+
+
+def painters(metadata: bool = False) -> Union[sparse.csr_matrix, Dataset]:
+    """Graph of links between some famous painters on Wikipedia.
+
+    * Directed graph
+    * 14 nodes, 50 edges
+    * Names of painters
+
+    Parameters
+    ----------
+    metadata :
+        If ``True``, return a `Dataset` object with metadata.
+
+    Returns
+    -------
+    adjacency or graph : Union[sparse.csr_matrix, Dataset]
+        Adjacency matrix or graph with metadata (names, positions).
+
+    Example
+    -------
+    >>> from sknetwork.data import painters
+    >>> adjacency = painters()
+    >>> adjacency.shape
+    (14, 14)
+    """
+    row = np.array(
+        [0, 0, 1, 1, 2, 3, 3, 3, 3, 3, 4, 4, 4, 5, 5, 5, 5,
+         6, 6, 7, 7, 7, 7, 7, 7, 8, 8, 8, 8, 8, 8, 8, 9, 9,
+         10, 10, 10, 10, 10, 11, 11, 11, 11, 11, 12, 12, 12, 12, 13, 13])
+    col = np.array(
+        [3, 10, 3, 12, 9, 0, 1, 7, 11, 12, 2, 5, 9, 2, 4, 8, 9,
+         0, 13, 1, 2, 3, 8, 11, 12, 0, 1, 4, 5, 7, 10, 11, 2, 4,
+         0, 3, 8, 11, 12, 0, 1, 3, 10, 12, 1, 3, 4, 7, 6, 8])
+    adjacency = sparse.csr_matrix((np.ones(len(row), dtype=bool), (row, col)), shape=(14, 14))
+
+    if metadata:
+        names = np.array(
+            ['Pablo Picasso', 'Claude Monet', 'Michel Angelo', 'Edouard Manet', 'Peter Paul Rubens', 'Rembrandt',
+             'Gustav Klimt', 'Edgar Degas', 'Vincent van Gogh', 'Leonardo da Vinci', 'Henri Matisse', 'Paul Cezanne',
+             'Pierre-Auguste Renoir', 'Egon Schiele'])
+        x = np.array(
+            [0.24, -0.47, -0.3, -0.31, -0.08, 0.12, 0.78, -0.36, 0.11,
+             -0.06, -0.02, -0.12, -0.24, 0.73])
+        y = np.array(
+            [0.53, 0.19, -0.71, 0.44, -0.48, -0.65, 0.69, -0.11, 0.01,
+             -1., 0.49, 0.28, 0.06, 0.27])
+        graph = Dataset()
+        graph.adjacency = adjacency
+        graph.names = names
+        graph.position = np.stack((x, y)).T
+        graph.name = 'painters'
+        return graph
+    else:
+        return adjacency
+
+
+def hourglass(metadata: bool = False) -> Union[sparse.csr_matrix, Dataset]:
+    """Hourglass graph.
+
+    * Bipartite graph
+    * 4 nodes, 4 edges
+
+    Returns
+    -------
+    biadjacency or graph : Union[sparse.csr_matrix, Dataset]
+        Biadjacency matrix or graph.
+
+    Example
+    -------
+    >>> from sknetwork.data import hourglass
+    >>> biadjacency = hourglass()
+    >>> biadjacency.shape
+    (2, 2)
+    """
+    biadjacency = sparse.csr_matrix(np.ones((2, 2), dtype=bool))
+    if metadata:
+        graph = Dataset()
+        graph.biadjacency = biadjacency
+        return graph
+    else:
+        return biadjacency
+
+
+def star_wars(metadata: bool = False) -> Union[sparse.csr_matrix, Dataset]:
+    """Bipartite graph connecting some Star Wars villains to the movies in which they appear.
+
+    * Bipartite graph
+    * 7 nodes (4 villains, 3 movies), 8 edges
+    * Names of villains and movies
+
+    Parameters
+    ----------
+    metadata :
+        If ``True``, return a `Dataset` object with metadata.
+
+    Returns
+    -------
+    biadjacency or graph : Union[sparse.csr_matrix, Dataset]
+        Biadjacency matrix or graph with metadata (names).
+
+    Example
+    -------
+    >>> from sknetwork.data import star_wars
+    >>> biadjacency = star_wars()
+    >>> biadjacency.shape
+    (4, 3)
+   """
+    row = np.array([0, 0, 1, 2, 2, 2, 3, 3])
+    col = np.array([0, 2, 0, 0, 1, 2, 1, 2])
+    biadjacency = sparse.csr_matrix((np.ones(len(row), dtype=bool), (row, col)), shape=(4, 3))
+
+    if metadata:
+        villains = np.array(['Jabba', 'Greedo', 'Vader', 'Boba'])
+        movies = np.array(['A New Hope', 'The Empire Strikes Back', 'Return Of The Jedi'])
+        graph = Dataset()
+        graph.biadjacency = biadjacency
+        graph.names = villains
+        graph.names_row = villains
+        graph.names_col = movies
+        graph.name = 'star_wars'
+        return graph
+    else:
+        return biadjacency
+
+
+def movie_actor(metadata: bool = False) -> Union[sparse.csr_matrix, Dataset]:
+    """Bipartite graph connecting movies to some actors starring in them.
+
+    * Bipartite graph
+    * 32 nodes (15 movies, 17 actors), 43 edges
+    * Names of movies (rows) and actors (columns)
+
+    Parameters
+    ----------
+    metadata :
+        If ``True``, return a `Dataset` object with metadata.
+
+    Returns
+    -------
+    biadjacency or dataset : Union[sparse.csr_matrix, Dataset]
+        Biadjacency matrix or dataset with metadata (names of movies and actors).
+
+    Example
+    -------
+    >>> from sknetwork.data import movie_actor
+    >>> biadjacency = movie_actor()
+    >>> biadjacency.shape
+    (15, 17)
+    """
+    row = np.array(
+        [0, 0, 0, 1, 1, 1, 2, 2, 2, 2, 3, 3, 4, 4, 5, 5, 6,
+         6, 6, 7, 7, 8, 8, 8, 8, 8, 9, 9, 9, 10, 10, 10, 10, 11, 11, 11,
+         12, 12, 12, 13, 13, 14, 14])
+    col = np.array(
+        [0, 1, 2, 1, 2, 3, 3, 4, 5, 8, 4, 6, 0, 6, 4, 7, 4,
+         7, 8, 3, 8, 9, 10, 11, 12, 15, 0, 11, 12, 9, 10, 13, 16, 5, 9, 13,
+         1, 9, 15, 12, 14, 14, 16])
+    biadjacency = sparse.csr_matrix((np.ones(len(row), dtype=bool), (row, col)), shape=(15, 17))
+
+    if metadata:
+        movies = np.array(
+            ['Inception', 'The Dark Knight Rises', 'The Big Short', 'Drive', 'The Great Gatsby', 'La La Land',
+             'Crazy Stupid Love', 'Vice', 'The Grand Budapest Hotel', 'Aviator', '007 Spectre', 'Inglourious Basterds',
+             'Midnight In Paris', 'Murder on the Orient Express', "Pirates of the Caribbean: At World's End"])
+        actors = np.array(
+            ['Leonardo DiCaprio', 'Marion Cotillard', 'Joseph Gordon Lewitt', 'Christian Bale', 'Ryan Gosling',
+             'Brad Pitt', 'Carey Mulligan', 'Emma Stone', 'Steve Carell', 'Lea Seydoux', 'Ralph Fiennes', 'Jude Law',
+             'Willem Dafoe', 'Christophe Waltz', 'Johnny Depp', 'Owen Wilson', 'Naomie Harris'])
+        dataset = Dataset()
+        dataset.biadjacency = biadjacency
+        dataset.names = movies
+        dataset.names_row = movies
+        dataset.names_col = actors
+        dataset.name = 'movie_actor'
+        return dataset
+    else:
+        return biadjacency
+
+
+def art_philo_science(metadata: bool = False) -> Union[sparse.csr_matrix, Dataset]:
+    """Wikipedia links between 30 articles (10 artists, 10 philosophers, 10 scientists).
+
+    * Directed graph
+    * 30 nodes, 240 edges
+    * Names of articles
+
+    Metadata includes the occurence of 11 words in the abstract of these articles.
+
+    Parameters
+    ----------
+    metadata :
+        If ``True``, return a `Dataset` object with metadata.
+
+    Returns
+    -------
+    adjacency or graph : Union[sparse.csr_matrix, Dataset]
+        Adjacency matrix or graph with metadata (names, positions, labels, names_labels,
+        biadjacency, names_col).
+
+    Example
+    -------
+    >>> from sknetwork.data import art_philo_science
+    >>> adjacency = art_philo_science()
+    >>> adjacency.shape
+    (30, 30)
+    """
+    row = np.array(
+        [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1,
+         1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 3, 3, 4, 4, 4, 4,
+         5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 5, 6, 6,
+         6, 6, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8,
+         8, 8, 8, 8, 8, 9, 9, 10, 10, 10, 10, 11, 11, 11, 12, 12, 12,
+         12, 12, 13, 13, 13, 14, 14, 14, 14, 14, 15, 15, 15, 16, 16, 16, 17,
+         17, 17, 17, 18, 19, 19, 19, 20, 20, 20, 20, 20, 20, 20, 20, 20, 20,
+         20, 20, 20, 20, 20, 20, 20, 21, 21, 21, 21, 21, 21, 21, 21, 21, 21,
+         21, 21, 21, 21, 21, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 23, 23,
+         23, 23, 23, 23, 23, 23, 23, 23, 23, 24, 24, 24, 24, 24, 24, 24, 24,
+         24, 24, 24, 24, 24, 24, 24, 24, 25, 25, 25, 25, 25, 25, 25, 25, 25,
+         25, 25, 25, 25, 25, 25, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26, 26,
+         26, 26, 26, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27, 27,
+         28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 28, 29, 29, 29,
+         29, 29])
+    col = np.array(
+        [1, 5, 6, 7, 20, 21, 23, 24, 25, 26, 27, 28, 0, 5, 7, 9, 12,
+         16, 20, 21, 24, 25, 26, 27, 28, 3, 20, 0, 2, 26, 7, 20, 21, 29,
+         0, 1, 6, 8, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 0, 1,
+         5, 7, 8, 24, 26, 27, 0, 1, 6, 20, 21, 24, 25, 26, 27, 28, 0,
+         5, 6, 7, 9, 27, 1, 25, 0, 18, 19, 20, 12, 16, 17, 11, 12, 14,
+         16, 17, 14, 15, 25, 11, 12, 16, 17, 19, 13, 14, 19, 12, 14, 16, 11,
+         12, 14, 16, 10, 14, 17, 18, 0, 1, 2, 3, 4, 5, 7, 18, 21, 22,
+         23, 24, 25, 26, 27, 28, 29, 0, 1, 4, 5, 7, 18, 20, 22, 23, 24,
+         25, 26, 27, 28, 29, 5, 20, 21, 23, 24, 25, 26, 27, 28, 29, 5, 20,
+         21, 22, 23, 24, 25, 26, 27, 28, 29, 0, 1, 2, 5, 6, 7, 10, 20,
+         21, 22, 23, 25, 26, 27, 28, 29, 0, 1, 5, 7, 9, 13, 20, 21, 22,
+         23, 24, 26, 27, 28, 29, 0, 1, 5, 6, 7, 20, 21, 22, 23, 24, 25,
+         27, 28, 29, 0, 1, 3, 5, 6, 7, 20, 21, 22, 23, 24, 25, 26, 28,
+         0, 1, 5, 7, 9, 20, 21, 22, 23, 24, 25, 26, 27, 29, 4, 18, 20,
+         21, 22])
+    adjacency = sparse.csr_matrix((np.ones(len(row), dtype=bool), (row, col)), shape=(30, 30))
+
+    if metadata:
+        names = np.array(
+            ['Isaac Newton',
+             'Albert Einstein',
+             'Carl Linnaeus',
+             'Charles Darwin',
+             'Ptolemy',
+             'Gottfried Wilhelm Leibniz',
+             'Carl Friedrich Gauss',
+             'Galileo Galilei',
+             'Leonhard Euler',
+             'John von Neumann',
+             'Leonardo da Vinci',
+             'Richard Wagner',
+             'Ludwig van Beethoven',
+             'Bob Dylan',
+             'Igor Stravinsky',
+             'The Beatles',
+             'Wolfgang Amadeus Mozart',
+             'Richard Strauss',
+             'Raphael',
+             'Pablo Picasso',
+             'Aristotle',
+             'Plato',
+             'Augustine of Hippo',
+             'Thomas Aquinas',
+             'Immanuel Kant',
+             'Bertrand Russell',
+             'David Hume',
+             'René Descartes',
+             'John Stuart Mill',
+             'Socrates'])
+        labels = np.array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 1, 1, 1,
+                           1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2])
+        names_labels = np.array(['science', 'arts', 'philosophy'])
+        position = np.array(
+            [[0.25, 0.57],
+             [0.28, 0.37],
+             [-0.08, 0.82],
+             [0.08, 0.87],
+             [-0.08, 0.49],
+             [0.31, 0.58],
+             [0.41, 0.66],
+             [0.31, 0.51],
+             [0.53, 0.65],
+             [0.48, 0.42],
+             [-0.02, 0.29],
+             [0.25, -0.44],
+             [0.23, -0.22],
+             [0.02, 0.03],
+             [0.07, -0.26],
+             [-0.16, -0.23],
+             [0.28, -0.15],
+             [0.12, -0.38],
+             [-0.14, 0.29],
+             [-0.09, -0.1],
+             [0.09, 0.57],
+             [0.12, 0.5],
+             [0.16, 0.7],
+             [0.12, 0.66],
+             [0.17, 0.57],
+             [0.2, 0.44],
+             [0.22, 0.64],
+             [0.28, 0.65],
+             [0.23, 0.51],
+             [-0., 0.57]])
+        row = np.array(
+            [0, 0, 0, 0, 0, 1, 1, 1, 1, 1, 2, 2, 2, 2, 3, 3, 3,
+             3, 3, 3, 4, 4, 5, 5, 5, 5, 5, 6, 7, 7, 7, 7, 8, 8,
+             8, 8, 8, 9, 9, 9, 10, 10, 10, 10, 10, 11, 11, 11, 12, 12, 12,
+             13, 13, 14, 15, 15, 16, 16, 17, 17, 18, 19, 19, 19, 19, 20, 20, 20,
+             20, 20, 20, 21, 21, 21, 21, 22, 22, 23, 23, 23, 23, 23, 24, 24, 24,
+             25, 25, 25, 26, 26, 27, 27, 27, 27, 28, 28, 28, 29, 29, 29, 29])
+        col = np.array(
+            [1, 2, 4, 5, 10, 2, 3, 4, 5, 8, 1, 4, 8, 10, 1, 2, 4,
+             5, 8, 10, 2, 9, 2, 5, 7, 8, 9, 5, 1, 4, 5, 8, 1, 2,
+             3, 5, 8, 2, 4, 5, 0, 4, 5, 6, 8, 5, 8, 9, 1, 4, 6,
+             4, 10, 9, 4, 9, 4, 6, 4, 8, 9, 0, 2, 8, 9, 1, 2, 3,
+             7, 8, 9, 2, 3, 4, 5, 2, 5, 1, 2, 3, 4, 8, 2, 4, 8,
+             2, 7, 9, 2, 4, 3, 4, 8, 9, 2, 9, 10, 5, 6, 8, 10])
+        data = np.array(
+            [2, 2, 3, 1, 1, 15, 1, 2, 2, 2, 1, 1, 3, 1, 1, 7, 2,
+             1, 1, 1, 1, 1, 1, 2, 2, 2, 3, 1, 1, 1, 1, 2, 3, 3,
+             1, 1, 1, 6, 1, 1, 1, 3, 1, 1, 1, 1, 1, 2, 1, 1, 2,
+             4, 1, 2, 2, 1, 3, 3, 1, 1, 1, 2, 1, 1, 3, 2, 1, 1,
+             4, 1, 2, 1, 1, 1, 1, 1, 1, 3, 1, 2, 2, 2, 3, 1, 2,
+             2, 5, 1, 1, 1, 3, 1, 5, 5, 3, 1, 1, 1, 1, 1, 2])
+        biadjacency = sparse.csr_matrix((data, (row, col)), shape=(30, 11))
+        words = np.array(
+            ['contribution', 'theory', 'invention', 'time', 'modern',
+             'century', 'study', 'logic', 'school', 'author', 'compose'])
+        graph = Dataset()
+        graph.adjacency = adjacency
+        graph.names = names
+        graph.position = position
+        graph.labels = labels
+        graph.names_labels = names_labels
+        graph.biadjacency = biadjacency
+        graph.names_col = words
+        graph.name = 'art-philo-science'
+        return graph
+    else:
+        return adjacency

sknetwork/embedding/__init__.py

@@ -0,0 +1,8 @@
+"""embedding module"""
+from sknetwork.embedding.base import BaseEmbedding
+from sknetwork.embedding.force_atlas import ForceAtlas
+from sknetwork.embedding.louvain_embedding import LouvainEmbedding
+from sknetwork.embedding.random_projection import RandomProjection
+from sknetwork.embedding.spectral import Spectral
+from sknetwork.embedding.spring import Spring
+from sknetwork.embedding.svd import SVD, GSVD, PCA