scikit-network 0.31.0__tar.gz → 0.32.0__tar.gz

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  1. {scikit-network-0.31.0 → scikit-network-0.32.0}/AUTHORS.rst +3 -0
  2. {scikit-network-0.31.0 → scikit-network-0.32.0}/HISTORY.rst +10 -0
  3. {scikit-network-0.31.0 → scikit-network-0.32.0}/PKG-INFO +11 -4
  4. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/clustering.rst +11 -0
  5. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/embedding.rst +0 -4
  6. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/topology.rst +6 -0
  7. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/visualization.rst +2 -2
  8. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/tutorials/clustering/index.rst +2 -1
  9. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/tutorials/embedding/index.rst +0 -1
  10. {scikit-network-0.31.0 → scikit-network-0.32.0}/scikit_network.egg-info/PKG-INFO +11 -4
  11. {scikit-network-0.31.0 → scikit-network-0.32.0}/scikit_network.egg-info/SOURCES.txt +9 -3
  12. {scikit-network-0.31.0 → scikit-network-0.32.0}/setup.cfg +1 -1
  13. {scikit-network-0.31.0 → scikit-network-0.32.0}/setup.py +1 -1
  14. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/__init__.py +1 -1
  15. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/base.py +1 -1
  16. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/base_rank.py +3 -3
  17. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/diffusion.py +21 -13
  18. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/knn.py +19 -13
  19. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/metrics.py +1 -1
  20. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/pagerank.py +12 -8
  21. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/propagation.py +22 -15
  22. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/tests/test_diffusion.py +10 -0
  23. scikit-network-0.31.0/sknetwork/clustering/louvain_core.cpp → scikit-network-0.32.0/sknetwork/classification/vote.cpp +12968 -11092
  24. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/clustering/__init__.py +3 -1
  25. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/clustering/base.py +1 -1
  26. scikit-network-0.32.0/sknetwork/clustering/kcenters.py +253 -0
  27. scikit-network-0.32.0/sknetwork/clustering/leiden.py +241 -0
  28. scikit-network-0.32.0/sknetwork/clustering/leiden_core.cpp +31531 -0
  29. scikit-network-0.32.0/sknetwork/clustering/leiden_core.pyx +124 -0
  30. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/clustering/louvain.py +118 -83
  31. scikit-network-0.32.0/sknetwork/clustering/louvain_core.cpp +31176 -0
  32. scikit-network-0.32.0/sknetwork/clustering/louvain_core.pyx +124 -0
  33. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/clustering/postprocess.py +2 -2
  34. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/clustering/propagation_clustering.py +4 -4
  35. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/clustering/tests/test_API.py +7 -3
  36. scikit-network-0.32.0/sknetwork/clustering/tests/test_kcenters.py +92 -0
  37. scikit-network-0.32.0/sknetwork/clustering/tests/test_leiden.py +34 -0
  38. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/clustering/tests/test_louvain.py +2 -3
  39. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/data/load.py +2 -4
  40. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/data/parse.py +41 -20
  41. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/data/tests/test_parse.py +9 -12
  42. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/embedding/__init__.py +0 -1
  43. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/embedding/base.py +20 -19
  44. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/embedding/force_atlas.py +3 -2
  45. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/embedding/louvain_embedding.py +1 -1
  46. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/embedding/random_projection.py +5 -3
  47. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/embedding/spectral.py +0 -73
  48. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/embedding/tests/test_API.py +4 -28
  49. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/embedding/tests/test_louvain_embedding.py +4 -9
  50. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/embedding/tests/test_spectral.py +2 -5
  51. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/embedding/tests/test_svd.py +1 -1
  52. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/base_layer.py +3 -3
  53. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/gnn_classifier.py +40 -86
  54. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/layer.py +1 -1
  55. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/loss.py +1 -1
  56. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/optimizer.py +4 -3
  57. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/tests/test_base_layer.py +4 -4
  58. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/tests/test_gnn_classifier.py +12 -39
  59. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/utils.py +8 -8
  60. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/hierarchy/base.py +27 -0
  61. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/hierarchy/louvain_hierarchy.py +45 -41
  62. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/hierarchy/paris.cpp +27346 -20632
  63. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/hierarchy/paris.pyx +7 -7
  64. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/hierarchy/postprocess.py +16 -16
  65. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/hierarchy/tests/test_algos.py +5 -0
  66. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/__init__.py +1 -1
  67. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/diteration.cpp +13927 -8097
  68. scikit-network-0.31.0/sknetwork/linalg/normalization.py → scikit-network-0.32.0/sknetwork/linalg/normalizer.py +17 -14
  69. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/operators.py +1 -1
  70. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/ppr_solver.py +1 -1
  71. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/push.cpp +23093 -16922
  72. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/tests/test_normalization.py +3 -7
  73. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/tests/test_operators.py +2 -6
  74. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/tests/test_ppr.py +1 -1
  75. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linkpred/base.py +12 -1
  76. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linkpred/nn.py +6 -6
  77. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/path/distances.py +11 -4
  78. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/path/shortest_path.py +1 -1
  79. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/path/tests/test_distances.py +7 -0
  80. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/path/tests/test_search.py +2 -2
  81. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/ranking/base.py +11 -6
  82. scikit-network-0.32.0/sknetwork/ranking/betweenness.cpp +9668 -0
  83. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/ranking/pagerank.py +13 -12
  84. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/ranking/tests/test_API.py +0 -2
  85. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/ranking/tests/test_betweenness.py +1 -1
  86. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/ranking/tests/test_pagerank.py +11 -5
  87. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/regression/base.py +18 -1
  88. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/regression/diffusion.py +24 -10
  89. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/regression/tests/test_diffusion.py +8 -0
  90. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/__init__.py +3 -1
  91. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/cliques.cpp +23502 -16858
  92. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/core.cpp +22743 -16511
  93. scikit-network-0.32.0/sknetwork/topology/cycles.py +243 -0
  94. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/minheap.cpp +19468 -13478
  95. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/structure.py +2 -42
  96. scikit-network-0.32.0/sknetwork/topology/tests/test_cycles.py +65 -0
  97. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/tests/test_structure.py +2 -16
  98. scikit-network-0.32.0/sknetwork/topology/triangles.cpp +8856 -0
  99. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/triangles.pyx +7 -4
  100. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/weisfeiler_lehman_core.cpp +14754 -8924
  101. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/utils/format.py +1 -1
  102. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/utils/membership.py +2 -2
  103. scikit-network-0.32.0/sknetwork/visualization/__init__.py +4 -0
  104. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/visualization/dendrograms.py +55 -7
  105. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/visualization/graphs.py +261 -44
  106. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/visualization/tests/test_dendrograms.py +9 -9
  107. scikit-network-0.32.0/sknetwork/visualization/tests/test_graphs.py +176 -0
  108. scikit-network-0.31.0/sknetwork/classification/vote.cpp +0 -21699
  109. scikit-network-0.31.0/sknetwork/clustering/louvain_core.pyx +0 -132
  110. scikit-network-0.31.0/sknetwork/embedding/louvain_hierarchy.py +0 -142
  111. scikit-network-0.31.0/sknetwork/embedding/tests/test_louvain_hierarchy.py +0 -19
  112. scikit-network-0.31.0/sknetwork/ranking/betweenness.cpp +0 -6638
  113. scikit-network-0.31.0/sknetwork/topology/triangles.cpp +0 -5006
  114. scikit-network-0.31.0/sknetwork/visualization/__init__.py +0 -4
  115. scikit-network-0.31.0/sknetwork/visualization/tests/test_graphs.py +0 -170
  116. {scikit-network-0.31.0 → scikit-network-0.32.0}/CONTRIBUTING.rst +0 -0
  117. {scikit-network-0.31.0 → scikit-network-0.32.0}/LICENSE +0 -0
  118. {scikit-network-0.31.0 → scikit-network-0.32.0}/MANIFEST.in +0 -0
  119. {scikit-network-0.31.0 → scikit-network-0.32.0}/README.rst +0 -0
  120. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/Makefile +0 -0
  121. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/authors.rst +0 -0
  122. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/conf.py +0 -0
  123. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/contributing.rst +0 -0
  124. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/first_steps.rst +0 -0
  125. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/genindex.rst +0 -0
  126. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/glossary.rst +0 -0
  127. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/history.rst +0 -0
  128. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/index.rst +0 -0
  129. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/make.bat +0 -0
  130. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/readme.rst +0 -0
  131. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/classification.rst +0 -0
  132. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/data.rst +0 -0
  133. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/gnn.rst +0 -0
  134. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/hierarchy.rst +0 -0
  135. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/linalg.rst +0 -0
  136. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/linkpred.rst +0 -0
  137. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/path.rst +0 -0
  138. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/ranking.rst +0 -0
  139. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/regression.rst +0 -0
  140. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/utils.rst +0 -0
  141. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/tutorials/classification/index.rst +0 -0
  142. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/tutorials/data/index.rst +0 -0
  143. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/tutorials/gnn/index.rst +0 -0
  144. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/tutorials/hierarchy/index.rst +0 -0
  145. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/tutorials/linkpred/index.rst +0 -0
  146. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/tutorials/overview/index.rst +0 -0
  147. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/tutorials/path/index.rst +0 -0
  148. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/tutorials/ranking/index.rst +0 -0
  149. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/tutorials/regression/index.rst +0 -0
  150. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/tutorials/topology/index.rst +0 -0
  151. {scikit-network-0.31.0 → scikit-network-0.32.0}/docs/tutorials/visualization/index.rst +0 -0
  152. {scikit-network-0.31.0 → scikit-network-0.32.0}/scikit_network.egg-info/dependency_links.txt +0 -0
  153. {scikit-network-0.31.0 → scikit-network-0.32.0}/scikit_network.egg-info/not-zip-safe +0 -0
  154. {scikit-network-0.31.0 → scikit-network-0.32.0}/scikit_network.egg-info/requires.txt +0 -0
  155. {scikit-network-0.31.0 → scikit-network-0.32.0}/scikit_network.egg-info/top_level.txt +0 -0
  156. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/base.py +0 -0
  157. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/__init__.py +0 -0
  158. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/tests/__init__.py +0 -0
  159. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/tests/test_API.py +0 -0
  160. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/tests/test_knn.py +0 -0
  161. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/tests/test_metrics.py +0 -0
  162. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/tests/test_pagerank.py +0 -0
  163. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/tests/test_propagation.py +0 -0
  164. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/vote.pyx +0 -0
  165. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/clustering/metrics.py +0 -0
  166. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/clustering/tests/__init__.py +0 -0
  167. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/clustering/tests/test_metrics.py +0 -0
  168. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/clustering/tests/test_postprocess.py +0 -0
  169. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/data/__init__.py +0 -0
  170. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/data/base.py +0 -0
  171. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/data/models.py +0 -0
  172. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/data/test_graphs.py +0 -0
  173. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/data/tests/__init__.py +0 -0
  174. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/data/tests/test_API.py +0 -0
  175. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/data/tests/test_base.py +0 -0
  176. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/data/tests/test_load.py +0 -0
  177. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/data/tests/test_models.py +0 -0
  178. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/data/tests/test_test_graphs.py +0 -0
  179. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/data/tests/test_toy_graphs.py +0 -0
  180. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/data/timeout.py +0 -0
  181. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/data/toy_graphs.py +0 -0
  182. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/embedding/spring.py +0 -0
  183. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/embedding/svd.py +0 -0
  184. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/embedding/tests/__init__.py +0 -0
  185. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/embedding/tests/test_force_atlas.py +0 -0
  186. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/embedding/tests/test_random_projection.py +0 -0
  187. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/embedding/tests/test_spring.py +0 -0
  188. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/__init__.py +0 -0
  189. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/activation.py +0 -0
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  191. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/base_activation.py +0 -0
  192. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/neighbor_sampler.py +0 -0
  193. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/tests/__init__.py +0 -0
  194. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/tests/test_activation.py +0 -0
  195. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/tests/test_base.py +0 -0
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  197. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/tests/test_loss.py +0 -0
  198. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/tests/test_neigh_sampler.py +0 -0
  199. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/tests/test_optimizer.py +0 -0
  200. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/gnn/tests/test_utils.py +0 -0
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  203. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/hierarchy/tests/__init__.py +0 -0
  204. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/hierarchy/tests/test_API.py +0 -0
  205. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/hierarchy/tests/test_metrics.py +0 -0
  206. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/hierarchy/tests/test_postprocess.py +0 -0
  207. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/basics.py +0 -0
  208. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/diteration.pyx +0 -0
  209. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/eig_solver.py +0 -0
  210. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/laplacian.py +0 -0
  211. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/polynome.py +0 -0
  212. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/push.pyx +0 -0
  213. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/sparse_lowrank.py +0 -0
  214. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/svd_solver.py +0 -0
  215. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/tests/__init__.py +0 -0
  216. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/tests/test_eig.py +0 -0
  217. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/tests/test_laplacian.py +0 -0
  218. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/tests/test_polynome.py +0 -0
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  220. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linalg/tests/test_svd.py +0 -0
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  222. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linkpred/tests/__init__.py +0 -0
  223. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/linkpred/tests/test_nn.py +0 -0
  224. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/log.py +0 -0
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  226. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/path/dag.py +0 -0
  227. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/path/search.py +0 -0
  228. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/path/tests/__init__.py +0 -0
  229. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/path/tests/test_dag.py +0 -0
  230. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/path/tests/test_shortest_path.py +0 -0
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  234. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/ranking/hits.py +0 -0
  235. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/ranking/katz.py +0 -0
  236. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/ranking/postprocess.py +0 -0
  237. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/ranking/tests/__init__.py +0 -0
  238. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/ranking/tests/test_closeness.py +0 -0
  239. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/ranking/tests/test_hits.py +0 -0
  240. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/ranking/tests/test_postprocess.py +0 -0
  241. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/regression/__init__.py +0 -0
  242. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/regression/tests/__init__.py +0 -0
  243. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/regression/tests/test_API.py +0 -0
  244. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/sknetwork.py +0 -0
  245. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/test_base.py +0 -0
  246. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/test_log.py +0 -0
  247. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/cliques.pyx +0 -0
  248. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/core.pyx +0 -0
  249. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/minheap.pxd +0 -0
  250. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/minheap.pyx +0 -0
  251. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/tests/__init__.py +0 -0
  252. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/tests/test_cliques.py +0 -0
  253. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/tests/test_core.py +0 -0
  254. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/tests/test_triangles.py +0 -0
  255. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/tests/test_wl.py +0 -0
  256. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/weisfeiler_lehman.py +0 -0
  257. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/topology/weisfeiler_lehman_core.pyx +0 -0
  258. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/utils/__init__.py +0 -0
  259. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/utils/check.py +0 -0
  260. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/utils/neighbors.py +0 -0
  261. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/utils/tests/__init__.py +0 -0
  262. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/utils/tests/test_check.py +0 -0
  263. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/utils/tests/test_format.py +0 -0
  264. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/utils/tests/test_membership.py +0 -0
  265. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/utils/tests/test_neighbors.py +0 -0
  266. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/utils/tests/test_tfidf.py +0 -0
  267. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/utils/tests/test_values.py +0 -0
  268. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/utils/tfidf.py +0 -0
  269. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/utils/values.py +0 -0
  270. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/visualization/colors.py +0 -0
  271. {scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/visualization/tests/__init__.py +0 -0
{scikit-network-0.31.0 → scikit-network-0.32.0}/AUTHORS.rst RENAMED
@@ -39,3 +39,6 @@ Contributors
39
39
  * Flávio Juvenal
40
40
  * Wenzhuo Zhao
41
41
  * Henry Carscadden
42
+ * Yiwen Peng
43
+ * Ahmed Zaiou
44
+ * Laurène David
{scikit-network-0.31.0 → scikit-network-0.32.0}/HISTORY.rst RENAMED
@@ -2,6 +2,16 @@
2
2
  History
3
3
  =======
4
4
 
5
+ 0.32.0 (2024-03-28)
6
+ -------------------
7
+
8
+ * Add Leiden clustering algorithm
9
+ * Add k-center clustering algorithm
10
+ * Add functions to detect and break cycles
11
+ * Add damping factor in diffusion
12
+ * Fix F1 scores
13
+ * Remove hierarchical Louvain embedding
14
+ * Get clustering coefficient for directed graphs
5
15
 
6
16
  0.31.0 (2023-05-22)
7
17
  -------------------
{scikit-network-0.31.0 → scikit-network-0.32.0}/PKG-INFO RENAMED
@@ -1,13 +1,12 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: scikit-network
3
- Version: 0.31.0
3
+ Version: 0.32.0
4
4
  Summary: Graph algorithms
5
5
  Home-page: https://github.com/sknetwork-team/scikit-network
6
6
  Author: Scikit-network team
7
7
  Author-email: bonald@enst.fr
8
8
  License: BSD license
9
9
  Keywords: sknetwork
10
- Platform: UNKNOWN
11
10
  Classifier: Development Status :: 3 - Alpha
12
11
  Classifier: Intended Audience :: Developers
13
12
  Classifier: Intended Audience :: Information Technology
@@ -117,6 +116,16 @@ the `Journal of Machine Learning Research <https://jmlr.org>`_:
117
116
  History
118
117
  =======
119
118
 
119
+ 0.32.0 (2024-03-28)
120
+ -------------------
121
+
122
+ * Add Leiden clustering algorithm
123
+ * Add k-center clustering algorithm
124
+ * Add functions to detect and break cycles
125
+ * Add damping factor in diffusion
126
+ * Fix F1 scores
127
+ * Remove hierarchical Louvain embedding
128
+ * Get clustering coefficient for directed graphs
120
129
 
121
130
  0.31.0 (2023-05-22)
122
131
  -------------------
@@ -492,5 +501,3 @@ History
492
501
  ------------------
493
502
 
494
503
  * First release on PyPI.
495
-
496
-
{scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/clustering.rst RENAMED
@@ -49,6 +49,17 @@ When the graph is weighted, the degree of a node is replaced by its weight (sum
49
49
 
50
50
  .. autoclass:: sknetwork.clustering.Louvain
51
51
 
52
+ Leiden
53
+ ------
54
+
55
+ .. autoclass:: sknetwork.clustering.Leiden
56
+
57
+ K-centers
58
+ ---------
59
+
60
+ .. autoclass:: sknetwork.clustering.KCenters
61
+
62
+
52
63
  Propagation
53
64
  -----------
54
65
  .. autoclass:: sknetwork.clustering.PropagationClustering
{scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/embedding.rst RENAMED
@@ -37,10 +37,6 @@ Louvain
37
37
 
38
38
  .. autoclass:: sknetwork.embedding.LouvainEmbedding
39
39
 
40
- Hierarchical Louvain
41
- --------------------
42
-
43
- .. autoclass:: sknetwork.embedding.LouvainNE
44
40
 
45
41
  Force Atlas
46
42
  -----------
{scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/topology.rst RENAMED
@@ -19,8 +19,14 @@ Structure
19
19
 
20
20
  .. autofunction:: sknetwork.topology.is_bipartite
21
21
 
22
+ Cycles
23
+ ------
24
+
22
25
  .. autofunction:: sknetwork.topology.is_acyclic
23
26
 
27
+ .. autofunction:: sknetwork.topology.get_cycles
28
+
29
+ .. autofunction:: sknetwork.topology.break_cycles
24
30
 
25
31
  Core decomposition
26
32
  ------------------
{scikit-network-0.31.0 → scikit-network-0.32.0}/docs/reference/visualization.rst RENAMED
@@ -10,9 +10,9 @@ Graphs
10
10
 
11
11
  .. autofunction:: sknetwork.visualization.graphs.svg_graph
12
12
 
13
- .. autofunction:: sknetwork.visualization.graphs.svg_bigraph
13
+ .. autofunction:: sknetwork.visualization.graphs.visualize_bigraph
14
14
 
15
15
  Dendrograms
16
16
  -----------
17
17
 
18
- .. autofunction:: sknetwork.visualization.dendrograms.svg_dendrogram
18
+ .. autofunction:: sknetwork.visualization.dendrograms.visualize_dendrogram
{scikit-network-0.31.0 → scikit-network-0.32.0}/docs/tutorials/clustering/index.rst RENAMED
@@ -7,5 +7,6 @@ Clustering
7
7
  .. toctree::
8
8
 
9
9
  louvain
10
+ leiden
11
+ kcenters
10
12
  propagation
11
-
{scikit-network-0.31.0 → scikit-network-0.32.0}/docs/tutorials/embedding/index.rst RENAMED
@@ -10,7 +10,6 @@ Embedding
10
10
  pca
11
11
  random_projection
12
12
  louvain_embedding
13
- louvain_hierarchy
14
13
  spring
15
14
  forceatlas
16
15
 
{scikit-network-0.31.0 → scikit-network-0.32.0}/scikit_network.egg-info/PKG-INFO RENAMED
@@ -1,13 +1,12 @@
1
1
  Metadata-Version: 2.1
2
2
  Name: scikit-network
3
- Version: 0.31.0
3
+ Version: 0.32.0
4
4
  Summary: Graph algorithms
5
5
  Home-page: https://github.com/sknetwork-team/scikit-network
6
6
  Author: Scikit-network team
7
7
  Author-email: bonald@enst.fr
8
8
  License: BSD license
9
9
  Keywords: sknetwork
10
- Platform: UNKNOWN
11
10
  Classifier: Development Status :: 3 - Alpha
12
11
  Classifier: Intended Audience :: Developers
13
12
  Classifier: Intended Audience :: Information Technology
@@ -117,6 +116,16 @@ the `Journal of Machine Learning Research <https://jmlr.org>`_:
117
116
  History
118
117
  =======
119
118
 
119
+ 0.32.0 (2024-03-28)
120
+ -------------------
121
+
122
+ * Add Leiden clustering algorithm
123
+ * Add k-center clustering algorithm
124
+ * Add functions to detect and break cycles
125
+ * Add damping factor in diffusion
126
+ * Fix F1 scores
127
+ * Remove hierarchical Louvain embedding
128
+ * Get clustering coefficient for directed graphs
120
129
 
121
130
  0.31.0 (2023-05-22)
122
131
  -------------------
@@ -492,5 +501,3 @@ History
492
501
  ------------------
493
502
 
494
503
  * First release on PyPI.
495
-
496
-
{scikit-network-0.31.0 → scikit-network-0.32.0}/scikit_network.egg-info/SOURCES.txt RENAMED
@@ -7,6 +7,7 @@ README.rst
7
7
  setup.cfg
8
8
  setup.py
9
9
  ./sknetwork/classification/vote.cpp
10
+ ./sknetwork/clustering/leiden_core.cpp
10
11
  ./sknetwork/clustering/louvain_core.cpp
11
12
  ./sknetwork/hierarchy/paris.cpp
12
13
  ./sknetwork/linalg/diteration.cpp
@@ -85,6 +86,9 @@ sknetwork/classification/tests/test_pagerank.py
85
86
  sknetwork/classification/tests/test_propagation.py
86
87
  sknetwork/clustering/__init__.py
87
88
  sknetwork/clustering/base.py
89
+ sknetwork/clustering/kcenters.py
90
+ sknetwork/clustering/leiden.py
91
+ sknetwork/clustering/leiden_core.pyx
88
92
  sknetwork/clustering/louvain.py
89
93
  sknetwork/clustering/louvain_core.pyx
90
94
  sknetwork/clustering/metrics.py
@@ -92,6 +96,8 @@ sknetwork/clustering/postprocess.py
92
96
  sknetwork/clustering/propagation_clustering.py
93
97
  sknetwork/clustering/tests/__init__.py
94
98
  sknetwork/clustering/tests/test_API.py
99
+ sknetwork/clustering/tests/test_kcenters.py
100
+ sknetwork/clustering/tests/test_leiden.py
95
101
  sknetwork/clustering/tests/test_louvain.py
96
102
  sknetwork/clustering/tests/test_metrics.py
97
103
  sknetwork/clustering/tests/test_postprocess.py
@@ -115,7 +121,6 @@ sknetwork/embedding/__init__.py
115
121
  sknetwork/embedding/base.py
116
122
  sknetwork/embedding/force_atlas.py
117
123
  sknetwork/embedding/louvain_embedding.py
118
- sknetwork/embedding/louvain_hierarchy.py
119
124
  sknetwork/embedding/random_projection.py
120
125
  sknetwork/embedding/spectral.py
121
126
  sknetwork/embedding/spring.py
@@ -124,7 +129,6 @@ sknetwork/embedding/tests/__init__.py
124
129
  sknetwork/embedding/tests/test_API.py
125
130
  sknetwork/embedding/tests/test_force_atlas.py
126
131
  sknetwork/embedding/tests/test_louvain_embedding.py
127
- sknetwork/embedding/tests/test_louvain_hierarchy.py
128
132
  sknetwork/embedding/tests/test_random_projection.py
129
133
  sknetwork/embedding/tests/test_spectral.py
130
134
  sknetwork/embedding/tests/test_spring.py
@@ -166,7 +170,7 @@ sknetwork/linalg/basics.py
166
170
  sknetwork/linalg/diteration.pyx
167
171
  sknetwork/linalg/eig_solver.py
168
172
  sknetwork/linalg/laplacian.py
169
- sknetwork/linalg/normalization.py
173
+ sknetwork/linalg/normalizer.py
170
174
  sknetwork/linalg/operators.py
171
175
  sknetwork/linalg/polynome.py
172
176
  sknetwork/linalg/ppr_solver.py
@@ -221,6 +225,7 @@ sknetwork/regression/tests/test_diffusion.py
221
225
  sknetwork/topology/__init__.py
222
226
  sknetwork/topology/cliques.pyx
223
227
  sknetwork/topology/core.pyx
228
+ sknetwork/topology/cycles.py
224
229
  sknetwork/topology/minheap.pxd
225
230
  sknetwork/topology/minheap.pyx
226
231
  sknetwork/topology/structure.py
@@ -230,6 +235,7 @@ sknetwork/topology/weisfeiler_lehman_core.pyx
230
235
  sknetwork/topology/tests/__init__.py
231
236
  sknetwork/topology/tests/test_cliques.py
232
237
  sknetwork/topology/tests/test_core.py
238
+ sknetwork/topology/tests/test_cycles.py
233
239
  sknetwork/topology/tests/test_structure.py
234
240
  sknetwork/topology/tests/test_triangles.py
235
241
  sknetwork/topology/tests/test_wl.py
{scikit-network-0.31.0 → scikit-network-0.32.0}/setup.cfg RENAMED
@@ -1,5 +1,5 @@
1
1
  [bumpversion]
2
- current_version = 0.31.0
2
+ current_version = 0.32.0
3
3
  commit = True
4
4
  tag = True
5
5
 
{scikit-network-0.31.0 → scikit-network-0.32.0}/setup.py RENAMED
@@ -153,7 +153,7 @@ setup(
153
153
  test_suite='tests',
154
154
  tests_require=test_requirements,
155
155
  url='https://github.com/sknetwork-team/scikit-network',
156
- version='0.31.0',
156
+ version='0.32.0',
157
157
  zip_safe=False,
158
158
  ext_modules=ext_modules,
159
159
  include_dirs=[numpy.get_include()],
{scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/__init__.py RENAMED
@@ -4,7 +4,7 @@
4
4
 
5
5
  __author__ = """scikit-network team"""
6
6
  __email__ = "thomas.bonald@telecom-paris.fr"
7
- __version__ = '0.31.0'
7
+ __version__ = '0.32.0'
8
8
 
9
9
  import sknetwork.topology
10
10
  import sknetwork.path
{scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/base.py RENAMED
@@ -38,7 +38,7 @@ class BaseClassifier(Algorithm, ABC):
38
38
  self.probs_row_ = None
39
39
  self.probs_col_ = None
40
40
 
41
- def predict(self, columns=False) -> np.ndarray:
41
+ def predict(self, columns: bool = False) -> np.ndarray:
42
42
  """Return the labels predicted by the algorithm.
43
43
 
44
44
  Parameters
{scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/base_rank.py RENAMED
@@ -1,7 +1,7 @@
1
1
  #!/usr/bin/env python3
2
2
  # -*- coding: utf-8 -*-
3
3
  """
4
- Created on March 2020
4
+ Created in March 2020
5
5
  @author: Nathan de Lara <nathan.delara@polytechnique.org>
6
6
  """
7
7
  from functools import partial
@@ -12,7 +12,7 @@ import numpy as np
12
12
  from scipy import sparse
13
13
 
14
14
  from sknetwork.classification.base import BaseClassifier
15
- from sknetwork.linalg.normalization import normalize
15
+ from sknetwork.linalg.normalizer import normalize
16
16
  from sknetwork.ranking.base import BaseRanking
17
17
  from sknetwork.utils.check import check_labels, check_n_jobs
18
18
  from sknetwork.utils.format import get_adjacency_values
@@ -114,7 +114,7 @@ class RankClassifier(BaseClassifier):
114
114
  seeds_labels = seeds_labels.astype(int)
115
115
  labels_unique, n_classes = check_labels(seeds_labels)
116
116
  seeds_all = self._process_labels(seeds_labels)
117
- local_function = partial(self.algorithm.fit_transform, adjacency)
117
+ local_function = partial(self.algorithm.fit_predict, adjacency)
118
118
  with Pool(self.n_jobs) as pool:
119
119
  scores = np.array(pool.map(local_function, seeds_all))
120
120
  scores = scores.T
{scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/diffusion.py RENAMED
@@ -11,7 +11,7 @@ from scipy import sparse
11
11
 
12
12
  from sknetwork.classification.base import BaseClassifier
13
13
  from sknetwork.path.distances import get_distances
14
- from sknetwork.linalg.normalization import normalize
14
+ from sknetwork.linalg.normalizer import normalize
15
15
  from sknetwork.utils.format import get_adjacency_values
16
16
  from sknetwork.utils.membership import get_membership
17
17
  from sknetwork.utils.neighbors import get_degrees
@@ -38,11 +38,14 @@ class DiffusionClassifier(BaseClassifier):
38
38
  Labels of nodes.
39
39
  probs_ : sparse.csr_matrix, shape (n_row, n_labels)
40
40
  Probability distribution over labels.
41
- labels_row_, labels_col_ : np.ndarray
42
- Labels of rows and columns, for bipartite graphs.
43
- probs_row_, probs_col_ : sparse.csr_matrix, shape (n_row, n_labels)
44
- Probability distributions over labels for rows and columns (for bipartite graphs).
45
-
41
+ labels_row_ : np.ndarray
42
+ Labels of rows, for bipartite graphs.
43
+ labels_col_ : np.ndarray
44
+ Labels of columns, for bipartite graphs.
45
+ probs_row_ : sparse.csr_matrix, shape (n_row, n_labels)
46
+ Probability distributions over labels of rows, for bipartite graphs.
47
+ probs_col_ : sparse.csr_matrix, shape (n_col, n_labels)
48
+ Probability distributions over labels of columns, for bipartite graphs.
46
49
  Example
47
50
  -------
48
51
  >>> from sknetwork.data import karate_club
@@ -78,13 +81,15 @@ class DiffusionClassifier(BaseClassifier):
78
81
 
79
82
  Parameters
80
83
  ----------
81
- input_matrix :
84
+ input_matrix : sparse.csr_matrix, np.ndarray
82
85
  Adjacency matrix or biadjacency matrix of the graph.
83
- labels :
86
+ labels : dict, np.ndarray
84
87
  Known labels (dictionary or vector of int). Negative values ignored.
85
- labels_row, labels_col :
86
- Labels of rows and columns for bipartite graphs. Negative values ignored.
87
- force_bipartite :
88
+ labels_row : dict, np.ndarray
89
+ Labels of rows for bipartite graphs. Negative values ignored.
90
+ labels_col : dict, np.ndarray
91
+ Labels of columns for bipartite graphs. Negative values ignored.
92
+ force_bipartite : bool
88
93
  If ``True``, consider the input matrix as a biadjacency matrix (default = ``False``).
89
94
 
90
95
  Returns
@@ -98,7 +103,10 @@ class DiffusionClassifier(BaseClassifier):
98
103
  labels = values.astype(int)
99
104
  if (labels < 0).all():
100
105
  raise ValueError('At least one node must be given a non-negative label.')
101
- temperatures = get_membership(labels).toarray()
106
+ labels_reindex = labels.copy()
107
+ labels_unique, inverse = np.unique(labels[labels >= 0], return_inverse=True)
108
+ labels_reindex[labels >= 0] = inverse
109
+ temperatures = get_membership(labels_reindex).toarray()
102
110
  temperatures_seeds = temperatures[labels >= 0]
103
111
  temperatures[labels < 0] = 0.5
104
112
  diffusion = normalize(adjacency)
@@ -107,7 +115,7 @@ class DiffusionClassifier(BaseClassifier):
107
115
  temperatures[labels >= 0] = temperatures_seeds
108
116
  if self.centering:
109
117
  temperatures -= temperatures.mean(axis=0)
110
- labels_ = temperatures.argmax(axis=1)
118
+ labels_ = labels_unique[temperatures.argmax(axis=1)]
111
119
 
112
120
  # softmax
113
121
  if self.centering:
{scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/knn.py RENAMED
@@ -12,7 +12,7 @@ from scipy import sparse
12
12
 
13
13
  from sknetwork.classification.base import BaseClassifier
14
14
  from sknetwork.embedding.base import BaseEmbedding
15
- from sknetwork.linalg.normalization import get_norms, normalize
15
+ from sknetwork.linalg.normalizer import get_norms, normalize
16
16
  from sknetwork.utils.check import check_n_neighbors
17
17
  from sknetwork.utils.format import get_adjacency_values
18
18
 
@@ -22,12 +22,12 @@ class NNClassifier(BaseClassifier):
22
22
 
23
23
  Parameters
24
24
  ----------
25
- n_neighbors :
25
+ n_neighbors : int
26
26
  Number of nearest neighbors .
27
- embedding_method :
27
+ embedding_method : :class:`BaseEmbedding`
28
28
  Embedding method used to represent nodes in vector space.
29
29
  If ``None`` (default), use identity.
30
- normalize :
30
+ normalize : bool
31
31
  If ``True``, apply normalization so that all vectors have norm 1 in the embedding space.
32
32
 
33
33
  Attributes
@@ -36,10 +36,14 @@ class NNClassifier(BaseClassifier):
36
36
  Labels of nodes.
37
37
  probs_ : sparse.csr_matrix, shape (n_row, n_labels)
38
38
  Probability distribution over labels.
39
- labels_row_, labels_col_ : np.ndarray
40
- Labels of rows and columns, for bipartite graphs.
41
- probs_row_, probs_col_ : sparse.csr_matrix, shape (n_row, n_labels)
42
- Probability distributions over labels for rows and columns (for bipartite graphs).
39
+ labels_row_ : np.ndarray
40
+ Labels of rows, for bipartite graphs.
41
+ labels_col_ : np.ndarray
42
+ Labels of columns, for bipartite graphs.
43
+ probs_row_ : sparse.csr_matrix, shape (n_row, n_labels)
44
+ Probability distributions over labels of rows, for bipartite graphs.
45
+ probs_col_ : sparse.csr_matrix, shape (n_col, n_labels)
46
+ Probability distributions over labels of columns, for bipartite graphs.
43
47
 
44
48
  Example
45
49
  -------
@@ -99,12 +103,14 @@ class NNClassifier(BaseClassifier):
99
103
 
100
104
  Parameters
101
105
  ----------
102
- input_matrix :
106
+ input_matrix : sparse.csr_matrix, np.ndarray
103
107
  Adjacency matrix or biadjacency matrix of the graph.
104
- labels :
105
- Known labels (dictionary or array). Negative values ignored.
106
- labels_row, labels_col :
107
- Known labels of rows and columns (for bipartite graphs).
108
+ labels : np.ndarray, dict
109
+ Known labels. Negative values ignored.
110
+ labels_row : np.ndarray, dict
111
+ Known labels of rows, for bipartite graphs.
112
+ labels_col : np.ndarray, dict
113
+ Known labels of columns, for bipartite graphs.
108
114
 
109
115
  Returns
110
116
  -------
{scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/metrics.py RENAMED
@@ -158,7 +158,7 @@ def get_f1_scores(labels_true: np.ndarray, labels_pred: np.ndarray, return_preci
158
158
  mask = counts_pred > 0
159
159
  precisions[mask] = counts_correct[mask] / counts_pred[mask]
160
160
  f1_scores = np.zeros(n_labels)
161
- mask = (counts_true > 0) & (counts_pred > 0)
161
+ mask = (precisions > 0) & (recalls > 0)
162
162
  f1_scores[mask] = 2 / (1 / precisions[mask] + 1 / recalls[mask])
163
163
  if return_precision_recall:
164
164
  return f1_scores, precisions, recalls
{scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/pagerank.py RENAMED
@@ -1,7 +1,7 @@
1
1
  #!/usr/bin/env python3
2
2
  # -*- coding: utf-8 -*-
3
3
  """
4
- Created on March 2020
4
+ Created in March 2020
5
5
  @author: Nathan de Lara <nathan.delara@polytechnique.org>
6
6
  """
7
7
  from typing import Optional
@@ -17,9 +17,9 @@ class PageRankClassifier(RankClassifier):
17
17
 
18
18
  Parameters
19
19
  ----------
20
- damping_factor:
20
+ damping_factor: float
21
21
  Probability to continue the random walk.
22
- solver : :obj:`str`
22
+ solver : str
23
23
  Which solver to use: 'piteration', 'diteration', 'bicgstab', 'lanczos'.
24
24
  n_iter : int
25
25
  Number of iterations for some solvers such as ``'piteration'`` or ``'diteration'``.
@@ -29,13 +29,17 @@ class PageRankClassifier(RankClassifier):
29
29
  Attributes
30
30
  ----------
31
31
  labels_ : np.ndarray, shape (n_labels,)
32
- Label of each node.
32
+ Labels of nodes.
33
33
  probs_ : sparse.csr_matrix, shape (n_row, n_labels)
34
34
  Probability distribution over labels.
35
- labels_row_, labels_col_ : np.ndarray
36
- Labels of rows and columns, for bipartite graphs.
37
- probs_row_, probs_col_ : sparse.csr_matrix, shape (n_row, n_labels)
38
- Probability distributions over labels for rows and columns (for bipartite graphs).
35
+ labels_row_ : np.ndarray
36
+ Labels of rows, for bipartite graphs.
37
+ labels_col_ : np.ndarray
38
+ Labels of columns, for bipartite graphs.
39
+ probs_row_ : sparse.csr_matrix, shape (n_row, n_labels)
40
+ Probability distributions over labels of rows, for bipartite graphs.
41
+ probs_col_ : sparse.csr_matrix, shape (n_col, n_labels)
42
+ Probability distributions over labels of columns, for bipartite graphs.
39
43
 
40
44
  Example
41
45
  -------
{scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/propagation.py RENAMED
@@ -1,7 +1,7 @@
1
1
  #!/usr/bin/env python3
2
2
  # coding: utf-8
3
3
  """
4
- Created on April 2020
4
+ Created in April 2020
5
5
  @author: Thomas Bonald <tbonald@enst.fr>
6
6
  """
7
7
 
@@ -12,7 +12,7 @@ from scipy import sparse
12
12
 
13
13
  from sknetwork.classification.base import BaseClassifier
14
14
  from sknetwork.classification.vote import vote_update
15
- from sknetwork.linalg.normalization import normalize
15
+ from sknetwork.linalg.normalizer import normalize
16
16
  from sknetwork.utils.format import get_adjacency_values
17
17
  from sknetwork.utils.membership import get_membership
18
18
 
@@ -25,9 +25,9 @@ class Propagation(BaseClassifier):
25
25
  n_iter : float
26
26
  Maximum number of iterations (-1 for infinity).
27
27
  node_order : str
28
- * `'random'`: node labels are updated in random order.
29
- * `'increasing'`: node labels are updated by increasing order of (in-)weight.
30
- * `'decreasing'`: node labels are updated by decreasing order of (in-)weight.
28
+ * ``'random'``: node labels are updated in random order.
29
+ * ``'increasing'``: node labels are updated by increasing order of (in-) weight.
30
+ * ``'decreasing'``: node labels are updated by decreasing order of (in-) weight.
31
31
  * Otherwise, node labels are updated by index order.
32
32
  weighted : bool
33
33
  If ``True``, the vote of each neighbor is proportional to the edge weight.
@@ -36,13 +36,17 @@ class Propagation(BaseClassifier):
36
36
  Attributes
37
37
  ----------
38
38
  labels_ : np.ndarray, shape (n_labels,)
39
- Label of each node.
39
+ Labels of nodes.
40
40
  probs_ : sparse.csr_matrix, shape (n_row, n_labels)
41
41
  Probability distribution over labels.
42
- labels_row_, labels_col_ : np.ndarray
43
- Labels of rows and columns, for bipartite graphs.
44
- probs_row_, probs_col_ : sparse.csr_matrix, shape (n_row, n_labels)
45
- Probability distributions over labels for rows and columns (for bipartite graphs).
42
+ labels_row_ : np.ndarray
43
+ Labels of rows, for bipartite graphs.
44
+ labels_col_ : np.ndarray
45
+ Labels of columns, for bipartite graphs.
46
+ probs_row_ : sparse.csr_matrix, shape (n_row, n_labels)
47
+ Probability distributions over labels of rows, for bipartite graphs.
48
+ probs_col_ : sparse.csr_matrix, shape (n_col, n_labels)
49
+ Probability distributions over labels of columns, for bipartite graphs.
46
50
 
47
51
  Example
48
52
  -------
@@ -93,12 +97,15 @@ class Propagation(BaseClassifier):
93
97
 
94
98
  Parameters
95
99
  ----------
96
- input_matrix :
100
+ input_matrix : sparse.csr_matrix, np.ndarray
97
101
  Adjacency matrix or biadjacency matrix of the graph.
98
- labels :
99
- Known labels (dictionary or array). Negative values ignored.
100
- labels_row, labels_col :
101
- Known labels of rows and columns (for bipartite graphs).
102
+ labels : np.ndarray, dict
103
+ Known labels. Negative values ignored.
104
+ labels_row : np.ndarray, dict
105
+ Known labels of rows, for bipartite graphs.
106
+ labels_col : np.ndarray, dict
107
+ Known labels of columns, for bipartite graphs.
108
+
102
109
  Returns
103
110
  -------
104
111
  self: :class:`Propagation`
{scikit-network-0.31.0 → scikit-network-0.32.0}/sknetwork/classification/tests/test_diffusion.py RENAMED
@@ -36,6 +36,7 @@ class TestDiffusionClassifier(unittest.TestCase):
36
36
  algo.fit(biadjacency, labels_row=labels_row, labels_col=labels_col)
37
37
  self.assertTrue(len(algo.labels_row_) == n_row)
38
38
  self.assertTrue(len(algo.labels_col_) == n_col)
39
+ self.assertTrue(all(algo.labels_col_ == algo.predict(columns=True)))
39
40
 
40
41
  def test_predict(self):
41
42
  adjacency = test_graph()
@@ -65,3 +66,12 @@ class TestDiffusionClassifier(unittest.TestCase):
65
66
  self.assertTrue(membership.shape == (n_row, 2))
66
67
  membership = algo.transform(columns=True)
67
68
  self.assertTrue(membership.shape == (n_col, 2))
69
+
70
+ def test_reindex_label(self):
71
+ adjacency = test_graph()
72
+ n_nodes = adjacency.shape[0]
73
+ labels = {0: 0, 1: 2, 2: 3}
74
+ algo = DiffusionClassifier()
75
+ labels_pred = algo.fit_predict(adjacency, labels=labels)
76
+ self.assertTrue(len(labels_pred) == n_nodes)
77
+ self.assertTrue(set(list(labels_pred)) == {0, 2, 3})