pyg-nightly 2.6.0.dev20240704__py3-none-any.whl → 2.8.0.dev20251207__py3-none-any.whl

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  1. {pyg_nightly-2.6.0.dev20240704.dist-info → pyg_nightly-2.8.0.dev20251207.dist-info}/METADATA +81 -58
  2. {pyg_nightly-2.6.0.dev20240704.dist-info → pyg_nightly-2.8.0.dev20251207.dist-info}/RECORD +265 -221
  3. {pyg_nightly-2.6.0.dev20240704.dist-info → pyg_nightly-2.8.0.dev20251207.dist-info}/WHEEL +1 -1
  4. pyg_nightly-2.8.0.dev20251207.dist-info/licenses/LICENSE +19 -0
  5. torch_geometric/__init__.py +34 -1
  6. torch_geometric/_compile.py +11 -3
  7. torch_geometric/_onnx.py +228 -0
  8. torch_geometric/config_mixin.py +8 -3
  9. torch_geometric/config_store.py +1 -1
  10. torch_geometric/contrib/__init__.py +1 -1
  11. torch_geometric/contrib/explain/pgm_explainer.py +1 -1
  12. torch_geometric/data/__init__.py +19 -1
  13. torch_geometric/data/batch.py +2 -2
  14. torch_geometric/data/collate.py +1 -3
  15. torch_geometric/data/data.py +110 -6
  16. torch_geometric/data/database.py +19 -5
  17. torch_geometric/data/dataset.py +14 -9
  18. torch_geometric/data/extract.py +1 -1
  19. torch_geometric/data/feature_store.py +17 -22
  20. torch_geometric/data/graph_store.py +3 -2
  21. torch_geometric/data/hetero_data.py +139 -7
  22. torch_geometric/data/hypergraph_data.py +2 -2
  23. torch_geometric/data/in_memory_dataset.py +2 -2
  24. torch_geometric/data/lightning/datamodule.py +42 -28
  25. torch_geometric/data/storage.py +9 -1
  26. torch_geometric/datasets/__init__.py +20 -1
  27. torch_geometric/datasets/actor.py +7 -9
  28. torch_geometric/datasets/airfrans.py +17 -20
  29. torch_geometric/datasets/airports.py +8 -10
  30. torch_geometric/datasets/amazon.py +8 -11
  31. torch_geometric/datasets/amazon_book.py +8 -9
  32. torch_geometric/datasets/amazon_products.py +7 -9
  33. torch_geometric/datasets/aminer.py +8 -9
  34. torch_geometric/datasets/aqsol.py +10 -13
  35. torch_geometric/datasets/attributed_graph_dataset.py +8 -10
  36. torch_geometric/datasets/ba_multi_shapes.py +10 -12
  37. torch_geometric/datasets/ba_shapes.py +5 -6
  38. torch_geometric/datasets/brca_tgca.py +1 -1
  39. torch_geometric/datasets/city.py +157 -0
  40. torch_geometric/datasets/dbp15k.py +1 -1
  41. torch_geometric/datasets/gdelt_lite.py +3 -2
  42. torch_geometric/datasets/ged_dataset.py +3 -2
  43. torch_geometric/datasets/git_mol_dataset.py +263 -0
  44. torch_geometric/datasets/gnn_benchmark_dataset.py +3 -2
  45. torch_geometric/datasets/hgb_dataset.py +2 -2
  46. torch_geometric/datasets/hm.py +1 -1
  47. torch_geometric/datasets/instruct_mol_dataset.py +134 -0
  48. torch_geometric/datasets/linkx_dataset.py +4 -3
  49. torch_geometric/datasets/lrgb.py +3 -5
  50. torch_geometric/datasets/malnet_tiny.py +2 -1
  51. torch_geometric/datasets/md17.py +3 -3
  52. torch_geometric/datasets/medshapenet.py +145 -0
  53. torch_geometric/datasets/mnist_superpixels.py +2 -3
  54. torch_geometric/datasets/modelnet.py +1 -1
  55. torch_geometric/datasets/molecule_gpt_dataset.py +492 -0
  56. torch_geometric/datasets/molecule_net.py +3 -2
  57. torch_geometric/datasets/neurograph.py +1 -3
  58. torch_geometric/datasets/ogb_mag.py +1 -1
  59. torch_geometric/datasets/opf.py +19 -5
  60. torch_geometric/datasets/pascal_pf.py +1 -1
  61. torch_geometric/datasets/pcqm4m.py +2 -1
  62. torch_geometric/datasets/ppi.py +2 -1
  63. torch_geometric/datasets/protein_mpnn_dataset.py +451 -0
  64. torch_geometric/datasets/qm7.py +1 -1
  65. torch_geometric/datasets/qm9.py +3 -2
  66. torch_geometric/datasets/shrec2016.py +2 -2
  67. torch_geometric/datasets/snap_dataset.py +8 -4
  68. torch_geometric/datasets/tag_dataset.py +462 -0
  69. torch_geometric/datasets/teeth3ds.py +269 -0
  70. torch_geometric/datasets/web_qsp_dataset.py +342 -0
  71. torch_geometric/datasets/wikics.py +2 -1
  72. torch_geometric/datasets/wikidata.py +2 -1
  73. torch_geometric/deprecation.py +1 -1
  74. torch_geometric/distributed/__init__.py +13 -0
  75. torch_geometric/distributed/dist_loader.py +2 -2
  76. torch_geometric/distributed/local_feature_store.py +3 -2
  77. torch_geometric/distributed/local_graph_store.py +2 -1
  78. torch_geometric/distributed/partition.py +9 -8
  79. torch_geometric/distributed/rpc.py +3 -3
  80. torch_geometric/edge_index.py +35 -22
  81. torch_geometric/explain/algorithm/attention_explainer.py +219 -29
  82. torch_geometric/explain/algorithm/base.py +2 -2
  83. torch_geometric/explain/algorithm/captum.py +1 -1
  84. torch_geometric/explain/algorithm/captum_explainer.py +2 -1
  85. torch_geometric/explain/algorithm/gnn_explainer.py +406 -69
  86. torch_geometric/explain/algorithm/graphmask_explainer.py +8 -8
  87. torch_geometric/explain/algorithm/pg_explainer.py +305 -47
  88. torch_geometric/explain/explainer.py +2 -2
  89. torch_geometric/explain/explanation.py +89 -5
  90. torch_geometric/explain/metric/faithfulness.py +1 -1
  91. torch_geometric/graphgym/checkpoint.py +2 -1
  92. torch_geometric/graphgym/config.py +3 -2
  93. torch_geometric/graphgym/imports.py +15 -4
  94. torch_geometric/graphgym/logger.py +1 -1
  95. torch_geometric/graphgym/loss.py +1 -1
  96. torch_geometric/graphgym/models/encoder.py +2 -2
  97. torch_geometric/graphgym/models/layer.py +1 -1
  98. torch_geometric/graphgym/utils/comp_budget.py +4 -3
  99. torch_geometric/hash_tensor.py +798 -0
  100. torch_geometric/index.py +16 -7
  101. torch_geometric/inspector.py +6 -2
  102. torch_geometric/io/fs.py +27 -0
  103. torch_geometric/io/tu.py +2 -3
  104. torch_geometric/llm/__init__.py +9 -0
  105. torch_geometric/llm/large_graph_indexer.py +741 -0
  106. torch_geometric/llm/models/__init__.py +23 -0
  107. torch_geometric/llm/models/g_retriever.py +251 -0
  108. torch_geometric/llm/models/git_mol.py +336 -0
  109. torch_geometric/llm/models/glem.py +397 -0
  110. torch_geometric/llm/models/llm.py +470 -0
  111. torch_geometric/llm/models/llm_judge.py +158 -0
  112. torch_geometric/llm/models/molecule_gpt.py +222 -0
  113. torch_geometric/llm/models/protein_mpnn.py +333 -0
  114. torch_geometric/llm/models/sentence_transformer.py +188 -0
  115. torch_geometric/llm/models/txt2kg.py +353 -0
  116. torch_geometric/llm/models/vision_transformer.py +38 -0
  117. torch_geometric/llm/rag_loader.py +154 -0
  118. torch_geometric/llm/utils/__init__.py +10 -0
  119. torch_geometric/llm/utils/backend_utils.py +443 -0
  120. torch_geometric/llm/utils/feature_store.py +169 -0
  121. torch_geometric/llm/utils/graph_store.py +199 -0
  122. torch_geometric/llm/utils/vectorrag.py +125 -0
  123. torch_geometric/loader/cluster.py +6 -5
  124. torch_geometric/loader/graph_saint.py +2 -1
  125. torch_geometric/loader/ibmb_loader.py +4 -4
  126. torch_geometric/loader/link_loader.py +1 -1
  127. torch_geometric/loader/link_neighbor_loader.py +2 -1
  128. torch_geometric/loader/mixin.py +6 -5
  129. torch_geometric/loader/neighbor_loader.py +1 -1
  130. torch_geometric/loader/neighbor_sampler.py +2 -2
  131. torch_geometric/loader/prefetch.py +4 -3
  132. torch_geometric/loader/temporal_dataloader.py +2 -2
  133. torch_geometric/loader/utils.py +10 -10
  134. torch_geometric/metrics/__init__.py +23 -2
  135. torch_geometric/metrics/link_pred.py +755 -85
  136. torch_geometric/nn/__init__.py +1 -0
  137. torch_geometric/nn/aggr/__init__.py +2 -0
  138. torch_geometric/nn/aggr/base.py +1 -1
  139. torch_geometric/nn/aggr/equilibrium.py +1 -1
  140. torch_geometric/nn/aggr/fused.py +1 -1
  141. torch_geometric/nn/aggr/patch_transformer.py +149 -0
  142. torch_geometric/nn/aggr/set_transformer.py +1 -1
  143. torch_geometric/nn/aggr/utils.py +9 -4
  144. torch_geometric/nn/attention/__init__.py +9 -1
  145. torch_geometric/nn/attention/polynormer.py +107 -0
  146. torch_geometric/nn/attention/qformer.py +71 -0
  147. torch_geometric/nn/attention/sgformer.py +99 -0
  148. torch_geometric/nn/conv/__init__.py +2 -0
  149. torch_geometric/nn/conv/appnp.py +1 -1
  150. torch_geometric/nn/conv/collect.jinja +6 -3
  151. torch_geometric/nn/conv/cugraph/gat_conv.py +8 -2
  152. torch_geometric/nn/conv/cugraph/rgcn_conv.py +3 -0
  153. torch_geometric/nn/conv/cugraph/sage_conv.py +3 -0
  154. torch_geometric/nn/conv/dna_conv.py +1 -1
  155. torch_geometric/nn/conv/eg_conv.py +7 -7
  156. torch_geometric/nn/conv/gat_conv.py +33 -4
  157. torch_geometric/nn/conv/gatv2_conv.py +35 -4
  158. torch_geometric/nn/conv/gen_conv.py +1 -1
  159. torch_geometric/nn/conv/general_conv.py +1 -1
  160. torch_geometric/nn/conv/gravnet_conv.py +2 -1
  161. torch_geometric/nn/conv/hetero_conv.py +3 -2
  162. torch_geometric/nn/conv/meshcnn_conv.py +487 -0
  163. torch_geometric/nn/conv/message_passing.py +6 -5
  164. torch_geometric/nn/conv/mixhop_conv.py +1 -1
  165. torch_geometric/nn/conv/rgcn_conv.py +2 -1
  166. torch_geometric/nn/conv/sg_conv.py +1 -1
  167. torch_geometric/nn/conv/spline_conv.py +2 -1
  168. torch_geometric/nn/conv/ssg_conv.py +1 -1
  169. torch_geometric/nn/conv/transformer_conv.py +5 -3
  170. torch_geometric/nn/data_parallel.py +5 -4
  171. torch_geometric/nn/dense/linear.py +5 -24
  172. torch_geometric/nn/encoding.py +17 -3
  173. torch_geometric/nn/fx.py +17 -15
  174. torch_geometric/nn/model_hub.py +5 -16
  175. torch_geometric/nn/models/__init__.py +11 -0
  176. torch_geometric/nn/models/attentive_fp.py +1 -1
  177. torch_geometric/nn/models/attract_repel.py +148 -0
  178. torch_geometric/nn/models/basic_gnn.py +2 -1
  179. torch_geometric/nn/models/captum.py +1 -1
  180. torch_geometric/nn/models/deep_graph_infomax.py +1 -1
  181. torch_geometric/nn/models/dimenet.py +2 -2
  182. torch_geometric/nn/models/dimenet_utils.py +4 -2
  183. torch_geometric/nn/models/gpse.py +1083 -0
  184. torch_geometric/nn/models/graph_unet.py +13 -4
  185. torch_geometric/nn/models/lpformer.py +783 -0
  186. torch_geometric/nn/models/metapath2vec.py +1 -1
  187. torch_geometric/nn/models/mlp.py +4 -2
  188. torch_geometric/nn/models/node2vec.py +1 -1
  189. torch_geometric/nn/models/polynormer.py +206 -0
  190. torch_geometric/nn/models/rev_gnn.py +3 -3
  191. torch_geometric/nn/models/schnet.py +2 -1
  192. torch_geometric/nn/models/sgformer.py +219 -0
  193. torch_geometric/nn/models/signed_gcn.py +1 -1
  194. torch_geometric/nn/models/visnet.py +2 -2
  195. torch_geometric/nn/norm/batch_norm.py +17 -7
  196. torch_geometric/nn/norm/diff_group_norm.py +7 -2
  197. torch_geometric/nn/norm/graph_norm.py +9 -4
  198. torch_geometric/nn/norm/instance_norm.py +5 -1
  199. torch_geometric/nn/norm/layer_norm.py +15 -7
  200. torch_geometric/nn/norm/msg_norm.py +8 -2
  201. torch_geometric/nn/pool/__init__.py +15 -9
  202. torch_geometric/nn/pool/cluster_pool.py +144 -0
  203. torch_geometric/nn/pool/connect/base.py +1 -3
  204. torch_geometric/nn/pool/edge_pool.py +1 -1
  205. torch_geometric/nn/pool/knn.py +13 -10
  206. torch_geometric/nn/pool/select/base.py +1 -4
  207. torch_geometric/nn/summary.py +1 -1
  208. torch_geometric/nn/to_hetero_module.py +4 -3
  209. torch_geometric/nn/to_hetero_transformer.py +3 -3
  210. torch_geometric/nn/to_hetero_with_bases_transformer.py +5 -5
  211. torch_geometric/profile/__init__.py +2 -0
  212. torch_geometric/profile/nvtx.py +66 -0
  213. torch_geometric/profile/profiler.py +18 -9
  214. torch_geometric/profile/utils.py +20 -5
  215. torch_geometric/sampler/__init__.py +2 -1
  216. torch_geometric/sampler/base.py +337 -8
  217. torch_geometric/sampler/hgt_sampler.py +11 -1
  218. torch_geometric/sampler/neighbor_sampler.py +298 -25
  219. torch_geometric/sampler/utils.py +93 -5
  220. torch_geometric/testing/__init__.py +4 -0
  221. torch_geometric/testing/decorators.py +35 -5
  222. torch_geometric/testing/distributed.py +1 -1
  223. torch_geometric/transforms/__init__.py +4 -0
  224. torch_geometric/transforms/add_gpse.py +49 -0
  225. torch_geometric/transforms/add_metapaths.py +10 -8
  226. torch_geometric/transforms/add_positional_encoding.py +2 -2
  227. torch_geometric/transforms/base_transform.py +2 -1
  228. torch_geometric/transforms/delaunay.py +65 -15
  229. torch_geometric/transforms/face_to_edge.py +32 -3
  230. torch_geometric/transforms/gdc.py +8 -9
  231. torch_geometric/transforms/largest_connected_components.py +1 -1
  232. torch_geometric/transforms/mask.py +5 -1
  233. torch_geometric/transforms/node_property_split.py +1 -1
  234. torch_geometric/transforms/normalize_features.py +3 -3
  235. torch_geometric/transforms/pad.py +1 -1
  236. torch_geometric/transforms/random_link_split.py +1 -1
  237. torch_geometric/transforms/remove_duplicated_edges.py +4 -2
  238. torch_geometric/transforms/remove_self_loops.py +36 -0
  239. torch_geometric/transforms/rooted_subgraph.py +1 -1
  240. torch_geometric/transforms/svd_feature_reduction.py +1 -1
  241. torch_geometric/transforms/virtual_node.py +2 -1
  242. torch_geometric/typing.py +82 -17
  243. torch_geometric/utils/__init__.py +6 -1
  244. torch_geometric/utils/_lexsort.py +0 -9
  245. torch_geometric/utils/_negative_sampling.py +28 -13
  246. torch_geometric/utils/_normalize_edge_index.py +46 -0
  247. torch_geometric/utils/_scatter.py +126 -164
  248. torch_geometric/utils/_sort_edge_index.py +0 -2
  249. torch_geometric/utils/_spmm.py +16 -14
  250. torch_geometric/utils/_subgraph.py +4 -0
  251. torch_geometric/utils/_tree_decomposition.py +1 -1
  252. torch_geometric/utils/_trim_to_layer.py +2 -2
  253. torch_geometric/utils/augmentation.py +1 -1
  254. torch_geometric/utils/convert.py +17 -10
  255. torch_geometric/utils/cross_entropy.py +34 -13
  256. torch_geometric/utils/embedding.py +91 -2
  257. torch_geometric/utils/geodesic.py +28 -25
  258. torch_geometric/utils/influence.py +279 -0
  259. torch_geometric/utils/map.py +14 -10
  260. torch_geometric/utils/nested.py +1 -1
  261. torch_geometric/utils/smiles.py +3 -3
  262. torch_geometric/utils/sparse.py +32 -24
  263. torch_geometric/visualization/__init__.py +2 -1
  264. torch_geometric/visualization/graph.py +250 -5
  265. torch_geometric/warnings.py +11 -2
  266. torch_geometric/nn/nlp/__init__.py +0 -7
  267. torch_geometric/nn/nlp/llm.py +0 -283
  268. torch_geometric/nn/nlp/sentence_transformer.py +0 -94
torch_geometric/nn/models/graph_unet.py CHANGED
@@ -64,7 +64,7 @@ class GraphUNet(torch.nn.Module):
64
64
  in_channels = channels if sum_res else 2 * channels
65
65
 
66
66
  self.up_convs = torch.nn.ModuleList()
67
- for i in range(depth - 1):
67
+ for _ in range(depth - 1):
68
68
  self.up_convs.append(GCNConv(in_channels, channels, improved=True))
69
69
  self.up_convs.append(GCNConv(in_channels, out_channels, improved=True))
70
70
 
@@ -79,12 +79,21 @@ class GraphUNet(torch.nn.Module):
79
79
  for conv in self.up_convs:
80
80
  conv.reset_parameters()
81
81
 
82
- def forward(self, x: Tensor, edge_index: Tensor,
83
- batch: OptTensor = None) -> Tensor:
82
+ def forward(
83
+ self,
84
+ x: Tensor,
85
+ edge_index: Tensor,
86
+ batch: OptTensor = None,
87
+ edge_weight: Tensor = None,
88
+ ) -> Tensor:
84
89
  """""" # noqa: D419
85
90
  if batch is None:
86
91
  batch = edge_index.new_zeros(x.size(0))
87
- edge_weight = x.new_ones(edge_index.size(1))
92
+
93
+ if edge_weight is None:
94
+ edge_weight = x.new_ones(edge_index.size(1))
95
+ assert edge_weight.dim() == 1
96
+ assert edge_weight.size(0) == edge_index.size(1)
88
97
 
89
98
  x = self.down_convs[0](x, edge_index, edge_weight)
90
99
  x = self.act(x)