pyg-nightly 2.6.0.dev20240511__py3-none-any.whl → 2.7.0.dev20250114__py3-none-any.whl

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  1. {pyg_nightly-2.6.0.dev20240511.dist-info → pyg_nightly-2.7.0.dev20250114.dist-info}/METADATA +30 -31
  2. {pyg_nightly-2.6.0.dev20240511.dist-info → pyg_nightly-2.7.0.dev20250114.dist-info}/RECORD +205 -181
  3. {pyg_nightly-2.6.0.dev20240511.dist-info → pyg_nightly-2.7.0.dev20250114.dist-info}/WHEEL +1 -1
  4. torch_geometric/__init__.py +26 -1
  5. torch_geometric/_compile.py +8 -1
  6. torch_geometric/_onnx.py +14 -0
  7. torch_geometric/config_mixin.py +113 -0
  8. torch_geometric/config_store.py +16 -14
  9. torch_geometric/data/__init__.py +24 -1
  10. torch_geometric/data/batch.py +2 -2
  11. torch_geometric/data/data.py +13 -8
  12. torch_geometric/data/database.py +15 -7
  13. torch_geometric/data/dataset.py +14 -6
  14. torch_geometric/data/feature_store.py +13 -22
  15. torch_geometric/data/graph_store.py +0 -4
  16. torch_geometric/data/hetero_data.py +4 -4
  17. torch_geometric/data/in_memory_dataset.py +2 -4
  18. torch_geometric/data/large_graph_indexer.py +677 -0
  19. torch_geometric/data/lightning/datamodule.py +4 -4
  20. torch_geometric/data/storage.py +15 -5
  21. torch_geometric/data/summary.py +14 -4
  22. torch_geometric/data/temporal.py +1 -2
  23. torch_geometric/datasets/__init__.py +11 -1
  24. torch_geometric/datasets/actor.py +9 -11
  25. torch_geometric/datasets/airfrans.py +15 -18
  26. torch_geometric/datasets/airports.py +10 -12
  27. torch_geometric/datasets/amazon.py +8 -11
  28. torch_geometric/datasets/amazon_book.py +9 -10
  29. torch_geometric/datasets/amazon_products.py +9 -10
  30. torch_geometric/datasets/aminer.py +8 -9
  31. torch_geometric/datasets/aqsol.py +10 -13
  32. torch_geometric/datasets/attributed_graph_dataset.py +10 -12
  33. torch_geometric/datasets/ba_multi_shapes.py +10 -12
  34. torch_geometric/datasets/ba_shapes.py +5 -6
  35. torch_geometric/datasets/bitcoin_otc.py +1 -1
  36. torch_geometric/datasets/brca_tgca.py +1 -1
  37. torch_geometric/datasets/dblp.py +2 -1
  38. torch_geometric/datasets/dbp15k.py +2 -2
  39. torch_geometric/datasets/fake.py +1 -3
  40. torch_geometric/datasets/flickr.py +2 -1
  41. torch_geometric/datasets/freebase.py +1 -1
  42. torch_geometric/datasets/gdelt_lite.py +3 -2
  43. torch_geometric/datasets/ged_dataset.py +3 -2
  44. torch_geometric/datasets/git_mol_dataset.py +263 -0
  45. torch_geometric/datasets/gnn_benchmark_dataset.py +6 -5
  46. torch_geometric/datasets/hgb_dataset.py +8 -8
  47. torch_geometric/datasets/imdb.py +2 -1
  48. torch_geometric/datasets/last_fm.py +2 -1
  49. torch_geometric/datasets/linkx_dataset.py +4 -3
  50. torch_geometric/datasets/lrgb.py +3 -5
  51. torch_geometric/datasets/malnet_tiny.py +4 -3
  52. torch_geometric/datasets/mnist_superpixels.py +2 -3
  53. torch_geometric/datasets/molecule_gpt_dataset.py +485 -0
  54. torch_geometric/datasets/molecule_net.py +7 -1
  55. torch_geometric/datasets/motif_generator/base.py +0 -1
  56. torch_geometric/datasets/neurograph.py +1 -3
  57. torch_geometric/datasets/ogb_mag.py +1 -1
  58. torch_geometric/datasets/opf.py +239 -0
  59. torch_geometric/datasets/ose_gvcs.py +1 -1
  60. torch_geometric/datasets/pascal_pf.py +1 -1
  61. torch_geometric/datasets/pcpnet_dataset.py +1 -1
  62. torch_geometric/datasets/pcqm4m.py +2 -1
  63. torch_geometric/datasets/ppi.py +1 -1
  64. torch_geometric/datasets/qm9.py +4 -3
  65. torch_geometric/datasets/reddit.py +2 -1
  66. torch_geometric/datasets/reddit2.py +2 -1
  67. torch_geometric/datasets/rel_link_pred_dataset.py +3 -3
  68. torch_geometric/datasets/s3dis.py +2 -2
  69. torch_geometric/datasets/shapenet.py +3 -3
  70. torch_geometric/datasets/shrec2016.py +2 -2
  71. torch_geometric/datasets/tag_dataset.py +350 -0
  72. torch_geometric/datasets/upfd.py +2 -1
  73. torch_geometric/datasets/web_qsp_dataset.py +246 -0
  74. torch_geometric/datasets/webkb.py +2 -2
  75. torch_geometric/datasets/wikics.py +1 -1
  76. torch_geometric/datasets/wikidata.py +3 -2
  77. torch_geometric/datasets/wikipedia_network.py +2 -2
  78. torch_geometric/datasets/word_net.py +2 -2
  79. torch_geometric/datasets/yelp.py +2 -1
  80. torch_geometric/datasets/zinc.py +1 -1
  81. torch_geometric/device.py +42 -0
  82. torch_geometric/distributed/local_feature_store.py +3 -2
  83. torch_geometric/distributed/local_graph_store.py +2 -1
  84. torch_geometric/distributed/partition.py +9 -8
  85. torch_geometric/edge_index.py +17 -8
  86. torch_geometric/explain/algorithm/base.py +0 -1
  87. torch_geometric/explain/algorithm/pg_explainer.py +1 -1
  88. torch_geometric/explain/explanation.py +2 -2
  89. torch_geometric/graphgym/checkpoint.py +2 -1
  90. torch_geometric/graphgym/logger.py +4 -4
  91. torch_geometric/graphgym/loss.py +1 -1
  92. torch_geometric/graphgym/utils/agg_runs.py +6 -6
  93. torch_geometric/index.py +20 -7
  94. torch_geometric/inspector.py +6 -2
  95. torch_geometric/io/fs.py +28 -2
  96. torch_geometric/io/npz.py +2 -1
  97. torch_geometric/io/off.py +2 -2
  98. torch_geometric/io/sdf.py +2 -2
  99. torch_geometric/io/tu.py +2 -3
  100. torch_geometric/loader/__init__.py +4 -0
  101. torch_geometric/loader/cluster.py +9 -3
  102. torch_geometric/loader/graph_saint.py +2 -1
  103. torch_geometric/loader/ibmb_loader.py +12 -4
  104. torch_geometric/loader/mixin.py +1 -1
  105. torch_geometric/loader/neighbor_loader.py +1 -1
  106. torch_geometric/loader/neighbor_sampler.py +2 -2
  107. torch_geometric/loader/prefetch.py +1 -1
  108. torch_geometric/loader/rag_loader.py +107 -0
  109. torch_geometric/loader/zip_loader.py +10 -0
  110. torch_geometric/metrics/__init__.py +11 -2
  111. torch_geometric/metrics/link_pred.py +159 -34
  112. torch_geometric/nn/aggr/__init__.py +2 -0
  113. torch_geometric/nn/aggr/attention.py +0 -2
  114. torch_geometric/nn/aggr/base.py +2 -4
  115. torch_geometric/nn/aggr/patch_transformer.py +143 -0
  116. torch_geometric/nn/aggr/set_transformer.py +1 -1
  117. torch_geometric/nn/attention/__init__.py +5 -1
  118. torch_geometric/nn/attention/qformer.py +71 -0
  119. torch_geometric/nn/conv/collect.jinja +6 -3
  120. torch_geometric/nn/conv/cugraph/base.py +0 -1
  121. torch_geometric/nn/conv/edge_conv.py +3 -2
  122. torch_geometric/nn/conv/gat_conv.py +35 -7
  123. torch_geometric/nn/conv/gatv2_conv.py +36 -6
  124. torch_geometric/nn/conv/general_conv.py +1 -1
  125. torch_geometric/nn/conv/gravnet_conv.py +3 -2
  126. torch_geometric/nn/conv/hetero_conv.py +3 -3
  127. torch_geometric/nn/conv/hgt_conv.py +1 -1
  128. torch_geometric/nn/conv/message_passing.py +100 -82
  129. torch_geometric/nn/conv/mixhop_conv.py +1 -1
  130. torch_geometric/nn/conv/rgcn_conv.py +2 -1
  131. torch_geometric/nn/conv/spline_conv.py +4 -4
  132. torch_geometric/nn/conv/x_conv.py +3 -2
  133. torch_geometric/nn/dense/linear.py +5 -4
  134. torch_geometric/nn/fx.py +3 -3
  135. torch_geometric/nn/model_hub.py +3 -1
  136. torch_geometric/nn/models/__init__.py +10 -2
  137. torch_geometric/nn/models/deep_graph_infomax.py +1 -2
  138. torch_geometric/nn/models/dimenet_utils.py +5 -7
  139. torch_geometric/nn/models/g_retriever.py +230 -0
  140. torch_geometric/nn/models/git_mol.py +336 -0
  141. torch_geometric/nn/models/glem.py +385 -0
  142. torch_geometric/nn/models/gnnff.py +0 -1
  143. torch_geometric/nn/models/graph_unet.py +12 -3
  144. torch_geometric/nn/models/jumping_knowledge.py +63 -4
  145. torch_geometric/nn/models/lightgcn.py +1 -1
  146. torch_geometric/nn/models/metapath2vec.py +3 -4
  147. torch_geometric/nn/models/molecule_gpt.py +222 -0
  148. torch_geometric/nn/models/node2vec.py +1 -2
  149. torch_geometric/nn/models/schnet.py +2 -1
  150. torch_geometric/nn/models/signed_gcn.py +3 -3
  151. torch_geometric/nn/module_dict.py +2 -2
  152. torch_geometric/nn/nlp/__init__.py +9 -0
  153. torch_geometric/nn/nlp/llm.py +322 -0
  154. torch_geometric/nn/nlp/sentence_transformer.py +134 -0
  155. torch_geometric/nn/nlp/vision_transformer.py +33 -0
  156. torch_geometric/nn/norm/batch_norm.py +1 -1
  157. torch_geometric/nn/parameter_dict.py +2 -2
  158. torch_geometric/nn/pool/__init__.py +7 -5
  159. torch_geometric/nn/pool/cluster_pool.py +145 -0
  160. torch_geometric/nn/pool/connect/base.py +0 -1
  161. torch_geometric/nn/pool/edge_pool.py +1 -1
  162. torch_geometric/nn/pool/graclus.py +4 -2
  163. torch_geometric/nn/pool/select/base.py +0 -1
  164. torch_geometric/nn/pool/voxel_grid.py +3 -2
  165. torch_geometric/nn/resolver.py +1 -1
  166. torch_geometric/nn/sequential.jinja +10 -23
  167. torch_geometric/nn/sequential.py +203 -77
  168. torch_geometric/nn/summary.py +1 -1
  169. torch_geometric/nn/to_hetero_with_bases_transformer.py +19 -19
  170. torch_geometric/profile/__init__.py +2 -0
  171. torch_geometric/profile/nvtx.py +66 -0
  172. torch_geometric/profile/profiler.py +24 -15
  173. torch_geometric/resolver.py +1 -1
  174. torch_geometric/sampler/base.py +34 -13
  175. torch_geometric/sampler/neighbor_sampler.py +11 -10
  176. torch_geometric/testing/decorators.py +17 -22
  177. torch_geometric/transforms/__init__.py +2 -0
  178. torch_geometric/transforms/add_metapaths.py +4 -4
  179. torch_geometric/transforms/add_positional_encoding.py +1 -1
  180. torch_geometric/transforms/delaunay.py +65 -14
  181. torch_geometric/transforms/face_to_edge.py +32 -3
  182. torch_geometric/transforms/gdc.py +7 -6
  183. torch_geometric/transforms/laplacian_lambda_max.py +2 -2
  184. torch_geometric/transforms/mask.py +5 -1
  185. torch_geometric/transforms/node_property_split.py +1 -2
  186. torch_geometric/transforms/pad.py +7 -6
  187. torch_geometric/transforms/random_link_split.py +1 -1
  188. torch_geometric/transforms/remove_self_loops.py +36 -0
  189. torch_geometric/transforms/svd_feature_reduction.py +1 -1
  190. torch_geometric/transforms/virtual_node.py +2 -1
  191. torch_geometric/typing.py +31 -5
  192. torch_geometric/utils/__init__.py +5 -1
  193. torch_geometric/utils/_negative_sampling.py +1 -1
  194. torch_geometric/utils/_normalize_edge_index.py +46 -0
  195. torch_geometric/utils/_scatter.py +37 -12
  196. torch_geometric/utils/_subgraph.py +4 -0
  197. torch_geometric/utils/_tree_decomposition.py +2 -2
  198. torch_geometric/utils/augmentation.py +1 -1
  199. torch_geometric/utils/convert.py +5 -5
  200. torch_geometric/utils/geodesic.py +24 -22
  201. torch_geometric/utils/hetero.py +1 -1
  202. torch_geometric/utils/map.py +1 -1
  203. torch_geometric/utils/smiles.py +66 -28
  204. torch_geometric/utils/sparse.py +25 -10
  205. torch_geometric/visualization/graph.py +3 -4
@@ -2,7 +2,7 @@ import copy
2
2
  import math
3
3
  import sys
4
4
  import warnings
5
- from typing import Callable, Dict, List, Optional, Tuple, Union
5
+ from typing import Callable, Dict, List, Literal, Optional, Tuple, Union
6
6
 
7
7
  import torch
8
8
  from torch import Tensor
@@ -168,7 +168,7 @@ class NeighborSampler(BaseSampler):
168
168
  attrs = [attr for attr in feature_store.get_all_tensor_attrs()]
169
169
 
170
170
  edge_attrs = graph_store.get_all_edge_attrs()
171
- self.edge_types = list(set(attr.edge_type for attr in edge_attrs))
171
+ self.edge_types = list({attr.edge_type for attr in edge_attrs})
172
172
 
173
173
  if weight_attr is not None:
174
174
  raise NotImplementedError(
@@ -593,7 +593,7 @@ def edge_sample(
593
593
  src_node_time = node_time
594
594
 
595
595
  src_neg = neg_sample(src, neg_sampling, num_src_nodes, src_time,
596
- src_node_time)
596
+ src_node_time, endpoint='src')
597
597
  src = torch.cat([src, src_neg], dim=0)
598
598
 
599
599
  if isinstance(node_time, dict):
@@ -602,7 +602,7 @@ def edge_sample(
602
602
  dst_node_time = node_time
603
603
 
604
604
  dst_neg = neg_sample(dst, neg_sampling, num_dst_nodes, dst_time,
605
- dst_node_time)
605
+ dst_node_time, endpoint='dst')
606
606
  dst = torch.cat([dst, dst_neg], dim=0)
607
607
 
608
608
  if edge_label is None:
@@ -623,7 +623,7 @@ def edge_sample(
623
623
  dst_node_time = node_time
624
624
 
625
625
  dst_neg = neg_sample(dst, neg_sampling, num_dst_nodes, dst_time,
626
- dst_node_time)
626
+ dst_node_time, endpoint='dst')
627
627
  dst = torch.cat([dst, dst_neg], dim=0)
628
628
 
629
629
  assert edge_label is None
@@ -631,7 +631,7 @@ def edge_sample(
631
631
  if edge_label_time is not None:
632
632
  dst_time = edge_label_time.repeat(1 + neg_sampling.amount)
633
633
 
634
- # Heterogeneus Neighborhood Sampling ######################################
634
+ # Heterogeneous Neighborhood Sampling #####################################
635
635
 
636
636
  if input_type is not None:
637
637
  seed_time_dict = None
@@ -724,7 +724,7 @@ def edge_sample(
724
724
  src_time,
725
725
  )
726
726
 
727
- # Homogeneus Neighborhood Sampling ########################################
727
+ # Homogeneous Neighborhood Sampling #######################################
728
728
 
729
729
  else:
730
730
 
@@ -781,12 +781,13 @@ def neg_sample(
781
781
  num_nodes: int,
782
782
  seed_time: Optional[Tensor],
783
783
  node_time: Optional[Tensor],
784
+ endpoint: Literal['str', 'dst'],
784
785
  ) -> Tensor:
785
786
  num_neg = math.ceil(seed.numel() * neg_sampling.amount)
786
787
 
787
788
  # TODO: Do not sample false negatives.
788
789
  if node_time is None:
789
- return neg_sampling.sample(num_neg, num_nodes)
790
+ return neg_sampling.sample(num_neg, endpoint, num_nodes)
790
791
 
791
792
  # If we are in a temporal-sampling scenario, we need to respect the
792
793
  # timestamp of the given nodes we can use as negative examples.
@@ -800,7 +801,7 @@ def neg_sample(
800
801
  num_samples = math.ceil(neg_sampling.amount)
801
802
  seed_time = seed_time.view(1, -1).expand(num_samples, -1)
802
803
 
803
- out = neg_sampling.sample(num_samples * seed.numel(), num_nodes)
804
+ out = neg_sampling.sample(num_samples * seed.numel(), endpoint, num_nodes)
804
805
  out = out.view(num_samples, seed.numel())
805
806
  mask = node_time[out] > seed_time # holds all invalid samples.
806
807
  neg_sampling_complete = False
@@ -811,7 +812,7 @@ def neg_sample(
811
812
  break
812
813
 
813
814
  # Greedily search for alternative negatives.
814
- out[mask] = tmp = neg_sampling.sample(num_invalid, num_nodes)
815
+ out[mask] = tmp = neg_sampling.sample(num_invalid, endpoint, num_nodes)
815
816
  mask[mask.clone()] = node_time[tmp] >= seed_time[mask]
816
817
 
817
818
  if not neg_sampling_complete: # pragma: no cover
@@ -7,7 +7,9 @@ from typing import Callable
7
7
 
8
8
  import torch
9
9
  from packaging.requirements import Requirement
10
+ from packaging.version import Version
10
11
 
12
+ import torch_geometric
11
13
  from torch_geometric.typing import WITH_METIS, WITH_PYG_LIB, WITH_TORCH_SPARSE
12
14
  from torch_geometric.visualization.graph import has_graphviz
13
15
 
@@ -112,13 +114,8 @@ def onlyCUDA(func: Callable) -> Callable:
112
114
  def onlyXPU(func: Callable) -> Callable:
113
115
  r"""A decorator to skip tests if XPU is not found."""
114
116
  import pytest
115
- try:
116
- import intel_extension_for_pytorch as ipex
117
- xpu_available = ipex.xpu.is_available()
118
- except ImportError:
119
- xpu_available = False
120
117
  return pytest.mark.skipif(
121
- not xpu_available,
118
+ not torch_geometric.is_xpu_available(),
122
119
  reason="XPU not available",
123
120
  )(func)
124
121
 
@@ -176,24 +173,23 @@ def has_package(package: str) -> bool:
176
173
  req = Requirement(package)
177
174
  if find_spec(req.name) is None:
178
175
  return False
179
- module = import_module(req.name)
180
- if not hasattr(module, '__version__'):
181
- return True
182
176
 
183
- version = module.__version__
184
- # `req.specifier` does not support `.dev` suffixes, e.g., for
185
- # `pyg_lib==0.1.0.dev*`, so we manually drop them:
186
- if '.dev' in version:
187
- version = '.'.join(version.split('.dev')[:-1])
177
+ try:
178
+ module = import_module(req.name)
179
+ if not hasattr(module, '__version__'):
180
+ return True
188
181
 
189
- return version in req.specifier
182
+ version = Version(module.__version__).base_version
183
+ return version in req.specifier
184
+ except Exception:
185
+ return False
190
186
 
191
187
 
192
188
  def withPackage(*args: str) -> Callable:
193
189
  r"""A decorator to skip tests if certain packages are not installed.
194
190
  Also supports version specification.
195
191
  """
196
- na_packages = set(package for package in args if not has_package(package))
192
+ na_packages = {package for package in args if not has_package(package)}
197
193
 
198
194
  if len(na_packages) == 1:
199
195
  reason = f"Package {list(na_packages)[0]} not found"
@@ -227,12 +223,11 @@ def withDevice(func: Callable) -> Callable:
227
223
  if torch.cuda.is_available():
228
224
  devices.append(pytest.param(torch.device('cuda:0'), id='cuda:0'))
229
225
 
230
- if hasattr(torch.backends, 'mps') and torch.backends.mps.is_available():
231
- try: # Github CI may not have access to MPS hardware. Confirm:
232
- torch.empty(1, device='mps')
233
- devices.append(pytest.param(torch.device('mps:0'), id='mps'))
234
- except RuntimeError:
235
- pass
226
+ if torch_geometric.is_mps_available():
227
+ devices.append(pytest.param(torch.device('mps:0'), id='mps'))
228
+
229
+ if torch_geometric.is_xpu_available():
230
+ devices.append(pytest.param(torch.device('xpu:0'), id='xpu'))
236
231
 
237
232
  # Additional devices can be registered through environment variables:
238
233
  device = os.getenv('TORCH_DEVICE')
@@ -20,6 +20,7 @@ from .target_indegree import TargetIndegree
20
20
  from .local_degree_profile import LocalDegreeProfile
21
21
  from .add_self_loops import AddSelfLoops
22
22
  from .add_remaining_self_loops import AddRemainingSelfLoops
23
+ from .remove_self_loops import RemoveSelfLoops
23
24
  from .remove_isolated_nodes import RemoveIsolatedNodes
24
25
  from .remove_duplicated_edges import RemoveDuplicatedEdges
25
26
  from .knn_graph import KNNGraph
@@ -87,6 +88,7 @@ graph_transforms = [
87
88
  'LocalDegreeProfile',
88
89
  'AddSelfLoops',
89
90
  'AddRemainingSelfLoops',
91
+ 'RemoveSelfLoops',
90
92
  'RemoveIsolatedNodes',
91
93
  'RemoveDuplicatedEdges',
92
94
  'KNNGraph',
@@ -37,7 +37,7 @@ class AddMetaPaths(BaseTransform):
37
37
  :class:`~torch_geometric.data.HeteroData` object as edge type
38
38
  :obj:`(src_node_type, "metapath_*", dst_node_type)`, where
39
39
  :obj:`src_node_type` and :obj:`dst_node_type` denote :math:`\mathcal{V}_1`
40
- and :math:`\mathcal{V}_{\ell}`, repectively.
40
+ and :math:`\mathcal{V}_{\ell}`, respectively.
41
41
 
42
42
  In addition, a :obj:`metapath_dict` object is added to the
43
43
  :class:`~torch_geometric.data.HeteroData` object which maps the
@@ -108,12 +108,12 @@ class AddMetaPaths(BaseTransform):
108
108
  **kwargs: bool,
109
109
  ) -> None:
110
110
  if 'drop_orig_edges' in kwargs:
111
- warnings.warn("'drop_orig_edges' is dprecated. Use "
111
+ warnings.warn("'drop_orig_edges' is deprecated. Use "
112
112
  "'drop_orig_edge_types' instead")
113
113
  drop_orig_edge_types = kwargs['drop_orig_edges']
114
114
 
115
115
  if 'drop_unconnected_nodes' in kwargs:
116
- warnings.warn("'drop_unconnected_nodes' is dprecated. Use "
116
+ warnings.warn("'drop_unconnected_nodes' is deprecated. Use "
117
117
  "'drop_unconnected_node_types' instead")
118
118
  drop_unconnected_node_types = kwargs['drop_unconnected_nodes']
119
119
 
@@ -231,7 +231,7 @@ class AddRandomMetaPaths(BaseTransform):
231
231
  will drop node types not connected by any edge type.
232
232
  (default: :obj:`False`)
233
233
  walks_per_node (int, List[int], optional): The number of random walks
234
- for each starting node in a metapth. (default: :obj:`1`)
234
+ for each starting node in a metapath. (default: :obj:`1`)
235
235
  sample_ratio (float, optional): The ratio of source nodes to start
236
236
  random walks from. (default: :obj:`1.0`)
237
237
  """
@@ -92,7 +92,7 @@ class AddLaplacianEigenvectorPE(BaseTransform):
92
92
  from numpy.linalg import eig, eigh
93
93
  eig_fn = eig if not self.is_undirected else eigh
94
94
 
95
- eig_vals, eig_vecs = eig_fn(L.todense()) # type: ignore
95
+ eig_vals, eig_vecs = eig_fn(L.todense())
96
96
  else:
97
97
  from scipy.sparse.linalg import eigs, eigsh
98
98
  eig_fn = eigs if not self.is_undirected else eigsh
@@ -1,4 +1,5 @@
1
- import scipy.spatial
1
+ from typing import List
2
+
2
3
  import torch
3
4
 
4
5
  from torch_geometric.data import Data
@@ -6,28 +7,78 @@ from torch_geometric.data.datapipes import functional_transform
6
7
  from torch_geometric.transforms import BaseTransform
7
8
 
8
9
 
10
+ class _QhullTransform(BaseTransform):
11
+ r"""Q-hull implementation of delaunay triangulation."""
12
+ def forward(self, data: Data) -> Data:
13
+ assert data.pos is not None
14
+ import scipy.spatial
15
+
16
+ pos = data.pos.cpu().numpy()
17
+ tri = scipy.spatial.Delaunay(pos, qhull_options='QJ')
18
+ face = torch.from_numpy(tri.simplices)
19
+
20
+ data.face = face.t().contiguous().to(data.pos.device, torch.long)
21
+ return data
22
+
23
+
24
+ class _ShullTransform(BaseTransform):
25
+ r"""Sweep-hull implementation of delaunay triangulation."""
26
+ def forward(self, data: Data) -> Data:
27
+ assert data.pos is not None
28
+ from torch_delaunay.functional import shull2d
29
+
30
+ face = shull2d(data.pos.cpu())
31
+ data.face = face.t().contiguous().to(data.pos.device)
32
+ return data
33
+
34
+
35
+ class _SequentialTransform(BaseTransform):
36
+ r"""Runs the first successful transformation.
37
+
38
+ All intermediate exceptions are suppressed except the last.
39
+ """
40
+ def __init__(self, transforms: List[BaseTransform]) -> None:
41
+ assert len(transforms) > 0
42
+ self.transforms = transforms
43
+
44
+ def forward(self, data: Data) -> Data:
45
+ for i, transform in enumerate(self.transforms):
46
+ try:
47
+ return transform.forward(data)
48
+ except ImportError as e:
49
+ if i == len(self.transforms) - 1:
50
+ raise e
51
+ return data
52
+
53
+
9
54
  @functional_transform('delaunay')
10
55
  class Delaunay(BaseTransform):
11
56
  r"""Computes the delaunay triangulation of a set of points
12
57
  (functional name: :obj:`delaunay`).
58
+
59
+ .. hint::
60
+ Consider installing the
61
+ `torch_delaunay <https://github.com/ybubnov/torch_delaunay>`_ package
62
+ to speed up computation.
13
63
  """
64
+ def __init__(self) -> None:
65
+ self._transform = _SequentialTransform([
66
+ _ShullTransform(),
67
+ _QhullTransform(),
68
+ ])
69
+
14
70
  def forward(self, data: Data) -> Data:
15
71
  assert data.pos is not None
72
+ device = data.pos.device
16
73
 
17
74
  if data.pos.size(0) < 2:
18
- data.edge_index = torch.tensor([], dtype=torch.long,
19
- device=data.pos.device).view(2, 0)
20
- if data.pos.size(0) == 2:
21
- data.edge_index = torch.tensor([[0, 1], [1, 0]], dtype=torch.long,
22
- device=data.pos.device)
75
+ data.edge_index = torch.empty(2, 0, dtype=torch.long,
76
+ device=device)
77
+ elif data.pos.size(0) == 2:
78
+ data.edge_index = torch.tensor([[0, 1], [1, 0]], device=device)
23
79
  elif data.pos.size(0) == 3:
24
- data.face = torch.tensor([[0], [1], [2]], dtype=torch.long,
25
- device=data.pos.device)
26
- if data.pos.size(0) > 3:
27
- pos = data.pos.cpu().numpy()
28
- tri = scipy.spatial.Delaunay(pos, qhull_options='QJ')
29
- face = torch.from_numpy(tri.simplices)
30
-
31
- data.face = face.t().contiguous().to(data.pos.device, torch.long)
80
+ data.face = torch.tensor([[0], [1], [2]], device=device)
81
+ else:
82
+ data = self._transform.forward(data)
32
83
 
33
84
  return data
@@ -8,8 +8,15 @@ from torch_geometric.utils import to_undirected
8
8
 
9
9
  @functional_transform('face_to_edge')
10
10
  class FaceToEdge(BaseTransform):
11
- r"""Converts mesh faces :obj:`[3, num_faces]` to edge indices
12
- :obj:`[2, num_edges]` (functional name: :obj:`face_to_edge`).
11
+ r"""Converts mesh faces of shape :obj:`[3, num_faces]` or
12
+ :obj:`[4, num_faces]` to edge indices of shape :obj:`[2, num_edges]`
13
+ (functional name: :obj:`face_to_edge`).
14
+
15
+ This transform supports both 2D triangular faces, represented by a
16
+ tensor of shape :obj:`[3, num_faces]`, and 3D tetrahedral mesh faces,
17
+ represented by a tensor of shape :obj:`[4, num_faces]`. It will convert
18
+ these faces into edge indices, where each edge is defined by the indices
19
+ of its two endpoints.
13
20
 
14
21
  Args:
15
22
  remove_faces (bool, optional): If set to :obj:`False`, the face tensor
@@ -22,7 +29,29 @@ class FaceToEdge(BaseTransform):
22
29
  if hasattr(data, 'face'):
23
30
  assert data.face is not None
24
31
  face = data.face
25
- edge_index = torch.cat([face[:2], face[1:], face[::2]], dim=1)
32
+
33
+ if face.size(0) not in [3, 4]:
34
+ raise RuntimeError(f"Expected 'face' tensor with shape "
35
+ f"[3, num_faces] or [4, num_faces] "
36
+ f"(got {list(face.size())})")
37
+
38
+ if face.size()[0] == 3:
39
+ edge_index = torch.cat([
40
+ face[:2],
41
+ face[1:],
42
+ face[::2],
43
+ ], dim=1)
44
+ else:
45
+ assert face.size()[0] == 4
46
+ edge_index = torch.cat([
47
+ face[:2],
48
+ face[1:3],
49
+ face[2:4],
50
+ face[::2],
51
+ face[1::2],
52
+ face[::3],
53
+ ], dim=1)
54
+
26
55
  edge_index = to_undirected(edge_index, num_nodes=data.num_nodes)
27
56
 
28
57
  data.edge_index = edge_index
@@ -2,7 +2,6 @@ from typing import Any, Dict, Tuple
2
2
 
3
3
  import numpy as np
4
4
  import torch
5
- from scipy.linalg import expm
6
5
  from torch import Tensor
7
6
 
8
7
  from torch_geometric.data import Data
@@ -22,7 +21,7 @@ from torch_geometric.utils import (
22
21
  @functional_transform('gdc')
23
22
  class GDC(BaseTransform):
24
23
  r"""Processes the graph via Graph Diffusion Convolution (GDC) from the
25
- `"Diffusion Improves Graph Learning" <https://www.kdd.in.tum.de/gdc>`_
24
+ `"Diffusion Improves Graph Learning" <https://arxiv.org/abs/1911.05485>`_
26
25
  paper (functional name: :obj:`gdc`).
27
26
 
28
27
  .. note::
@@ -338,10 +337,10 @@ class GDC(BaseTransform):
338
337
 
339
338
  elif method == 'heat':
340
339
  raise NotImplementedError(
341
- ('Currently no fast heat kernel is implemented. You are '
342
- 'welcome to create one yourself, e.g., based on '
343
- '"Kloster and Gleich: Heat kernel based community detection '
344
- '(KDD 2014)."'))
340
+ 'Currently no fast heat kernel is implemented. You are '
341
+ 'welcome to create one yourself, e.g., based on '
342
+ '"Kloster and Gleich: Heat kernel based community detection '
343
+ '(KDD 2014)."')
345
344
  else:
346
345
  raise ValueError(f"Approximate GDC diffusion '{method}' unknown")
347
346
 
@@ -473,6 +472,8 @@ class GDC(BaseTransform):
473
472
 
474
473
  :rtype: (:class:`Tensor`)
475
474
  """
475
+ from scipy.linalg import expm
476
+
476
477
  if symmetric:
477
478
  e, V = torch.linalg.eigh(matrix, UPLO='U')
478
479
  diff_mat = V @ torch.diag(e.exp()) @ V.t()
@@ -1,7 +1,5 @@
1
1
  from typing import Optional
2
2
 
3
- from scipy.sparse.linalg import eigs, eigsh
4
-
5
3
  from torch_geometric.data import Data
6
4
  from torch_geometric.data.datapipes import functional_transform
7
5
  from torch_geometric.transforms import BaseTransform
@@ -41,6 +39,8 @@ class LaplacianLambdaMax(BaseTransform):
41
39
  self.is_undirected = is_undirected
42
40
 
43
41
  def forward(self, data: Data) -> Data:
42
+ from scipy.sparse.linalg import eigs, eigsh
43
+
44
44
  assert data.edge_index is not None
45
45
  num_nodes = data.num_nodes
46
46
 
@@ -19,7 +19,11 @@ def get_attrs_with_suffix(
19
19
  return [key for key in store.keys() if key.endswith(suffix)]
20
20
 
21
21
 
22
- def get_mask_size(attr: str, store: BaseStorage, size: Optional[int]) -> int:
22
+ def get_mask_size(
23
+ attr: str,
24
+ store: BaseStorage,
25
+ size: Optional[int],
26
+ ) -> Optional[int]:
23
27
  if size is not None:
24
28
  return size
25
29
  return store.num_edges if store.is_edge_attr(attr) else store.num_nodes
@@ -44,7 +44,6 @@ class NodePropertySplit(BaseTransform):
44
44
  of the node property, so that nodes with greater values of the
45
45
  property are considered to be OOD (default: :obj:`True`)
46
46
 
47
- Example:
48
47
  .. code-block:: python
49
48
 
50
49
  from torch_geometric.transforms import NodePropertySplit
@@ -54,7 +53,7 @@ class NodePropertySplit(BaseTransform):
54
53
 
55
54
  property_name = 'popularity'
56
55
  ratios = [0.3, 0.1, 0.1, 0.3, 0.2]
57
- tranaform = NodePropertySplit(property_name, ratios)
56
+ transform = NodePropertySplit(property_name, ratios)
58
57
 
59
58
  data = transform(data)
60
59
  """
@@ -262,15 +262,14 @@ class Pad(BaseTransform):
262
262
  All the attributes of node types other than :obj:`v0` and :obj:`v1` are
263
263
  padded using a value of :obj:`1.0`.
264
264
  All the attributes of the :obj:`('v0', 'e0', 'v1')` edge type are padded
265
- usin a value of :obj:`3.5`.
265
+ using a value of :obj:`3.5`.
266
266
  The :obj:`edge_attr` attributes of the :obj:`('v1', 'e0', 'v0')` edge type
267
267
  are padded using a value of :obj:`-1.5`, and any other attributes of this
268
268
  edge type are padded using a value of :obj:`5.5`.
269
269
  All the attributes of edge types other than these two are padded using a
270
270
  value of :obj:`1.5`.
271
271
 
272
- Example:
273
- .. code-block::
272
+ .. code-block:: python
274
273
 
275
274
  num_nodes = {'v0': 10, 'v1': 20, 'v2':30}
276
275
  num_edges = {('v0', 'e0', 'v1'): 80}
@@ -467,9 +466,11 @@ class Pad(BaseTransform):
467
466
  edge_type: Optional[EdgeType] = None,
468
467
  ) -> None:
469
468
 
470
- attrs_to_pad = set(
471
- attr for attr in store.keys()
472
- if store.is_edge_attr(attr) and self.__should_pad_edge_attr(attr))
469
+ attrs_to_pad = {
470
+ attr
471
+ for attr in store.keys()
472
+ if store.is_edge_attr(attr) and self.__should_pad_edge_attr(attr)
473
+ }
473
474
  if not attrs_to_pad:
474
475
  return
475
476
  num_target_edges = self.max_num_edges.get_value(edge_type)
@@ -23,7 +23,7 @@ class RandomLinkSplit(BaseTransform):
23
23
  in validation and test splits; and the validation split does not include
24
24
  edges in the test split.
25
25
 
26
- .. code-block::
26
+ .. code-block:: python
27
27
 
28
28
  from torch_geometric.transforms import RandomLinkSplit
29
29
 
@@ -0,0 +1,36 @@
1
+ from typing import Union
2
+
3
+ from torch_geometric.data import Data, HeteroData
4
+ from torch_geometric.data.datapipes import functional_transform
5
+ from torch_geometric.transforms import BaseTransform
6
+ from torch_geometric.utils import remove_self_loops
7
+
8
+
9
+ @functional_transform('remove_self_loops')
10
+ class RemoveSelfLoops(BaseTransform):
11
+ r"""Removes all self-loops in the given homogeneous or heterogeneous
12
+ graph (functional name: :obj:`remove_self_loops`).
13
+
14
+ Args:
15
+ attr (str, optional): The name of the attribute of edge weights
16
+ or multi-dimensional edge features to pass to
17
+ :meth:`torch_geometric.utils.remove_self_loops`.
18
+ (default: :obj:`"edge_weight"`)
19
+ """
20
+ def __init__(self, attr: str = 'edge_weight') -> None:
21
+ self.attr = attr
22
+
23
+ def forward(
24
+ self,
25
+ data: Union[Data, HeteroData],
26
+ ) -> Union[Data, HeteroData]:
27
+ for store in data.edge_stores:
28
+ if store.is_bipartite() or 'edge_index' not in store:
29
+ continue
30
+
31
+ store.edge_index, store[self.attr] = remove_self_loops(
32
+ store.edge_index,
33
+ edge_attr=store.get(self.attr, None),
34
+ )
35
+
36
+ return data
@@ -11,7 +11,7 @@ class SVDFeatureReduction(BaseTransform):
11
11
  Decomposition (SVD) (functional name: :obj:`svd_feature_reduction`).
12
12
 
13
13
  Args:
14
- out_channels (int): The dimensionlity of node features after
14
+ out_channels (int): The dimensionality of node features after
15
15
  reduction.
16
16
  """
17
17
  def __init__(self, out_channels: int):
@@ -37,7 +37,8 @@ class VirtualNode(BaseTransform):
37
37
  col = torch.cat([col, full, arange], dim=0)
38
38
  edge_index = torch.stack([row, col], dim=0)
39
39
 
40
- new_type = edge_type.new_full((num_nodes, ), int(edge_type.max()) + 1)
40
+ num_edge_types = int(edge_type.max()) if edge_type.numel() > 0 else 0
41
+ new_type = edge_type.new_full((num_nodes, ), num_edge_types + 1)
41
42
  edge_type = torch.cat([edge_type, new_type, new_type + 1], dim=0)
42
43
 
43
44
  old_data = copy.copy(data)
torch_geometric/typing.py CHANGED
@@ -13,6 +13,9 @@ WITH_PT20 = int(torch.__version__.split('.')[0]) >= 2
13
13
  WITH_PT21 = WITH_PT20 and int(torch.__version__.split('.')[1]) >= 1
14
14
  WITH_PT22 = WITH_PT20 and int(torch.__version__.split('.')[1]) >= 2
15
15
  WITH_PT23 = WITH_PT20 and int(torch.__version__.split('.')[1]) >= 3
16
+ WITH_PT24 = WITH_PT20 and int(torch.__version__.split('.')[1]) >= 4
17
+ WITH_PT25 = WITH_PT20 and int(torch.__version__.split('.')[1]) >= 5
18
+ WITH_PT26 = WITH_PT20 and int(torch.__version__.split('.')[1]) >= 6
16
19
  WITH_PT111 = WITH_PT20 or int(torch.__version__.split('.')[1]) >= 11
17
20
  WITH_PT112 = WITH_PT20 or int(torch.__version__.split('.')[1]) >= 12
18
21
  WITH_PT113 = WITH_PT20 or int(torch.__version__.split('.')[1]) >= 13
@@ -304,6 +307,8 @@ class EdgeTypeStr(str):
304
307
  r"""A helper class to construct serializable edge types by merging an edge
305
308
  type tuple into a single string.
306
309
  """
310
+ edge_type: tuple[str, str, str]
311
+
307
312
  def __new__(cls, *args: Any) -> 'EdgeTypeStr':
308
313
  if isinstance(args[0], (list, tuple)):
309
314
  # Unwrap `EdgeType((src, rel, dst))` and `EdgeTypeStr((src, dst))`:
@@ -311,27 +316,37 @@ class EdgeTypeStr(str):
311
316
 
312
317
  if len(args) == 1 and isinstance(args[0], str):
313
318
  arg = args[0] # An edge type string was passed.
319
+ edge_type = tuple(arg.split(EDGE_TYPE_STR_SPLIT))
320
+ if len(edge_type) != 3:
321
+ raise ValueError(f"Cannot convert the edge type '{arg}' to a "
322
+ f"tuple since it holds invalid characters")
314
323
 
315
324
  elif len(args) == 2 and all(isinstance(arg, str) for arg in args):
316
325
  # A `(src, dst)` edge type was passed - add `DEFAULT_REL`:
317
- arg = EDGE_TYPE_STR_SPLIT.join((args[0], DEFAULT_REL, args[1]))
326
+ edge_type = (args[0], DEFAULT_REL, args[1])
327
+ arg = EDGE_TYPE_STR_SPLIT.join(edge_type)
318
328
 
319
329
  elif len(args) == 3 and all(isinstance(arg, str) for arg in args):
320
330
  # A `(src, rel, dst)` edge type was passed:
331
+ edge_type = tuple(args)
321
332
  arg = EDGE_TYPE_STR_SPLIT.join(args)
322
333
 
323
334
  else:
324
335
  raise ValueError(f"Encountered invalid edge type '{args}'")
325
336
 
326
- return str.__new__(cls, arg)
337
+ out = str.__new__(cls, arg)
338
+ out.edge_type = edge_type # type: ignore
339
+ return out
327
340
 
328
341
  def to_tuple(self) -> EdgeType:
329
342
  r"""Returns the original edge type."""
330
- out = tuple(self.split(EDGE_TYPE_STR_SPLIT))
331
- if len(out) != 3:
343
+ if len(self.edge_type) != 3:
332
344
  raise ValueError(f"Cannot convert the edge type '{self}' to a "
333
345
  f"tuple since it holds invalid characters")
334
- return out
346
+ return self.edge_type
347
+
348
+ def __reduce__(self) -> tuple[Any, Any]:
349
+ return (self.__class__, (self.edge_type, ))
335
350
 
336
351
 
337
352
  # There exist some short-cuts to query edge-types (given that the full triplet
@@ -369,3 +384,14 @@ MaybeHeteroEdgeTensor = Union[Tensor, Dict[EdgeType, Tensor]]
369
384
 
370
385
  InputNodes = Union[OptTensor, NodeType, Tuple[NodeType, OptTensor]]
371
386
  InputEdges = Union[OptTensor, EdgeType, Tuple[EdgeType, OptTensor]]
387
+
388
+ # Serialization ###############################################################
389
+
390
+ if WITH_PT24:
391
+ torch.serialization.add_safe_globals([
392
+ SparseTensor,
393
+ SparseStorage,
394
+ TensorFrame,
395
+ MockTorchCSCTensor,
396
+ EdgeTypeStr,
397
+ ])