k3-node 1.0.0__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (459) hide show
  1. k3_node/__init__.py +122 -0
  2. k3_node/applications/__init__.py +17 -0
  3. k3_node/applications/bio/__init__.py +21 -0
  4. k3_node/applications/chemistry/__init__.py +155 -0
  5. k3_node/applications/materials/__init__.py +127 -0
  6. k3_node/applications/materials/basis.py +449 -0
  7. k3_node/applications/materials/chgnet.py +360 -0
  8. k3_node/applications/materials/core.py +351 -0
  9. k3_node/applications/materials/grace.py +246 -0
  10. k3_node/applications/materials/io.py +230 -0
  11. k3_node/applications/materials/m3gnet.py +462 -0
  12. k3_node/applications/materials/megnet.py +395 -0
  13. k3_node/applications/materials/qet.py +220 -0
  14. k3_node/applications/materials/readout.py +235 -0
  15. k3_node/applications/materials/so3net.py +234 -0
  16. k3_node/applications/materials/tensornet.py +381 -0
  17. k3_node/applications/materials/test_materials.py +167 -0
  18. k3_node/applications/materials/wrappers.py +95 -0
  19. k3_node/data/__init__.py +47 -0
  20. k3_node/data/batch.py +102 -0
  21. k3_node/data/collate.py +282 -0
  22. k3_node/data/data.py +532 -0
  23. k3_node/data/database.py +154 -0
  24. k3_node/data/dataset.py +182 -0
  25. k3_node/data/download.py +49 -0
  26. k3_node/data/extract.py +45 -0
  27. k3_node/data/feature_store.py +70 -0
  28. k3_node/data/graph_store.py +92 -0
  29. k3_node/data/hetero_data.py +374 -0
  30. k3_node/data/hypergraph_data.py +59 -0
  31. k3_node/data/in_memory_dataset.py +177 -0
  32. k3_node/data/makedirs.py +7 -0
  33. k3_node/data/on_disk_dataset.py +77 -0
  34. k3_node/data/separate.py +115 -0
  35. k3_node/data/storage.py +593 -0
  36. k3_node/data/temporal.py +154 -0
  37. k3_node/data/test_batch.py +67 -0
  38. k3_node/data/test_data.py +68 -0
  39. k3_node/data/test_dataset_and_stores.py +111 -0
  40. k3_node/data/test_hetero_data.py +33 -0
  41. k3_node/data/test_temporal_and_hyper.py +32 -0
  42. k3_node/data/view.py +43 -0
  43. k3_node/datasets/__init__.py +88 -0
  44. k3_node/datasets/actor.py +101 -0
  45. k3_node/datasets/airports.py +84 -0
  46. k3_node/datasets/amazon.py +66 -0
  47. k3_node/datasets/ba2motif_dataset.py +73 -0
  48. k3_node/datasets/ba_shapes.py +81 -0
  49. k3_node/datasets/bitcoin_otc.py +77 -0
  50. k3_node/datasets/citation_full.py +81 -0
  51. k3_node/datasets/coauthor.py +66 -0
  52. k3_node/datasets/dblp.py +106 -0
  53. k3_node/datasets/digits.py +63 -0
  54. k3_node/datasets/email_eu_core.py +60 -0
  55. k3_node/datasets/entities.py +158 -0
  56. k3_node/datasets/explainer_dataset.py +101 -0
  57. k3_node/datasets/facebook.py +51 -0
  58. k3_node/datasets/fake.py +256 -0
  59. k3_node/datasets/freebase.py +90 -0
  60. k3_node/datasets/geometric_shapes.py +69 -0
  61. k3_node/datasets/github.py +51 -0
  62. k3_node/datasets/graph_generator/__init__.py +6 -0
  63. k3_node/datasets/graph_generator/ba_graph.py +20 -0
  64. k3_node/datasets/graph_generator/base.py +29 -0
  65. k3_node/datasets/graph_generator/er_graph.py +21 -0
  66. k3_node/datasets/icews.py +58 -0
  67. k3_node/datasets/imdb.py +96 -0
  68. k3_node/datasets/jodie.py +56 -0
  69. k3_node/datasets/karate.py +56 -0
  70. k3_node/datasets/lastfm_asia.py +51 -0
  71. k3_node/datasets/mesh_correspondence.py +50 -0
  72. k3_node/datasets/molecule_net.py +148 -0
  73. k3_node/datasets/motif_generator/__init__.py +7 -0
  74. k3_node/datasets/motif_generator/base.py +29 -0
  75. k3_node/datasets/motif_generator/custom.py +17 -0
  76. k3_node/datasets/motif_generator/cycle.py +25 -0
  77. k3_node/datasets/motif_generator/house.py +27 -0
  78. k3_node/datasets/movielens.py +55 -0
  79. k3_node/datasets/planetoid.py +137 -0
  80. k3_node/datasets/polblogs.py +63 -0
  81. k3_node/datasets/ppi.py +189 -0
  82. k3_node/datasets/qm7.py +65 -0
  83. k3_node/datasets/qm9.py +132 -0
  84. k3_node/datasets/reddit.py +121 -0
  85. k3_node/datasets/sbm_dataset.py +165 -0
  86. k3_node/datasets/seal.py +74 -0
  87. k3_node/datasets/shape_scenes.py +92 -0
  88. k3_node/datasets/test_datasets.py +322 -0
  89. k3_node/datasets/tu_dataset.py +131 -0
  90. k3_node/datasets/twitch.py +66 -0
  91. k3_node/datasets/webkb.py +102 -0
  92. k3_node/datasets/wikics.py +85 -0
  93. k3_node/datasets/word_net.py +184 -0
  94. k3_node/etl/__init__.py +37 -0
  95. k3_node/etl/encoders.py +248 -0
  96. k3_node/etl/graph_builders.py +270 -0
  97. k3_node/etl/relational_to_graph.py +201 -0
  98. k3_node/etl/table_to_graph.py +244 -0
  99. k3_node/etl/test_etl.py +318 -0
  100. k3_node/export/__init__.py +15 -0
  101. k3_node/export/cross_backend.py +172 -0
  102. k3_node/export/onnx_exporter.py +190 -0
  103. k3_node/export/runtime.py +254 -0
  104. k3_node/export/tensorrt_exporter.py +201 -0
  105. k3_node/export/test_export.py +337 -0
  106. k3_node/export/tflite_exporter.py +112 -0
  107. k3_node/hub/__init__.py +29 -0
  108. k3_node/hub/dataset_hub.py +242 -0
  109. k3_node/hub/hub_mixin.py +599 -0
  110. k3_node/hub/model_card.py +133 -0
  111. k3_node/hub/test_hub.py +419 -0
  112. k3_node/io/__init__.py +22 -0
  113. k3_node/io/fs.py +117 -0
  114. k3_node/io/npz.py +45 -0
  115. k3_node/io/off.py +29 -0
  116. k3_node/io/planetoid.py +98 -0
  117. k3_node/io/tu.py +137 -0
  118. k3_node/io/txt_array.py +58 -0
  119. k3_node/layers/__init__.py +14 -0
  120. k3_node/layers/aggr/__init__.py +70 -0
  121. k3_node/layers/aggr/attention.py +77 -0
  122. k3_node/layers/aggr/base.py +403 -0
  123. k3_node/layers/aggr/basic.py +412 -0
  124. k3_node/layers/aggr/deep_sets.py +65 -0
  125. k3_node/layers/aggr/deepsets.py +29 -0
  126. k3_node/layers/aggr/equilibrium.py +107 -0
  127. k3_node/layers/aggr/fused.py +43 -0
  128. k3_node/layers/aggr/gmt.py +89 -0
  129. k3_node/layers/aggr/gru.py +58 -0
  130. k3_node/layers/aggr/lcm.py +143 -0
  131. k3_node/layers/aggr/lstm.py +58 -0
  132. k3_node/layers/aggr/mlp.py +75 -0
  133. k3_node/layers/aggr/multi.py +154 -0
  134. k3_node/layers/aggr/patch_transformer.py +137 -0
  135. k3_node/layers/aggr/quantile.py +125 -0
  136. k3_node/layers/aggr/resolver.py +68 -0
  137. k3_node/layers/aggr/scaler.py +133 -0
  138. k3_node/layers/aggr/set2set.py +87 -0
  139. k3_node/layers/aggr/set_transformer.py +107 -0
  140. k3_node/layers/aggr/sort.py +68 -0
  141. k3_node/layers/aggr/test_aggr.py +337 -0
  142. k3_node/layers/aggr/utils.py +210 -0
  143. k3_node/layers/aggr/variance_preserving.py +54 -0
  144. k3_node/layers/attention/__init__.py +5 -0
  145. k3_node/layers/attention/pair_attention.py +448 -0
  146. k3_node/layers/attention/performer.py +187 -0
  147. k3_node/layers/attention/polynormer.py +160 -0
  148. k3_node/layers/attention/qformer.py +143 -0
  149. k3_node/layers/attention/sgformer.py +106 -0
  150. k3_node/layers/attention/test_attention.py +68 -0
  151. k3_node/layers/attention/test_pair_attention.py +91 -0
  152. k3_node/layers/conv/__init__.py +149 -0
  153. k3_node/layers/conv/agnn_conv.py +120 -0
  154. k3_node/layers/conv/antisymmetric_conv.py +94 -0
  155. k3_node/layers/conv/appnp.py +105 -0
  156. k3_node/layers/conv/appnp_conv.py +157 -0
  157. k3_node/layers/conv/arma_conv.py +231 -0
  158. k3_node/layers/conv/cg_conv.py +92 -0
  159. k3_node/layers/conv/cheb_conv.py +137 -0
  160. k3_node/layers/conv/cluster_gcn_conv.py +102 -0
  161. k3_node/layers/conv/conv.py +100 -0
  162. k3_node/layers/conv/crystal_conv.py +140 -0
  163. k3_node/layers/conv/cugraph.py +84 -0
  164. k3_node/layers/conv/diffusion_conv.py +144 -0
  165. k3_node/layers/conv/dir_gnn_conv.py +93 -0
  166. k3_node/layers/conv/dna_conv.py +192 -0
  167. k3_node/layers/conv/edge_conv.py +107 -0
  168. k3_node/layers/conv/eg_conv.py +155 -0
  169. k3_node/layers/conv/fa_conv.py +107 -0
  170. k3_node/layers/conv/feast_conv.py +126 -0
  171. k3_node/layers/conv/film_conv.py +143 -0
  172. k3_node/layers/conv/gat_conv.py +244 -0
  173. k3_node/layers/conv/gated_graph_conv.py +136 -0
  174. k3_node/layers/conv/gatv2_conv.py +205 -0
  175. k3_node/layers/conv/gcn.py +144 -0
  176. k3_node/layers/conv/gcn2_conv.py +126 -0
  177. k3_node/layers/conv/gcn_conv.py +135 -0
  178. k3_node/layers/conv/gen_conv.py +163 -0
  179. k3_node/layers/conv/general_conv.py +218 -0
  180. k3_node/layers/conv/gin_conv.py +218 -0
  181. k3_node/layers/conv/gmm_conv.py +172 -0
  182. k3_node/layers/conv/gps_conv.py +153 -0
  183. k3_node/layers/conv/graph_attention.py +262 -0
  184. k3_node/layers/conv/graph_conv.py +84 -0
  185. k3_node/layers/conv/gravnet_conv.py +93 -0
  186. k3_node/layers/conv/han_conv.py +175 -0
  187. k3_node/layers/conv/heat_conv.py +131 -0
  188. k3_node/layers/conv/hetero_conv.py +128 -0
  189. k3_node/layers/conv/hgt_conv.py +218 -0
  190. k3_node/layers/conv/hypergraph_conv.py +182 -0
  191. k3_node/layers/conv/le_conv.py +81 -0
  192. k3_node/layers/conv/lg_conv.py +58 -0
  193. k3_node/layers/conv/meshcnn_conv.py +84 -0
  194. k3_node/layers/conv/message_passing.py +451 -0
  195. k3_node/layers/conv/mf_conv.py +95 -0
  196. k3_node/layers/conv/mixhop_conv.py +108 -0
  197. k3_node/layers/conv/nn_conv.py +110 -0
  198. k3_node/layers/conv/pan_conv.py +100 -0
  199. k3_node/layers/conv/pdn_conv.py +109 -0
  200. k3_node/layers/conv/pna_conv.py +177 -0
  201. k3_node/layers/conv/point_conv.py +101 -0
  202. k3_node/layers/conv/point_gnn_conv.py +90 -0
  203. k3_node/layers/conv/point_transformer_conv.py +132 -0
  204. k3_node/layers/conv/ppf_conv.py +135 -0
  205. k3_node/layers/conv/ppnp.py +89 -0
  206. k3_node/layers/conv/res_gated_graph_conv.py +126 -0
  207. k3_node/layers/conv/rgat_conv.py +251 -0
  208. k3_node/layers/conv/rgcn_conv.py +321 -0
  209. k3_node/layers/conv/sage_conv.py +154 -0
  210. k3_node/layers/conv/sg_conv.py +96 -0
  211. k3_node/layers/conv/signed_conv.py +100 -0
  212. k3_node/layers/conv/simple_conv.py +75 -0
  213. k3_node/layers/conv/spline_conv.py +182 -0
  214. k3_node/layers/conv/ssg_conv.py +101 -0
  215. k3_node/layers/conv/supergat_conv.py +195 -0
  216. k3_node/layers/conv/tag_conv.py +98 -0
  217. k3_node/layers/conv/test_backend_consistency.py +164 -0
  218. k3_node/layers/conv/test_conv.py +176 -0
  219. k3_node/layers/conv/test_conv_pyg.py +566 -0
  220. k3_node/layers/conv/transformer_conv.py +168 -0
  221. k3_node/layers/conv/utils.py +403 -0
  222. k3_node/layers/conv/wl_conv.py +151 -0
  223. k3_node/layers/conv/x_conv.py +187 -0
  224. k3_node/layers/dense/__init__.py +40 -0
  225. k3_node/layers/dense/dense_gat_conv.py +149 -0
  226. k3_node/layers/dense/dense_gcn_conv.py +117 -0
  227. k3_node/layers/dense/dense_gin_conv.py +88 -0
  228. k3_node/layers/dense/dense_graph_conv.py +95 -0
  229. k3_node/layers/dense/dense_sage_conv.py +85 -0
  230. k3_node/layers/dense/diff_pool.py +76 -0
  231. k3_node/layers/dense/dmon_pool.py +223 -0
  232. k3_node/layers/dense/linear.py +327 -0
  233. k3_node/layers/dense/mincut_pool.py +92 -0
  234. k3_node/layers/dense/test_dense.py +377 -0
  235. k3_node/layers/functional/__init__.py +13 -0
  236. k3_node/layers/functional/bro.py +49 -0
  237. k3_node/layers/functional/edge_dropout.py +55 -0
  238. k3_node/layers/functional/gini.py +44 -0
  239. k3_node/layers/functional/test_functional.py +34 -0
  240. k3_node/layers/kge/__init__.py +17 -0
  241. k3_node/layers/kge/base.py +255 -0
  242. k3_node/layers/kge/complex.py +98 -0
  243. k3_node/layers/kge/distmult.py +79 -0
  244. k3_node/layers/kge/loader.py +50 -0
  245. k3_node/layers/kge/rotate.py +103 -0
  246. k3_node/layers/kge/test_kge.py +76 -0
  247. k3_node/layers/kge/transe.py +96 -0
  248. k3_node/layers/norm/__init__.py +23 -0
  249. k3_node/layers/norm/batch_norm.py +328 -0
  250. k3_node/layers/norm/diff_group_norm.py +141 -0
  251. k3_node/layers/norm/graph_norm.py +105 -0
  252. k3_node/layers/norm/graph_size_norm.py +57 -0
  253. k3_node/layers/norm/instance_norm.py +163 -0
  254. k3_node/layers/norm/layer_norm.py +245 -0
  255. k3_node/layers/norm/mean_subtraction_norm.py +57 -0
  256. k3_node/layers/norm/msg_norm.py +58 -0
  257. k3_node/layers/norm/pair_norm.py +94 -0
  258. k3_node/layers/norm/test_norm.py +275 -0
  259. k3_node/layers/pool/__init__.py +83 -0
  260. k3_node/layers/pool/approx_knn.py +101 -0
  261. k3_node/layers/pool/asap.py +173 -0
  262. k3_node/layers/pool/avg_pool.py +165 -0
  263. k3_node/layers/pool/cluster_pool.py +168 -0
  264. k3_node/layers/pool/connect/__init__.py +10 -0
  265. k3_node/layers/pool/connect/base.py +103 -0
  266. k3_node/layers/pool/connect/filter_edges.py +113 -0
  267. k3_node/layers/pool/consecutive.py +30 -0
  268. k3_node/layers/pool/decimation.py +48 -0
  269. k3_node/layers/pool/edge_pool.py +189 -0
  270. k3_node/layers/pool/glob.py +139 -0
  271. k3_node/layers/pool/graclus.py +66 -0
  272. k3_node/layers/pool/knn.py +253 -0
  273. k3_node/layers/pool/max_pool.py +159 -0
  274. k3_node/layers/pool/mem_pool.py +145 -0
  275. k3_node/layers/pool/pan_pool.py +144 -0
  276. k3_node/layers/pool/point_cloud.py +212 -0
  277. k3_node/layers/pool/pool.py +119 -0
  278. k3_node/layers/pool/sag_pool.py +174 -0
  279. k3_node/layers/pool/select/__init__.py +10 -0
  280. k3_node/layers/pool/select/base.py +112 -0
  281. k3_node/layers/pool/select/topk.py +206 -0
  282. k3_node/layers/pool/test_pool.py +456 -0
  283. k3_node/layers/pool/topk_pool.py +103 -0
  284. k3_node/layers/pool/voxel_grid.py +70 -0
  285. k3_node/layers/unpool/__init__.py +9 -0
  286. k3_node/layers/unpool/knn_interpolate.py +57 -0
  287. k3_node/layers/unpool/test_unpool.py +31 -0
  288. k3_node/loader/__init__.py +62 -0
  289. k3_node/loader/base.py +69 -0
  290. k3_node/loader/cache.py +68 -0
  291. k3_node/loader/cluster.py +127 -0
  292. k3_node/loader/data_list_loader.py +45 -0
  293. k3_node/loader/dataloader.py +117 -0
  294. k3_node/loader/dense_data_loader.py +62 -0
  295. k3_node/loader/dynamic_batch_sampler.py +93 -0
  296. k3_node/loader/graph_saint.py +188 -0
  297. k3_node/loader/hgt_loader.py +90 -0
  298. k3_node/loader/imbalanced_sampler.py +87 -0
  299. k3_node/loader/keras_dataset.py +334 -0
  300. k3_node/loader/link_loader.py +179 -0
  301. k3_node/loader/link_neighbor_loader.py +202 -0
  302. k3_node/loader/mixin.py +190 -0
  303. k3_node/loader/neighbor_loader.py +159 -0
  304. k3_node/loader/neighbor_sampler.py +167 -0
  305. k3_node/loader/node_loader.py +185 -0
  306. k3_node/loader/prefetch.py +115 -0
  307. k3_node/loader/random_node_loader.py +89 -0
  308. k3_node/loader/sampler_utils.py +499 -0
  309. k3_node/loader/shadow.py +115 -0
  310. k3_node/loader/temporal_dataloader.py +98 -0
  311. k3_node/loader/test_dataloader.py +113 -0
  312. k3_node/loader/test_keras_dataset.py +221 -0
  313. k3_node/loader/test_neighbor_loader.py +122 -0
  314. k3_node/loader/test_sampler_utils.py +82 -0
  315. k3_node/loader/test_samplers.py +96 -0
  316. k3_node/loader/test_subgraph_loaders.py +89 -0
  317. k3_node/loader/utils.py +232 -0
  318. k3_node/loader/zip_loader.py +88 -0
  319. k3_node/metrics.py +94 -0
  320. k3_node/models/__init__.py +424 -0
  321. k3_node/models/attentive_fp.py +232 -0
  322. k3_node/models/attract_repel.py +108 -0
  323. k3_node/models/autoencoder.py +318 -0
  324. k3_node/models/basic_gnn.py +443 -0
  325. k3_node/models/bio/__init__.py +4 -0
  326. k3_node/models/captum.py +52 -0
  327. k3_node/models/chemistry/__init__.py +4 -0
  328. k3_node/models/correct_and_smooth.py +146 -0
  329. k3_node/models/deep_graph_infomax.py +113 -0
  330. k3_node/models/deepgcn.py +121 -0
  331. k3_node/models/dimenet.py +737 -0
  332. k3_node/models/dimenet_utils.py +153 -0
  333. k3_node/models/gnnff.py +263 -0
  334. k3_node/models/gps_model.py +1122 -0
  335. k3_node/models/gpse.py +638 -0
  336. k3_node/models/graph_unet.py +199 -0
  337. k3_node/models/graphmae2.py +954 -0
  338. k3_node/models/graphormer.py +1258 -0
  339. k3_node/models/graphormer_3d.py +868 -0
  340. k3_node/models/grover.py +1066 -0
  341. k3_node/models/jumping_knowledge.py +200 -0
  342. k3_node/models/label_prop.py +110 -0
  343. k3_node/models/lightgcn.py +171 -0
  344. k3_node/models/linkx.py +181 -0
  345. k3_node/models/lpformer.py +404 -0
  346. k3_node/models/mask_label.py +114 -0
  347. k3_node/models/materials/__init__.py +33 -0
  348. k3_node/models/meta.py +133 -0
  349. k3_node/models/metapath2vec.py +234 -0
  350. k3_node/models/mlp.py +264 -0
  351. k3_node/models/mole_bert.py +379 -0
  352. k3_node/models/neural_fingerprint.py +95 -0
  353. k3_node/models/node2vec.py +213 -0
  354. k3_node/models/pmlp.py +157 -0
  355. k3_node/models/polynormer.py +229 -0
  356. k3_node/models/rect.py +93 -0
  357. k3_node/models/renet.py +221 -0
  358. k3_node/models/rev_gnn.py +128 -0
  359. k3_node/models/schnet.py +484 -0
  360. k3_node/models/sgformer.py +195 -0
  361. k3_node/models/signed_gcn.py +185 -0
  362. k3_node/models/test_attentive_fp.py +32 -0
  363. k3_node/models/test_attract_repel.py +33 -0
  364. k3_node/models/test_autoencoder.py +119 -0
  365. k3_node/models/test_basic_gnn.py +102 -0
  366. k3_node/models/test_correct_and_smooth.py +40 -0
  367. k3_node/models/test_deep_graph_infomax.py +68 -0
  368. k3_node/models/test_deepgcn.py +21 -0
  369. k3_node/models/test_dimenet.py +86 -0
  370. k3_node/models/test_domain_apis.py +138 -0
  371. k3_node/models/test_gnnff.py +24 -0
  372. k3_node/models/test_gps_model.py +271 -0
  373. k3_node/models/test_gpse.py +34 -0
  374. k3_node/models/test_graph_unet.py +26 -0
  375. k3_node/models/test_graphmae2.py +226 -0
  376. k3_node/models/test_graphormer.py +233 -0
  377. k3_node/models/test_graphormer3d.py +163 -0
  378. k3_node/models/test_grover.py +287 -0
  379. k3_node/models/test_jumping_knowledge.py +129 -0
  380. k3_node/models/test_label_prop.py +37 -0
  381. k3_node/models/test_lightgcn.py +38 -0
  382. k3_node/models/test_linkx.py +31 -0
  383. k3_node/models/test_lpformer.py +22 -0
  384. k3_node/models/test_mask_label.py +90 -0
  385. k3_node/models/test_meta.py +159 -0
  386. k3_node/models/test_metapath2vec.py +45 -0
  387. k3_node/models/test_mlp.py +62 -0
  388. k3_node/models/test_mole_bert.py +164 -0
  389. k3_node/models/test_neural_fingerprint.py +13 -0
  390. k3_node/models/test_node2vec.py +57 -0
  391. k3_node/models/test_pmlp.py +81 -0
  392. k3_node/models/test_polynormer.py +104 -0
  393. k3_node/models/test_rect.py +23 -0
  394. k3_node/models/test_renet.py +32 -0
  395. k3_node/models/test_rev_gnn.py +24 -0
  396. k3_node/models/test_schnet.py +43 -0
  397. k3_node/models/test_sgformer.py +48 -0
  398. k3_node/models/test_signed_gcn.py +28 -0
  399. k3_node/models/test_tgn.py +77 -0
  400. k3_node/models/test_unimol.py +179 -0
  401. k3_node/models/test_unimol2.py +114 -0
  402. k3_node/models/test_unimol_plus.py +131 -0
  403. k3_node/models/test_visnet.py +44 -0
  404. k3_node/models/tgn.py +382 -0
  405. k3_node/models/unimol.py +1156 -0
  406. k3_node/models/unimol2.py +616 -0
  407. k3_node/models/unimol_docking_v2.py +301 -0
  408. k3_node/models/unimol_plus.py +456 -0
  409. k3_node/models/utils.py +97 -0
  410. k3_node/models/visnet.py +759 -0
  411. k3_node/ops/__init__.py +4 -0
  412. k3_node/ops/conv.py +56 -0
  413. k3_node/ops/creation.py +43 -0
  414. k3_node/ops/graph.py +27 -0
  415. k3_node/ops/host.py +41 -0
  416. k3_node/ops/matmul.py +49 -0
  417. k3_node/ops/numpy.py +24 -0
  418. k3_node/ops/segment.py +54 -0
  419. k3_node/ops/sparse.py +51 -0
  420. k3_node/rag/__init__.py +49 -0
  421. k3_node/rag/encoders.py +312 -0
  422. k3_node/rag/pipeline.py +192 -0
  423. k3_node/rag/projector.py +184 -0
  424. k3_node/rag/subgraph.py +270 -0
  425. k3_node/rag/test_rag.py +347 -0
  426. k3_node/rag/verbalizer.py +162 -0
  427. k3_node/tasks/__init__.py +19 -0
  428. k3_node/tasks/backbone_resolver.py +125 -0
  429. k3_node/tasks/base.py +67 -0
  430. k3_node/tasks/graph_classification.py +270 -0
  431. k3_node/tasks/graph_regression.py +228 -0
  432. k3_node/tasks/link_prediction.py +306 -0
  433. k3_node/tasks/node_classification.py +194 -0
  434. k3_node/tasks/node_regression.py +138 -0
  435. k3_node/tasks/test_tasks.py +319 -0
  436. k3_node/test_docstring_examples.py +106 -0
  437. k3_node/test_training_forwarding.py +116 -0
  438. k3_node/training.py +115 -0
  439. k3_node/transforms/__init__.py +166 -0
  440. k3_node/transforms/base_transform.py +32 -0
  441. k3_node/transforms/compose.py +58 -0
  442. k3_node/transforms/general.py +676 -0
  443. k3_node/transforms/graph.py +1070 -0
  444. k3_node/transforms/spatial.py +797 -0
  445. k3_node/transforms/test_random_link_split.py +45 -0
  446. k3_node/transforms/test_spatial_transforms.py +65 -0
  447. k3_node/transforms/test_transforms.py +253 -0
  448. k3_node/transforms/utils.py +102 -0
  449. k3_node/utils/__init__.py +5 -0
  450. k3_node/utils/backend_import.py +12 -0
  451. k3_node/utils/graph.py +286 -0
  452. k3_node/utils/keras.py +94 -0
  453. k3_node/utils/random.py +103 -0
  454. k3_node/utils/smiles.py +235 -0
  455. k3_node-1.0.0.dist-info/METADATA +284 -0
  456. k3_node-1.0.0.dist-info/RECORD +459 -0
  457. k3_node-1.0.0.dist-info/WHEEL +5 -0
  458. k3_node-1.0.0.dist-info/licenses/LICENSE +21 -0
  459. k3_node-1.0.0.dist-info/top_level.txt +1 -0
@@ -0,0 +1,68 @@
1
+ from typing import Optional
2
+ from keras import ops
3
+ import numpy as np
4
+
5
+ from .base import Aggregation
6
+ from k3_node.ops.creation import repeat
7
+
8
+
9
+ class SortAggregation(Aggregation):
10
+ r"""The pooling operator from the `"An End-to-End Deep Learning
11
+ Architecture for Graph Classification"
12
+ <https://www.cse.wustl.edu/~muhan/papers/AAAI_2018_DGCNN.pdf>`_ paper,
13
+ where node features are sorted in descending order based on their last
14
+ feature channel. The first :math:`k` nodes form the output of the layer.
15
+
16
+ Example:
17
+ ```python
18
+ import numpy as np
19
+ from k3_node.layers import SortAggregation
20
+
21
+ x = np.random.rand(10, 8).astype("float32") # 10 nodes with 8 features each
22
+ index = np.repeat([0, 1], 5) # aggregate nodes 0-4 into set 0 and nodes 5-9 into set 1
23
+
24
+ aggr = SortAggregation(k=2)
25
+ out = aggr(x, index=index, dim_size=2)
26
+ print(tuple(out.shape)) # (2, 16)
27
+ ```
28
+ """
29
+
30
+ def __init__(self, k: int, **kwargs):
31
+ super().__init__(**kwargs)
32
+ self.k = k
33
+
34
+ def call(
35
+ self,
36
+ x,
37
+ index: Optional[any] = None,
38
+ ptr: Optional[any] = None,
39
+ dim_size: Optional[int] = None,
40
+ dim: int = -2,
41
+ max_num_elements: Optional[int] = None,
42
+ **kwargs,
43
+ ):
44
+ fill_value = -1e9
45
+ batch_x, mask = self.to_dense_batch(
46
+ x, index=index, ptr=ptr, dim_size=dim_size, dim=dim,
47
+ fill_value=fill_value, max_num_elements=max_num_elements,
48
+ )
49
+
50
+ B = ops.shape(batch_x)[0]
51
+ N = ops.shape(batch_x)[1]
52
+ D = ops.shape(batch_x)[2]
53
+
54
+ scores = batch_x[:, :, -1] # [B, N]
55
+ k = self.k
56
+ k_val = min(k, int(scores.shape[1])) if hasattr(scores, "shape") and isinstance(scores.shape[1], int) else k
57
+ _, perm = ops.top_k(scores, k=k_val, sorted=True) # [B, k]
58
+ perm_expanded = repeat(ops.expand_dims(perm, -1), D, axis=-1)
59
+ out_x = ops.take_along_axis(batch_x, perm_expanded, axis=1)
60
+ out_x = ops.where(ops.equal(out_x, fill_value), ops.zeros_like(out_x), out_x)
61
+ static_d = x.shape[-1]
62
+ out_x = ops.reshape(out_x, (-1, k_val * static_d) if isinstance(static_d, int) else (B, -1))
63
+
64
+ return out_x
65
+
66
+ def __repr__(self) -> str:
67
+ return f"{self.__class__.__name__}(k={self.k})"
68
+
@@ -0,0 +1,337 @@
1
+ import numpy as np
2
+ import pytest
3
+ from keras import layers, ops
4
+
5
+ from k3_node.layers.aggr import (
6
+ Aggregation,
7
+ AttentionalAggregation,
8
+ DeepSetsAggregation,
9
+ DegreeScalerAggregation,
10
+ EquilibriumAggregation,
11
+ FusedAggregation,
12
+ GRUAggregation,
13
+ GraphMultisetTransformer,
14
+ LCMAggregation,
15
+ LSTMAggregation,
16
+ MLPAggregation,
17
+ MaxAggregation,
18
+ MeanAggregation,
19
+ MedianAggregation,
20
+ MinAggregation,
21
+ MulAggregation,
22
+ MultiAggregation,
23
+ PatchTransformerAggregation,
24
+ PowerMeanAggregation,
25
+ QuantileAggregation,
26
+ Set2Set,
27
+ SetTransformerAggregation,
28
+ SoftmaxAggregation,
29
+ SortAggregation,
30
+ StdAggregation,
31
+ SumAggregation,
32
+ VarAggregation,
33
+ VariancePreservingAggregation,
34
+ aggregation_resolver,
35
+ ptr2index,
36
+ to_dense_batch,
37
+ )
38
+
39
+
40
+ def test_ptr2index_and_to_dense_batch():
41
+ ptr = ops.convert_to_tensor([0, 2, 5, 6], dtype="int32")
42
+ index = ptr2index(ptr)
43
+ assert np.array_equal(ops.convert_to_numpy(index), [0, 0, 1, 1, 1, 2])
44
+
45
+ x = ops.convert_to_tensor([
46
+ [1.0, 2.0],
47
+ [3.0, 4.0],
48
+ [5.0, 6.0],
49
+ [7.0, 8.0],
50
+ [9.0, 10.0],
51
+ [11.0, 12.0],
52
+ ], dtype="float32")
53
+
54
+ dense_x, mask = to_dense_batch(x, index)
55
+ assert ops.shape(dense_x) == (3, 3, 2)
56
+ assert ops.shape(mask) == (3, 3)
57
+ assert np.array_equal(ops.convert_to_numpy(mask), [
58
+ [True, True, False],
59
+ [True, True, True],
60
+ [True, False, False],
61
+ ])
62
+
63
+
64
+ @pytest.mark.parametrize(
65
+ "AggrClass,expected",
66
+ [
67
+ (SumAggregation, [[4.0, 6.0], [21.0, 24.0], [11.0, 12.0]]),
68
+ (MeanAggregation, [[2.0, 3.0], [7.0, 8.0], [11.0, 12.0]]),
69
+ (MaxAggregation, [[3.0, 4.0], [9.0, 10.0], [11.0, 12.0]]),
70
+ (MinAggregation, [[1.0, 2.0], [5.0, 6.0], [11.0, 12.0]]),
71
+ (MulAggregation, [[3.0, 8.0], [315.0, 480.0], [11.0, 12.0]]),
72
+ ],
73
+ )
74
+ def test_basic_reductions(AggrClass, expected):
75
+ x = ops.convert_to_tensor([
76
+ [1.0, 2.0],
77
+ [3.0, 4.0],
78
+ [5.0, 6.0],
79
+ [7.0, 8.0],
80
+ [9.0, 10.0],
81
+ [11.0, 12.0],
82
+ ], dtype="float32")
83
+ index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
84
+
85
+ aggr = AggrClass()
86
+ out = aggr(x, index)
87
+ assert np.allclose(ops.convert_to_numpy(out), expected)
88
+
89
+ # Test with ptr
90
+ ptr = ops.convert_to_tensor([0, 2, 5, 6], dtype="int32")
91
+ out_ptr = aggr(x, ptr=ptr)
92
+ assert np.allclose(ops.convert_to_numpy(out_ptr), expected)
93
+
94
+
95
+ def test_var_and_std_aggregation():
96
+ x = ops.convert_to_tensor([
97
+ [1.0, 2.0],
98
+ [3.0, 4.0],
99
+ [5.0, 6.0],
100
+ [7.0, 8.0],
101
+ [9.0, 10.0],
102
+ [11.0, 12.0],
103
+ ], dtype="float32")
104
+ index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
105
+
106
+ var_aggr = VarAggregation()
107
+ var_out = var_aggr(x, index)
108
+ assert ops.shape(var_out) == (3, 2)
109
+ assert np.all(ops.convert_to_numpy(var_out) >= 0.0)
110
+
111
+ std_aggr = StdAggregation()
112
+ std_out = std_aggr(x, index)
113
+ assert ops.shape(std_out) == (3, 2)
114
+ assert np.all(ops.convert_to_numpy(std_out) >= 0.0)
115
+
116
+
117
+ def test_softmax_aggregation():
118
+ x = ops.convert_to_tensor([
119
+ [1.0, 2.0],
120
+ [3.0, 4.0],
121
+ [5.0, 6.0],
122
+ [7.0, 8.0],
123
+ [9.0, 10.0],
124
+ [11.0, 12.0],
125
+ ], dtype="float32")
126
+ index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
127
+
128
+ # Fixed temperature
129
+ aggr = SoftmaxAggregation(t=1.0)
130
+ out = aggr(x, index)
131
+ assert ops.shape(out) == (3, 2)
132
+
133
+ # Learnable multi-channel temperature
134
+ learnable_aggr = SoftmaxAggregation(t=1.0, learn=True, channels=2)
135
+ out_learn = learnable_aggr(x, index)
136
+ assert ops.shape(out_learn) == (3, 2)
137
+
138
+
139
+ def test_powermean_aggregation():
140
+ x = ops.convert_to_tensor([
141
+ [1.0, 2.0],
142
+ [3.0, 4.0],
143
+ [5.0, 6.0],
144
+ [7.0, 8.0],
145
+ [9.0, 10.0],
146
+ [11.0, 12.0],
147
+ ], dtype="float32")
148
+ index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
149
+
150
+ # Fixed p
151
+ aggr = PowerMeanAggregation(p=2.0)
152
+ out = aggr(x, index)
153
+ assert ops.shape(out) == (3, 2)
154
+
155
+ # Learnable p
156
+ learnable_aggr = PowerMeanAggregation(p=1.0, learn=True, channels=2)
157
+ out_learn = learnable_aggr(x, index)
158
+ assert ops.shape(out_learn) == (3, 2)
159
+
160
+
161
+ def test_quantile_and_median_aggregation():
162
+ x = ops.convert_to_tensor([
163
+ [1.0, 2.0],
164
+ [3.0, 4.0],
165
+ [5.0, 6.0],
166
+ [7.0, 8.0],
167
+ [9.0, 10.0],
168
+ [11.0, 12.0],
169
+ ], dtype="float32")
170
+ index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
171
+
172
+ # Median
173
+ med_aggr = MedianAggregation()
174
+ med_out = med_aggr(x, index)
175
+ assert ops.shape(med_out) == (3, 2)
176
+
177
+ # Quantile with multiple q
178
+ q_aggr = QuantileAggregation(q=[0.25, 0.75], interpolation="linear")
179
+ q_out = q_aggr(x, index)
180
+ assert ops.shape(q_out) == (3, 4)
181
+
182
+ # Interpolations
183
+ for interp in ["lower", "higher", "nearest", "midpoint"]:
184
+ q_interp = QuantileAggregation(q=0.5, interpolation=interp)
185
+ res = q_interp(x, index)
186
+ assert ops.shape(res) == (3, 2)
187
+
188
+
189
+ def test_attentional_aggregation():
190
+ x = ops.convert_to_tensor([
191
+ [1.0, 2.0],
192
+ [3.0, 4.0],
193
+ [5.0, 6.0],
194
+ [7.0, 8.0],
195
+ [9.0, 10.0],
196
+ [11.0, 12.0],
197
+ ], dtype="float32")
198
+ index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
199
+
200
+ gate_nn = layers.Dense(1)
201
+ nn = layers.Dense(8)
202
+ aggr = AttentionalAggregation(gate_nn=gate_nn, nn=nn)
203
+
204
+ out = aggr(x, index)
205
+ assert ops.shape(out) == (3, 8)
206
+
207
+
208
+ def test_set2set_aggregation():
209
+ in_channels = 4
210
+ x = ops.ones((6, in_channels), dtype="float32")
211
+ index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
212
+
213
+ s2s = Set2Set(in_channels=in_channels, processing_steps=2)
214
+ out = s2s(x, index)
215
+ assert ops.shape(out) == (3, 2 * in_channels)
216
+
217
+
218
+ def test_degree_scaler_aggregation():
219
+ x = ops.ones((6, 4), dtype="float32")
220
+ index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
221
+ deg = ops.convert_to_tensor([0.0, 1.0, 2.0, 3.0], dtype="float32")
222
+
223
+ scalers = ["identity", "amplification", "attenuation", "linear", "inverse_linear"]
224
+ aggr = DegreeScalerAggregation(aggr="mean", scaler=scalers, deg=deg)
225
+
226
+ out = aggr(x, index)
227
+ assert ops.shape(out) == (3, 4 * len(scalers))
228
+
229
+
230
+ def test_sort_aggregation():
231
+ x = ops.convert_to_tensor([
232
+ [1.0, 2.0],
233
+ [3.0, 1.0],
234
+ [5.0, 9.0],
235
+ [7.0, 8.0],
236
+ [9.0, 10.0],
237
+ [11.0, 5.0],
238
+ ], dtype="float32")
239
+ index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
240
+
241
+ aggr = SortAggregation(k=2)
242
+ out = aggr(x, index)
243
+ assert ops.shape(out) == (3, 2 * 2)
244
+
245
+
246
+ def test_multi_aggregation():
247
+ x = ops.ones((6, 4), dtype="float32")
248
+ index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
249
+
250
+ # Cat mode
251
+ aggr_cat = MultiAggregation(["mean", "max"], mode="cat")
252
+ assert ops.shape(aggr_cat(x, index)) == (3, 8)
253
+
254
+ # Proj mode
255
+ aggr_proj = MultiAggregation(["mean", "max"], mode="proj", mode_kwargs={"in_channels": 4, "out_channels": 16})
256
+ assert ops.shape(aggr_proj(x, index)) == (3, 16)
257
+
258
+ # Elementwise modes
259
+ for m in ["sum", "mean", "max", "min", "var", "std"]:
260
+ aggr_m = MultiAggregation(["sum", "mean"], mode=m)
261
+ assert ops.shape(aggr_m(x, index)) == (3, 4)
262
+
263
+
264
+ def test_deep_sets_and_mlp_aggregation():
265
+ x = ops.ones((6, 4), dtype="float32")
266
+ index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
267
+
268
+ # DeepSets
269
+ ds = DeepSetsAggregation(local_nn=layers.Dense(8), global_nn=layers.Dense(16))
270
+ assert ops.shape(ds(x, index)) == (3, 16)
271
+
272
+ # MLP
273
+ mlp_aggr = MLPAggregation(in_channels=4, out_channels=16, max_num_elements=3)
274
+ assert ops.shape(mlp_aggr(x, index)) == (3, 16)
275
+
276
+
277
+ def test_lstm_and_gru_aggregation():
278
+ x = ops.ones((6, 4), dtype="float32")
279
+ index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
280
+
281
+ lstm_aggr = LSTMAggregation(in_channels=4, out_channels=8)
282
+ assert ops.shape(lstm_aggr(x, index)) == (3, 8)
283
+
284
+ gru_aggr = GRUAggregation(in_channels=4, out_channels=8)
285
+ assert ops.shape(gru_aggr(x, index)) == (3, 8)
286
+
287
+
288
+ def test_set_transformer_and_gmt():
289
+ x = ops.ones((6, 4), dtype="float32")
290
+ index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
291
+
292
+ st = SetTransformerAggregation(channels=4, num_seed_points=2, heads=1, concat=True)
293
+ out_st = st(x, index)
294
+ assert ops.shape(out_st) == (3, 8)
295
+
296
+ gmt = GraphMultisetTransformer(channels=4, k=2, heads=1)
297
+ out_gmt = gmt(x, index)
298
+ assert ops.shape(out_gmt) == (3, 4)
299
+
300
+
301
+ def test_variance_preserving_and_patch_transformer():
302
+ x = ops.ones((6, 4), dtype="float32")
303
+ index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
304
+
305
+ vpa = VariancePreservingAggregation()
306
+ assert ops.shape(vpa(x, index)) == (3, 4)
307
+
308
+ pt = PatchTransformerAggregation(in_channels=4, out_channels=8, patch_size=2, hidden_channels=4)
309
+ assert ops.shape(pt(x, index)) == (3, 8)
310
+
311
+
312
+ def test_lcm_and_equilibrium_aggregation():
313
+ x = ops.ones((6, 4), dtype="float32")
314
+ index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
315
+
316
+ lcm = LCMAggregation(in_channels=4, out_channels=4, project=False)
317
+ assert ops.shape(lcm(x, index)) == (3, 4)
318
+
319
+ eq = EquilibriumAggregation(in_channels=4, out_channels=4, num_layers=[8])
320
+ assert ops.shape(eq(x, index)) == (3, 4)
321
+
322
+
323
+ def test_fused_and_resolver():
324
+ x = ops.ones((6, 4), dtype="float32")
325
+ index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
326
+
327
+ fused = FusedAggregation(["sum", "mean", "max"])
328
+ outs = fused(x, index)
329
+ assert len(outs) == 3
330
+ for o in outs:
331
+ assert ops.shape(o) == (3, 4)
332
+
333
+ # Resolver
334
+ res_sum = aggregation_resolver("sum")
335
+ assert isinstance(res_sum, SumAggregation)
336
+ res_mean = aggregation_resolver("mean")
337
+ assert isinstance(res_mean, MeanAggregation)
@@ -0,0 +1,210 @@
1
+ from typing import Optional
2
+ from keras import initializers, layers, ops
3
+
4
+
5
+ class MultiheadAttentionBlock(layers.Layer):
6
+ r"""The Multihead Attention Block (MAB) from the `"Set Transformer: A
7
+ Framework for Attention-based Permutation-Invariant Neural Networks"
8
+ <https://arxiv.org/abs/1810.00825>`_ paper.
9
+ """
10
+
11
+ def __init__(
12
+ self,
13
+ channels: int,
14
+ heads: int = 1,
15
+ layer_norm: bool = True,
16
+ dropout: float = 0.0,
17
+ **kwargs,
18
+ ):
19
+ super().__init__(**kwargs)
20
+ self.supports_masking = True
21
+ self.channels = channels
22
+ self.heads = heads
23
+ self.dropout = dropout
24
+
25
+ key_dim = max(channels // heads, 1)
26
+ self.attn = layers.MultiHeadAttention(
27
+ num_heads=heads,
28
+ key_dim=key_dim,
29
+ dropout=dropout,
30
+ )
31
+ self.lin = layers.Dense(channels)
32
+ self.layer_norm1 = layers.LayerNormalization() if layer_norm else None
33
+ self.layer_norm2 = layers.LayerNormalization() if layer_norm else None
34
+
35
+ def compute_mask(self, inputs, mask=None):
36
+ return mask
37
+
38
+ def reset_parameters(self):
39
+ pass
40
+
41
+ def call(
42
+ self,
43
+ x,
44
+ y,
45
+ x_mask: Optional[any] = None,
46
+ y_mask: Optional[any] = None,
47
+ training: bool = False,
48
+ ):
49
+ attn_mask = None
50
+ if y_mask is not None:
51
+ # y_mask shape: [B, S], expand to [B, 1, S]
52
+ attn_mask = ops.expand_dims(ops.cast(y_mask, "bool"), axis=1)
53
+
54
+ out = self.attn(
55
+ query=x,
56
+ value=y,
57
+ key=y,
58
+ attention_mask=attn_mask,
59
+ training=training,
60
+ )
61
+
62
+ if x_mask is not None:
63
+ out = out * ops.cast(ops.expand_dims(x_mask, axis=-1), out.dtype)
64
+
65
+ out = out + x
66
+ if self.layer_norm1 is not None:
67
+ out = self.layer_norm1(out)
68
+
69
+ out = out + ops.relu(self.lin(out))
70
+ if self.layer_norm2 is not None:
71
+ out = self.layer_norm2(out)
72
+
73
+ return out
74
+
75
+ def __repr__(self) -> str:
76
+ return (
77
+ f"{self.__class__.__name__}({self.channels}, "
78
+ f"heads={self.heads}, layer_norm={self.layer_norm1 is not None}, "
79
+ f"dropout={self.dropout})"
80
+ )
81
+
82
+
83
+ class SetAttentionBlock(layers.Layer):
84
+ r"""The Set Attention Block (SAB) from the `"Set Transformer"` paper."""
85
+
86
+ def __init__(
87
+ self,
88
+ channels: int,
89
+ heads: int = 1,
90
+ layer_norm: bool = True,
91
+ dropout: float = 0.0,
92
+ **kwargs,
93
+ ):
94
+ super().__init__(**kwargs)
95
+ self.supports_masking = True
96
+ self.mab = MultiheadAttentionBlock(channels, heads, layer_norm, dropout)
97
+
98
+ def compute_mask(self, inputs, mask=None):
99
+ return mask
100
+
101
+ def reset_parameters(self):
102
+ self.mab.reset_parameters()
103
+
104
+ def call(self, x, mask: Optional[any] = None, training: bool = False):
105
+ return self.mab(x, x, x_mask=mask, y_mask=mask, training=training)
106
+
107
+ def __repr__(self) -> str:
108
+ return (
109
+ f"{self.__class__.__name__}({self.mab.channels}, "
110
+ f"heads={self.mab.heads}, layer_norm={self.mab.layer_norm1 is not None}, "
111
+ f"dropout={self.mab.dropout})"
112
+ )
113
+
114
+
115
+ class InducedSetAttentionBlock(layers.Layer):
116
+ r"""The Induced Set Attention Block (ISAB) from the `"Set Transformer"` paper."""
117
+
118
+ def __init__(
119
+ self,
120
+ channels: int,
121
+ num_induced_points: int,
122
+ heads: int = 1,
123
+ layer_norm: bool = True,
124
+ dropout: float = 0.0,
125
+ **kwargs,
126
+ ):
127
+ super().__init__(**kwargs)
128
+ self.supports_masking = True
129
+ self.channels = channels
130
+ self.num_induced_points = num_induced_points
131
+
132
+ self.ind = self.add_weight(
133
+ shape=(1, num_induced_points, channels),
134
+ initializer=initializers.GlorotUniform(),
135
+ trainable=True,
136
+ name="ind",
137
+ )
138
+ self.mab1 = MultiheadAttentionBlock(channels, heads, layer_norm, dropout)
139
+ self.mab2 = MultiheadAttentionBlock(channels, heads, layer_norm, dropout)
140
+
141
+ def compute_mask(self, inputs, mask=None):
142
+ return mask
143
+
144
+ def reset_parameters(self):
145
+ init = initializers.GlorotUniform()
146
+ self.ind.assign(init(self.ind.shape, dtype=self.ind.dtype))
147
+ self.mab1.reset_parameters()
148
+ self.mab2.reset_parameters()
149
+
150
+ def call(self, x, mask: Optional[any] = None, training: bool = False):
151
+ B = ops.shape(x)[0]
152
+ ind_expanded = ops.broadcast_to(self.ind, (B, self.num_induced_points, self.channels))
153
+ h = self.mab1(ind_expanded, x, y_mask=mask, training=training)
154
+ return self.mab2(x, h, x_mask=mask, training=training)
155
+
156
+ def __repr__(self) -> str:
157
+ return (
158
+ f"{self.__class__.__name__}({self.channels}, "
159
+ f"num_induced_points={self.num_induced_points}, "
160
+ f"heads={self.mab1.heads})"
161
+ )
162
+
163
+
164
+ class PoolingByMultiheadAttention(layers.Layer):
165
+ r"""The Pooling by Multihead Attention (PMA) layer from the `"Set Transformer"` paper."""
166
+
167
+ def __init__(
168
+ self,
169
+ channels: int,
170
+ num_seed_points: int = 1,
171
+ heads: int = 1,
172
+ layer_norm: bool = True,
173
+ dropout: float = 0.0,
174
+ **kwargs,
175
+ ):
176
+ super().__init__(**kwargs)
177
+ self.supports_masking = True
178
+ self.channels = channels
179
+ self.num_seed_points = num_seed_points
180
+ self.lin = layers.Dense(channels)
181
+ self.seed = self.add_weight(
182
+ shape=(1, num_seed_points, channels),
183
+ initializer=initializers.GlorotUniform(),
184
+ trainable=True,
185
+ name="seed",
186
+ )
187
+ self.mab = MultiheadAttentionBlock(channels, heads, layer_norm, dropout)
188
+
189
+ def compute_mask(self, inputs, mask=None):
190
+ return None
191
+
192
+ def reset_parameters(self):
193
+ self.lin.reset_parameters()
194
+ init = initializers.GlorotUniform()
195
+ self.seed.assign(init(self.seed.shape, dtype=self.seed.dtype))
196
+ self.mab.reset_parameters()
197
+
198
+ def call(self, x, mask: Optional[any] = None, training: bool = False):
199
+ B = ops.shape(x)[0]
200
+ x_proj = ops.relu(self.lin(x))
201
+ seed_expanded = ops.broadcast_to(self.seed, (B, self.num_seed_points, self.channels))
202
+ return self.mab(seed_expanded, x_proj, y_mask=mask, training=training)
203
+
204
+ def __repr__(self) -> str:
205
+ return (
206
+ f"{self.__class__.__name__}({self.channels}, "
207
+ f"num_seed_points={self.num_seed_points}, "
208
+ f"heads={self.mab.heads})"
209
+ )
210
+
@@ -0,0 +1,54 @@
1
+ from typing import Optional
2
+ from keras import ops
3
+
4
+ from .base import Aggregation
5
+ from k3_node.ops.segment import segment_sum
6
+
7
+
8
+ class VariancePreservingAggregation(Aggregation):
9
+ r"""Performs the Variance Preserving Aggregation (VPA) from the `"GNN-VPA:
10
+ A Variance-Preserving Aggregation Strategy for Graph Neural Networks"
11
+ <https://arxiv.org/abs/2403.04747>`_ paper.
12
+
13
+ Example:
14
+ ```python
15
+ import numpy as np
16
+ from k3_node.layers import VariancePreservingAggregation
17
+
18
+ x = np.random.rand(10, 8).astype("float32") # 10 nodes with 8 features each
19
+ index = np.repeat([0, 1], 5) # aggregate nodes 0-4 into set 0 and nodes 5-9 into set 1
20
+
21
+ aggr = VariancePreservingAggregation()
22
+ out = aggr(x, index=index, dim_size=2)
23
+ print(tuple(out.shape)) # (2, 8)
24
+ ```
25
+ """
26
+
27
+ def call(
28
+ self,
29
+ x,
30
+ index: Optional[any] = None,
31
+ ptr: Optional[any] = None,
32
+ dim_size: Optional[int] = None,
33
+ dim: int = -2,
34
+ **kwargs,
35
+ ):
36
+ out = self.reduce(x, index, ptr, dim_size, dim, reduce="sum")
37
+
38
+ if ptr is not None and index is None:
39
+ from .base import ptr2index
40
+ index = ptr2index(ptr)
41
+
42
+ index = ops.cast(index, dtype="int32")
43
+ if dim_size is None: # a tensor while tracing; don't test its truth value
44
+ dim_size = int(ops.max(index)) + 1 if ops.shape(index)[0] > 0 else 0
45
+
46
+ ones = ops.ones((ops.shape(index)[0], 1), dtype=out.dtype)
47
+ count = segment_sum(ones, index, num_segments=dim_size)
48
+ count = ops.maximum(ops.sqrt(count), 1.0)
49
+
50
+ return out / count
51
+
52
+ def __repr__(self) -> str:
53
+ return f"{self.__class__.__name__}()"
54
+
@@ -0,0 +1,5 @@
1
+ from .performer import *
2
+ from .polynormer import *
3
+ from .qformer import *
4
+ from .sgformer import *
5
+ from .pair_attention import *