k3-node 1.0.0__py3-none-any.whl

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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 +1,287 @@
1
+ import os
2
+ import pytest
3
+ import numpy as np
4
+ import keras
5
+ from keras import ops
6
+ try:
7
+ import torch
8
+ except ImportError:
9
+ torch = None
10
+
11
+ from k3_node.models.grover import (
12
+ GROVER,
13
+ GroverPReLU,
14
+ MPNEncoder,
15
+ MTBlock,
16
+ Readout,
17
+ GTransEncoder,
18
+ load_grover_weights,
19
+ download_grover_checkpoint,
20
+ )
21
+
22
+
23
+ def _make_dummy_batch(num_atoms=5, num_bonds=7, atom_fdim=151, bond_fdim=165, edge_fdim=None):
24
+ if edge_fdim is not None:
25
+ bond_fdim = edge_fdim
26
+ np.random.seed(42)
27
+ f_atoms = np.random.randn(num_atoms, atom_fdim).astype(np.float32)
28
+ f_atoms[0] = 0.0
29
+ f_bonds = np.random.randn(num_bonds, bond_fdim).astype(np.float32)
30
+ f_bonds[0] = 0.0
31
+
32
+ a2b = np.array([[0, 0], [2, 0], [1, 4], [3, 0], [0, 0]], dtype=np.int64)
33
+ b2a = np.array([0, 1, 2, 2, 3, 1, 3], dtype=np.int64)
34
+ b2revb = np.array([0, 2, 1, 4, 3, 6, 5], dtype=np.int64)
35
+ a_scope = np.array([[1, 2], [3, 2]], dtype=np.int64)
36
+ b_scope = np.array([[1, 3], [4, 3]], dtype=np.int64)
37
+ a2a = b2a[a2b]
38
+
39
+ return (
40
+ ops.convert_to_tensor(f_atoms),
41
+ ops.convert_to_tensor(f_bonds),
42
+ ops.convert_to_tensor(a2b),
43
+ ops.convert_to_tensor(b2a),
44
+ ops.convert_to_tensor(b2revb),
45
+ ops.convert_to_tensor(a_scope),
46
+ ops.convert_to_tensor(b_scope),
47
+ ops.convert_to_tensor(a2a),
48
+ )
49
+
50
+
51
+ def test_grover_prelu():
52
+ layer = GroverPReLU(init_val=0.25)
53
+ x = ops.convert_to_tensor([-2.0, 0.0, 3.0], dtype="float32")
54
+ y = layer(x)
55
+ np.testing.assert_allclose(ops.convert_to_numpy(y), [-0.5, 0.0, 3.0], atol=1e-6)
56
+
57
+ # Config test
58
+ config = layer.get_config()
59
+ assert config["init_val"] == 0.25
60
+
61
+
62
+ def test_mpn_encoder():
63
+ hidden_size = 32
64
+ depth = 3
65
+ num_atoms = 4
66
+ num_bonds = 4
67
+ atom_dim = 16
68
+ bond_dim = 20
69
+
70
+ # 1. Atom messages
71
+ encoder_atom = MPNEncoder(
72
+ hidden_size=hidden_size,
73
+ depth=depth,
74
+ atom_messages=True,
75
+ input_layer="fc",
76
+ input_dim=atom_dim,
77
+ )
78
+ init_msg = ops.convert_to_tensor(np.random.randn(num_atoms, atom_dim).astype(np.float32))
79
+ a2nei = ops.convert_to_tensor(np.array([[0, 0], [2, 0], [1, 3], [2, 0]]), dtype="int64")
80
+
81
+ out = encoder_atom(
82
+ init_messages=init_msg,
83
+ init_attached_features=None,
84
+ a2nei=a2nei,
85
+ a2attached=None,
86
+ )
87
+ assert ops.shape(out) == (num_atoms, hidden_size)
88
+
89
+ # 2. Bond messages (non-backtracking)
90
+ encoder_bond = MPNEncoder(
91
+ hidden_size=hidden_size,
92
+ depth=depth,
93
+ atom_messages=False,
94
+ input_layer="fc",
95
+ input_dim=bond_dim,
96
+ )
97
+ init_bond = ops.convert_to_tensor(np.random.randn(num_bonds, bond_dim).astype(np.float32))
98
+ a2b = ops.convert_to_tensor(np.array([[0], [2], [1], [3]]), dtype="int64")
99
+ b2a = ops.convert_to_tensor(np.array([0, 1, 2, 2]), dtype="int64")
100
+ b2revb = ops.convert_to_tensor(np.array([0, 2, 1, 3]), dtype="int64")
101
+
102
+ out_bond = encoder_bond(
103
+ init_messages=init_bond,
104
+ init_attached_features=None,
105
+ a2nei=a2b,
106
+ a2attached=None,
107
+ b2a=b2a,
108
+ b2revb=b2revb,
109
+ )
110
+ assert ops.shape(out_bond) == (num_bonds, hidden_size)
111
+
112
+
113
+ def test_mt_block():
114
+ hidden_size = 32
115
+ num_attn_head = 2
116
+ depth = 3
117
+ num_atoms = 5
118
+ num_bonds = 7
119
+ atom_dim = 16
120
+ bond_dim = 20
121
+
122
+ block = MTBlock(
123
+ hidden_size=hidden_size,
124
+ input_dim=bond_dim,
125
+ num_attn_head=num_attn_head,
126
+ depth=depth,
127
+ atom_messages=False,
128
+ )
129
+
130
+ batch = _make_dummy_batch(num_atoms, num_bonds, atom_dim, bond_dim)
131
+ f_atoms, f_bonds, a2b, b2a, b2revb, a_scope, b_scope, a2a = batch
132
+
133
+ out_atoms, out_bonds = block(f_atoms, f_bonds, a2b, b2a, b2revb, a2a)
134
+ assert ops.shape(out_bonds) == (num_bonds, hidden_size)
135
+
136
+
137
+ def test_readout():
138
+ hidden_size = 32
139
+ emb = ops.convert_to_tensor(np.random.randn(8, hidden_size).astype(np.float32))
140
+ scope = ops.convert_to_tensor(np.array([[0, 3], [3, 4], [7, 1]]), dtype="int64")
141
+
142
+ # Mean Readout
143
+ readout_mean = Readout(rtype="mean", hidden_size=hidden_size)
144
+ out_mean = readout_mean(emb, scope)
145
+ assert ops.shape(out_mean) == (3, hidden_size)
146
+
147
+ # Self-attention Readout
148
+ readout_sa = Readout(rtype="self_attention", hidden_size=hidden_size, attn_hidden=16, attn_out=4)
149
+ out_sa = readout_sa(emb, scope)
150
+ assert ops.shape(out_sa) == (3, 4 * hidden_size)
151
+
152
+
153
+ def test_gtrans_encoder():
154
+ hidden_size = 32
155
+ batch = _make_dummy_batch(num_atoms=5, num_bonds=7, atom_fdim=151, edge_fdim=165)
156
+ f_atoms, f_bonds, a2b, b2a, b2revb, a_scope, b_scope, a2a = batch
157
+
158
+ # 'both'
159
+ encoder = GTransEncoder(
160
+ hidden_size=hidden_size,
161
+ edge_fdim=165,
162
+ node_fdim=151,
163
+ num_mt_block=1,
164
+ num_attn_head=2,
165
+ depth=3,
166
+ atom_emb_output="both",
167
+ )
168
+ res = encoder(f_atoms, f_bonds, a2b, b2a, b2revb, a2a)
169
+ assert "atom_from_atom" in res
170
+ assert "bond_from_bond" in res
171
+ assert ops.shape(res["atom_from_atom"]) == (5, hidden_size)
172
+ assert ops.shape(res["bond_from_bond"]) == (7, hidden_size)
173
+
174
+
175
+ def test_grover_model_and_fingerprint():
176
+ hidden_size = 32
177
+ model = GROVER(
178
+ hidden_size=hidden_size,
179
+ edge_fdim=165,
180
+ node_fdim=151,
181
+ num_mt_block=1,
182
+ num_attn_head=2,
183
+ depth=3,
184
+ atom_emb_output="both",
185
+ readout_type="mean",
186
+ )
187
+
188
+ batch = _make_dummy_batch(num_atoms=5, num_bonds=7, atom_fdim=151, edge_fdim=165)
189
+ out = model(batch)
190
+ assert ops.shape(out["atom_from_atom"]) == (5, hidden_size)
191
+
192
+ # Fingerprint
193
+ fp = model.get_fingerprint(batch, fingerprint_source="both")
194
+ # 2 molecules in scope, 4 branches * 32 = 128
195
+ assert ops.shape(fp) == (2, 4 * hidden_size)
196
+
197
+
198
+ def test_load_grover_weights_synthetic(tmp_path):
199
+ if torch is None:
200
+ pytest.skip("PyTorch is required for checkpoint loading test")
201
+ hidden_size = 16
202
+ num_attn_head = 2
203
+ depth = 2
204
+ node_fdim = 151
205
+ edge_fdim = 165
206
+
207
+ model = GROVER(
208
+ hidden_size=hidden_size,
209
+ edge_fdim=edge_fdim,
210
+ node_fdim=node_fdim,
211
+ num_mt_block=1,
212
+ num_attn_head=num_attn_head,
213
+ depth=depth,
214
+ atom_emb_output="both",
215
+ )
216
+ model.build(None)
217
+
218
+ # Create dummy torch state dict
219
+ state_dict = {}
220
+ for block_name, dim in [("edge_blocks", edge_fdim), ("node_blocks", node_fdim)]:
221
+ prefix = f"grover.encoders.{block_name}.0"
222
+ state_dict[f"{prefix}.W_i.weight"] = torch.randn(hidden_size, dim)
223
+ state_dict[f"{prefix}.act_func.weight"] = torch.tensor([0.25])
224
+ state_dict[f"{prefix}.layernorm.weight"] = torch.ones(hidden_size)
225
+ state_dict[f"{prefix}.layernorm.bias"] = torch.zeros(hidden_size)
226
+ state_dict[f"{prefix}.sublayer.norm.weight"] = torch.ones(hidden_size)
227
+ state_dict[f"{prefix}.sublayer.norm.bias"] = torch.zeros(hidden_size)
228
+ state_dict[f"{prefix}.W_o.weight"] = torch.randn(hidden_size, hidden_size * num_attn_head)
229
+ for i in range(3):
230
+ state_dict[f"{prefix}.attn.linear_layers.{i}.weight"] = torch.randn(hidden_size, hidden_size)
231
+ state_dict[f"{prefix}.attn.linear_layers.{i}.bias"] = torch.zeros(hidden_size)
232
+ state_dict[f"{prefix}.attn.output_linear.weight"] = torch.randn(hidden_size, hidden_size)
233
+ for hi in range(num_attn_head):
234
+ for mpn in ["mpn_q", "mpn_k", "mpn_v"]:
235
+ state_dict[f"{prefix}.heads.{hi}.{mpn}.W_h.weight"] = torch.randn(hidden_size, hidden_size)
236
+ state_dict[f"{prefix}.heads.{hi}.{mpn}.act_func.weight"] = torch.tensor([0.25])
237
+
238
+ for ffn_key, in_dim in [
239
+ ("ffn_atom_from_atom", hidden_size + node_fdim),
240
+ ("ffn_atom_from_bond", hidden_size + node_fdim),
241
+ ("ffn_bond_from_atom", hidden_size + edge_fdim),
242
+ ("ffn_bond_from_bond", hidden_size + edge_fdim),
243
+ ]:
244
+ prefix = f"grover.encoders.{ffn_key}"
245
+ state_dict[f"{prefix}.W_1.weight"] = torch.randn(hidden_size * 4, in_dim)
246
+ state_dict[f"{prefix}.W_1.bias"] = torch.zeros(hidden_size * 4)
247
+ state_dict[f"{prefix}.W_2.weight"] = torch.randn(hidden_size, hidden_size * 4)
248
+ state_dict[f"{prefix}.W_2.bias"] = torch.zeros(hidden_size)
249
+ state_dict[f"{prefix}.act_func.weight"] = torch.tensor([0.25])
250
+
251
+ for sub in ["atom_from_atom", "atom_from_bond", "bond_from_atom", "bond_from_bond"]:
252
+ state_dict[f"grover.encoders.{sub}_sublayer.norm.weight"] = torch.ones(hidden_size)
253
+ state_dict[f"grover.encoders.{sub}_sublayer.norm.bias"] = torch.zeros(hidden_size)
254
+
255
+ state_dict["grover.encoders.act_func_node.weight"] = torch.tensor([0.25])
256
+ state_dict["grover.encoders.act_func_edge.weight"] = torch.tensor([0.25])
257
+
258
+ save_path = str(tmp_path / "mock_grover.pt")
259
+ torch.save({"state_dict": state_dict}, save_path)
260
+
261
+ load_grover_weights(model, save_path)
262
+ # verify forward pass succeeds
263
+ batch = _make_dummy_batch(num_atoms=5, num_bonds=7, atom_fdim=node_fdim, edge_fdim=edge_fdim)
264
+ out = model(batch)
265
+ assert ops.shape(out["atom_from_atom"]) == (5, hidden_size)
266
+
267
+
268
+ def test_grover_official_pretrained_load():
269
+ ckpt_path = "/tmp/grover_download_test/grover_base.pt"
270
+ if not os.path.exists(ckpt_path):
271
+ pytest.skip("Official checkpoint not present at /tmp/grover_download_test/grover_base.pt")
272
+
273
+ model = GROVER(
274
+ hidden_size=800,
275
+ edge_fdim=165,
276
+ node_fdim=151,
277
+ num_mt_block=1,
278
+ num_attn_head=4,
279
+ depth=6,
280
+ atom_emb_output="both",
281
+ )
282
+ load_grover_weights(model, ckpt_path)
283
+
284
+ batch = _make_dummy_batch(num_atoms=5, num_bonds=7, atom_fdim=151, edge_fdim=165)
285
+ out = model(batch)
286
+ assert ops.shape(out["atom_from_atom"]) == (5, 800)
287
+ assert ops.shape(out["bond_from_bond"]) == (7, 800)
@@ -0,0 +1,129 @@
1
+ import pytest
2
+ from keras import ops
3
+
4
+ from k3_node.models import JumpingKnowledge, HeteroJumpingKnowledge
5
+
6
+
7
+ def test_jumping_knowledge_cat():
8
+ num_nodes, channels, num_layers = 100, 17, 5
9
+ xs = [ops.ones((num_nodes, channels)) for _ in range(num_layers)]
10
+
11
+ model = JumpingKnowledge('cat')
12
+ assert str(model) == 'JumpingKnowledge(cat)'
13
+
14
+ out = model(xs)
15
+ assert ops.shape(out) == (num_nodes, channels * num_layers)
16
+
17
+
18
+ def test_jumping_knowledge_max():
19
+ num_nodes, channels, num_layers = 100, 17, 5
20
+ xs = [ops.ones((num_nodes, channels)) for _ in range(num_layers)]
21
+
22
+ model = JumpingKnowledge('max')
23
+ assert str(model) == 'JumpingKnowledge(max)'
24
+
25
+ out = model(xs)
26
+ assert ops.shape(out) == (num_nodes, channels)
27
+
28
+
29
+ def test_jumping_knowledge_lstm():
30
+ num_nodes, channels, num_layers = 100, 17, 5
31
+ xs = [ops.ones((num_nodes, channels)) for _ in range(num_layers)]
32
+
33
+ model = JumpingKnowledge('lstm', channels, num_layers)
34
+ assert str(model) == (
35
+ f'JumpingKnowledge(lstm, channels={channels}, layers={num_layers})'
36
+ )
37
+
38
+ out = model(xs)
39
+ assert ops.shape(out) == (num_nodes, channels)
40
+
41
+
42
+ def test_jumping_knowledge_invalid_mode():
43
+ with pytest.raises(AssertionError):
44
+ JumpingKnowledge('invalid')
45
+
46
+
47
+ def test_jumping_knowledge_lstm_missing_args():
48
+ with pytest.raises(AssertionError):
49
+ JumpingKnowledge('lstm')
50
+
51
+
52
+ def test_hetero_jumping_knowledge_cat():
53
+ num_nodes, channels, num_layers = 100, 17, 5
54
+ types = ["author", "paper"]
55
+ xs_dict = {
56
+ key: [ops.ones((num_nodes, channels)) for _ in range(num_layers)]
57
+ for key in types
58
+ }
59
+
60
+ model = HeteroJumpingKnowledge(types, mode='cat')
61
+ model.reset_parameters()
62
+ assert str(model) == 'HeteroJumpingKnowledge(num_types=2, mode=cat)'
63
+
64
+ out_dict = model(xs_dict)
65
+ for out in out_dict.values():
66
+ assert ops.shape(out) == (num_nodes, channels * num_layers)
67
+
68
+
69
+ def test_hetero_jumping_knowledge_max():
70
+ num_nodes, channels, num_layers = 100, 17, 5
71
+ types = ["author", "paper"]
72
+ xs_dict = {
73
+ key: [ops.ones((num_nodes, channels)) for _ in range(num_layers)]
74
+ for key in types
75
+ }
76
+
77
+ model = HeteroJumpingKnowledge(types, mode='max')
78
+ assert str(model) == 'HeteroJumpingKnowledge(num_types=2, mode=max)'
79
+
80
+ out_dict = model(xs_dict)
81
+ for out in out_dict.values():
82
+ assert ops.shape(out) == (num_nodes, channels)
83
+
84
+
85
+ def test_hetero_jumping_knowledge_lstm():
86
+ num_nodes, channels, num_layers = 50, 8, 3
87
+ types = ["author", "paper"]
88
+ xs_dict = {
89
+ key: [ops.ones((num_nodes, channels)) for _ in range(num_layers)]
90
+ for key in types
91
+ }
92
+
93
+ model = HeteroJumpingKnowledge(types, mode='lstm', channels=channels,
94
+ num_layers=num_layers)
95
+ assert str(model) == (
96
+ f'HeteroJumpingKnowledge(num_types=2, mode=lstm, '
97
+ f'channels={channels}, layers={num_layers})'
98
+ )
99
+
100
+ out_dict = model(xs_dict)
101
+ for out in out_dict.values():
102
+ assert ops.shape(out) == (num_nodes, channels)
103
+
104
+
105
+ def test_jumping_knowledge_cat_aggregates_correctly():
106
+ """Values in cat mode should be the concatenation of all layer reps."""
107
+ xs = [
108
+ ops.convert_to_tensor([[1.0, 2.0], [3.0, 4.0]]),
109
+ ops.convert_to_tensor([[5.0, 6.0], [7.0, 8.0]]),
110
+ ]
111
+ model = JumpingKnowledge('cat')
112
+ out = model(xs)
113
+ assert ops.shape(out) == (2, 4)
114
+
115
+
116
+ def test_jumping_knowledge_max_aggregates_correctly():
117
+ """Values in max mode should be the element-wise max across layers."""
118
+ xs = [
119
+ ops.convert_to_tensor([[1.0, 8.0], [3.0, 4.0]]),
120
+ ops.convert_to_tensor([[5.0, 6.0], [7.0, 2.0]]),
121
+ ]
122
+ import numpy as np
123
+ model = JumpingKnowledge('max')
124
+ out = model(xs)
125
+ assert ops.shape(out) == (2, 2)
126
+ out_np = ops.convert_to_numpy(out)
127
+ assert np.allclose(out_np[0], [5.0, 8.0])
128
+ assert np.allclose(out_np[1], [7.0, 4.0])
129
+
@@ -0,0 +1,37 @@
1
+ from keras import ops
2
+
3
+ from k3_node.models import LabelPropagation
4
+
5
+
6
+ def test_label_prop():
7
+ y = ops.convert_to_tensor([1, 0, 0, 2, 1, 1])
8
+ edge_index = ops.convert_to_tensor([[0, 1, 1, 2, 4, 5], [1, 0, 2, 1, 5, 4]])
9
+ mask = ops.convert_to_tensor([True, False, True, False, True, False])
10
+
11
+ model = LabelPropagation(num_layers=2, alpha=0.5)
12
+ assert str(model) == 'LabelPropagation(num_layers=2, alpha=0.5)'
13
+
14
+ # Without mask:
15
+ out = model(y, edge_index)
16
+ assert ops.shape(out) == (6, 3)
17
+
18
+ # With mask:
19
+ out = model(y, edge_index, mask)
20
+ assert ops.shape(out) == (6, 3)
21
+
22
+ # With post_step:
23
+ out = model(y, edge_index, mask, post_step=lambda y: ops.zeros_like(y))
24
+ assert float(ops.sum(out)) == 0.0
25
+
26
+
27
+
28
+ def test_label_prop_with_boolean_mask_matches_index_mask():
29
+ import numpy as np
30
+
31
+ y = np.array([0, 1, 2, 0, 1, 2])
32
+ edge_index = np.array([[0, 1, 2, 3, 4, 5], [3, 4, 5, 0, 1, 2]])
33
+ model = LabelPropagation(num_layers=3, alpha=0.9)
34
+ by_bool = model(y, edge_index, mask=np.array([True, True, True, False, False, False]))
35
+ by_index = model(y, edge_index, mask=np.array([0, 1, 2]))
36
+ np.testing.assert_allclose(ops.convert_to_numpy(by_bool), ops.convert_to_numpy(by_index), rtol=1e-6)
37
+ assert (ops.convert_to_numpy(by_bool).argmax(-1) == y).all()
@@ -0,0 +1,38 @@
1
+ import pytest
2
+ from keras import ops
3
+ import numpy as np
4
+
5
+ from k3_node.models import LightGCN
6
+
7
+
8
+ @pytest.mark.parametrize('embedding_dim', [16, 32])
9
+ def test_lightgcn(embedding_dim):
10
+ num_nodes = 50
11
+ edge_index = ops.convert_to_tensor([
12
+ [0, 1, 2, 3, 4, 5, 6, 7],
13
+ [1, 2, 3, 4, 5, 6, 7, 0],
14
+ ])
15
+ edge_label_index = ops.convert_to_tensor([
16
+ [0, 1, 2, 3],
17
+ [4, 5, 6, 7],
18
+ ])
19
+
20
+ model = LightGCN(num_nodes, embedding_dim, num_layers=2)
21
+ assert str(model) == f'LightGCN({num_nodes}, {embedding_dim}, num_layers=2)'
22
+
23
+ pred = model(edge_index, edge_label_index)
24
+ assert ops.shape(pred) == (4,)
25
+
26
+ prob = model.predict_link(edge_index, edge_label_index, prob=True)
27
+ assert ops.shape(prob) == (4,)
28
+
29
+ loss = model.recommendation_loss(
30
+ pos_edge_rank=pred[:2],
31
+ neg_edge_rank=pred[2:],
32
+ lambda_reg=1e-4,
33
+ )
34
+ assert float(ops.convert_to_numpy(loss)) > 0.0
35
+
36
+ recs = model.recommend(edge_index, k=2)
37
+ assert ops.shape(recs) == (num_nodes, 2)
38
+
@@ -0,0 +1,31 @@
1
+ import pytest
2
+ from keras import ops
3
+
4
+ from k3_node.models import LINKX
5
+
6
+
7
+ @pytest.mark.parametrize('num_edge_layers', [1, 2])
8
+ def test_linkx(num_edge_layers):
9
+ x = ops.ones((4, 16))
10
+ edge_index = ops.convert_to_tensor([[0, 1, 2], [1, 2, 3]])
11
+ edge_weight = ops.convert_to_tensor([0.5, 0.8, 1.0])
12
+
13
+ model = LINKX(
14
+ num_nodes=4,
15
+ in_channels=16,
16
+ hidden_channels=32,
17
+ out_channels=8,
18
+ num_layers=2,
19
+ num_edge_layers=num_edge_layers,
20
+ )
21
+ assert str(model) == 'LINKX(num_nodes=4, in_channels=16, out_channels=8)'
22
+
23
+ out = model(x, edge_index)
24
+ assert ops.shape(out) == (4, 8)
25
+
26
+ out_no_x = model(None, edge_index)
27
+ assert ops.shape(out_no_x) == (4, 8)
28
+
29
+ out_weighted = model(x, edge_index, edge_weight)
30
+ assert ops.shape(out_weighted) == (4, 8)
31
+
@@ -0,0 +1,22 @@
1
+ import numpy as np
2
+ from keras import ops
3
+
4
+ from k3_node.models.lpformer import LPFormer, get_ppr
5
+
6
+
7
+ def test_get_ppr():
8
+ ppr = get_ppr(np.array([[0, 1, 1, 2, 2, 0], [1, 0, 2, 1, 0, 2]]), num_nodes=3)
9
+ assert ppr.shape == (3, 3)
10
+ np.testing.assert_allclose(np.asarray(ppr.sum(axis=1)).ravel(), 1.0, atol=0.05) # (approximate) distributions
11
+
12
+
13
+ def test_lpformer():
14
+ rng = np.random.default_rng(0)
15
+ x = rng.random((20, 16)).astype("float32")
16
+ edge_index = rng.integers(0, 20, (2, 60))
17
+ edge_index = np.concatenate([edge_index, edge_index[::-1]], axis=1)
18
+ batch = np.array([[0, 1, 5], [2, 3, 9]])
19
+ model = LPFormer(in_channels=16, hidden_channels=16, num_gnn_layers=2)
20
+ ppr = model.calc_sparse_ppr(edge_index, 20)
21
+ assert tuple(model(batch, x, edge_index, ppr_matrix=ppr).shape) == (3,)
22
+ assert tuple(model(batch, x, edge_index, ppr_matrix=ppr, training=True).shape) == (3,)
@@ -0,0 +1,90 @@
1
+ import numpy as np
2
+ from keras import ops
3
+
4
+ from k3_node.models import MaskLabel
5
+
6
+
7
+ def test_mask_label_add():
8
+ model = MaskLabel(2, 10)
9
+ assert str(model) == 'MaskLabel()'
10
+
11
+ x = ops.ones((4, 10))
12
+ y = ops.convert_to_tensor([1, 0, 1, 0])
13
+ mask = ops.convert_to_tensor([False, False, True, True])
14
+
15
+ out = model(x, y, mask)
16
+ assert ops.shape(out) == (4, 10)
17
+
18
+ # Non-masked nodes should have same features as input (plus zero embedding)
19
+ out_np = ops.convert_to_numpy(out)
20
+ x_np = ops.convert_to_numpy(x)
21
+ mask_np = ops.convert_to_numpy(mask)
22
+ # Non-masked embeddings are zero so output matches input exactly
23
+ assert np.allclose(out_np[~mask_np], x_np[~mask_np])
24
+
25
+
26
+ def test_mask_label_concat():
27
+ model = MaskLabel(2, 10, method='concat')
28
+
29
+ x = ops.ones((4, 10))
30
+ y = ops.convert_to_tensor([1, 0, 1, 0])
31
+ mask = ops.convert_to_tensor([False, False, True, True])
32
+
33
+ out = model(x, y, mask)
34
+ assert ops.shape(out) == (4, 20)
35
+
36
+ # First 10 features should be identical to x
37
+ out_np = ops.convert_to_numpy(out)
38
+ x_np = ops.convert_to_numpy(x)
39
+ assert np.allclose(out_np[:, :10], x_np)
40
+
41
+
42
+ def test_mask_label_concat_non_masked_zero():
43
+ """For concat method, non-masked nodes' label embedding part should be 0."""
44
+ model = MaskLabel(3, 8, method='concat')
45
+
46
+ x = ops.ones((6, 16))
47
+ y = ops.convert_to_tensor([0, 1, 2, 0, 1, 2])
48
+ mask = ops.convert_to_tensor([True, True, False, False, False, False])
49
+
50
+ out = model(x, y, mask)
51
+ assert ops.shape(out) == (6, 24)
52
+
53
+ out_np = ops.convert_to_numpy(out)
54
+ mask_np = ops.convert_to_numpy(mask)
55
+ # Non-masked embedding portion should be all zeros
56
+ assert np.allclose(out_np[~mask_np, 16:], 0.0)
57
+
58
+
59
+ def test_mask_label_invalid_method():
60
+ import pytest
61
+ with pytest.raises(ValueError, match="'method' must be either 'add' or 'concat'"):
62
+ MaskLabel(2, 10, method='multiply')
63
+
64
+
65
+ def test_ratio_mask():
66
+ mask = ops.convert_to_tensor([True, True, True, True, False, False, False, False])
67
+ out = MaskLabel.ratio_mask(mask, 0.5)
68
+ out_np = ops.convert_to_numpy(out)
69
+ mask_np = ops.convert_to_numpy(mask)
70
+ # True entries in original False positions should stay False
71
+ assert out_np[~mask_np].sum() == 0
72
+ # Number of remaining True entries should be <= original count
73
+ assert out_np[:4].sum() <= 4
74
+
75
+
76
+ def test_ratio_mask_zero():
77
+ """ratio=0 should mask all True entries."""
78
+ mask = ops.convert_to_tensor([True, True, True, False])
79
+ out = MaskLabel.ratio_mask(mask, 0.0)
80
+ out_np = ops.convert_to_numpy(out)
81
+ assert out_np.sum() == 0
82
+
83
+
84
+ def test_ratio_mask_one():
85
+ """ratio=1.0 should keep all True entries."""
86
+ mask = ops.convert_to_tensor([True, True, False, False])
87
+ out = MaskLabel.ratio_mask(mask, 1.0)
88
+ out_np = ops.convert_to_numpy(out)
89
+ assert out_np.sum() == 2
90
+