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.
- k3_node/__init__.py +122 -0
- k3_node/applications/__init__.py +17 -0
- k3_node/applications/bio/__init__.py +21 -0
- k3_node/applications/chemistry/__init__.py +155 -0
- k3_node/applications/materials/__init__.py +127 -0
- k3_node/applications/materials/basis.py +449 -0
- k3_node/applications/materials/chgnet.py +360 -0
- k3_node/applications/materials/core.py +351 -0
- k3_node/applications/materials/grace.py +246 -0
- k3_node/applications/materials/io.py +230 -0
- k3_node/applications/materials/m3gnet.py +462 -0
- k3_node/applications/materials/megnet.py +395 -0
- k3_node/applications/materials/qet.py +220 -0
- k3_node/applications/materials/readout.py +235 -0
- k3_node/applications/materials/so3net.py +234 -0
- k3_node/applications/materials/tensornet.py +381 -0
- k3_node/applications/materials/test_materials.py +167 -0
- k3_node/applications/materials/wrappers.py +95 -0
- k3_node/data/__init__.py +47 -0
- k3_node/data/batch.py +102 -0
- k3_node/data/collate.py +282 -0
- k3_node/data/data.py +532 -0
- k3_node/data/database.py +154 -0
- k3_node/data/dataset.py +182 -0
- k3_node/data/download.py +49 -0
- k3_node/data/extract.py +45 -0
- k3_node/data/feature_store.py +70 -0
- k3_node/data/graph_store.py +92 -0
- k3_node/data/hetero_data.py +374 -0
- k3_node/data/hypergraph_data.py +59 -0
- k3_node/data/in_memory_dataset.py +177 -0
- k3_node/data/makedirs.py +7 -0
- k3_node/data/on_disk_dataset.py +77 -0
- k3_node/data/separate.py +115 -0
- k3_node/data/storage.py +593 -0
- k3_node/data/temporal.py +154 -0
- k3_node/data/test_batch.py +67 -0
- k3_node/data/test_data.py +68 -0
- k3_node/data/test_dataset_and_stores.py +111 -0
- k3_node/data/test_hetero_data.py +33 -0
- k3_node/data/test_temporal_and_hyper.py +32 -0
- k3_node/data/view.py +43 -0
- k3_node/datasets/__init__.py +88 -0
- k3_node/datasets/actor.py +101 -0
- k3_node/datasets/airports.py +84 -0
- k3_node/datasets/amazon.py +66 -0
- k3_node/datasets/ba2motif_dataset.py +73 -0
- k3_node/datasets/ba_shapes.py +81 -0
- k3_node/datasets/bitcoin_otc.py +77 -0
- k3_node/datasets/citation_full.py +81 -0
- k3_node/datasets/coauthor.py +66 -0
- k3_node/datasets/dblp.py +106 -0
- k3_node/datasets/digits.py +63 -0
- k3_node/datasets/email_eu_core.py +60 -0
- k3_node/datasets/entities.py +158 -0
- k3_node/datasets/explainer_dataset.py +101 -0
- k3_node/datasets/facebook.py +51 -0
- k3_node/datasets/fake.py +256 -0
- k3_node/datasets/freebase.py +90 -0
- k3_node/datasets/geometric_shapes.py +69 -0
- k3_node/datasets/github.py +51 -0
- k3_node/datasets/graph_generator/__init__.py +6 -0
- k3_node/datasets/graph_generator/ba_graph.py +20 -0
- k3_node/datasets/graph_generator/base.py +29 -0
- k3_node/datasets/graph_generator/er_graph.py +21 -0
- k3_node/datasets/icews.py +58 -0
- k3_node/datasets/imdb.py +96 -0
- k3_node/datasets/jodie.py +56 -0
- k3_node/datasets/karate.py +56 -0
- k3_node/datasets/lastfm_asia.py +51 -0
- k3_node/datasets/mesh_correspondence.py +50 -0
- k3_node/datasets/molecule_net.py +148 -0
- k3_node/datasets/motif_generator/__init__.py +7 -0
- k3_node/datasets/motif_generator/base.py +29 -0
- k3_node/datasets/motif_generator/custom.py +17 -0
- k3_node/datasets/motif_generator/cycle.py +25 -0
- k3_node/datasets/motif_generator/house.py +27 -0
- k3_node/datasets/movielens.py +55 -0
- k3_node/datasets/planetoid.py +137 -0
- k3_node/datasets/polblogs.py +63 -0
- k3_node/datasets/ppi.py +189 -0
- k3_node/datasets/qm7.py +65 -0
- k3_node/datasets/qm9.py +132 -0
- k3_node/datasets/reddit.py +121 -0
- k3_node/datasets/sbm_dataset.py +165 -0
- k3_node/datasets/seal.py +74 -0
- k3_node/datasets/shape_scenes.py +92 -0
- k3_node/datasets/test_datasets.py +322 -0
- k3_node/datasets/tu_dataset.py +131 -0
- k3_node/datasets/twitch.py +66 -0
- k3_node/datasets/webkb.py +102 -0
- k3_node/datasets/wikics.py +85 -0
- k3_node/datasets/word_net.py +184 -0
- k3_node/etl/__init__.py +37 -0
- k3_node/etl/encoders.py +248 -0
- k3_node/etl/graph_builders.py +270 -0
- k3_node/etl/relational_to_graph.py +201 -0
- k3_node/etl/table_to_graph.py +244 -0
- k3_node/etl/test_etl.py +318 -0
- k3_node/export/__init__.py +15 -0
- k3_node/export/cross_backend.py +172 -0
- k3_node/export/onnx_exporter.py +190 -0
- k3_node/export/runtime.py +254 -0
- k3_node/export/tensorrt_exporter.py +201 -0
- k3_node/export/test_export.py +337 -0
- k3_node/export/tflite_exporter.py +112 -0
- k3_node/hub/__init__.py +29 -0
- k3_node/hub/dataset_hub.py +242 -0
- k3_node/hub/hub_mixin.py +599 -0
- k3_node/hub/model_card.py +133 -0
- k3_node/hub/test_hub.py +419 -0
- k3_node/io/__init__.py +22 -0
- k3_node/io/fs.py +117 -0
- k3_node/io/npz.py +45 -0
- k3_node/io/off.py +29 -0
- k3_node/io/planetoid.py +98 -0
- k3_node/io/tu.py +137 -0
- k3_node/io/txt_array.py +58 -0
- k3_node/layers/__init__.py +14 -0
- k3_node/layers/aggr/__init__.py +70 -0
- k3_node/layers/aggr/attention.py +77 -0
- k3_node/layers/aggr/base.py +403 -0
- k3_node/layers/aggr/basic.py +412 -0
- k3_node/layers/aggr/deep_sets.py +65 -0
- k3_node/layers/aggr/deepsets.py +29 -0
- k3_node/layers/aggr/equilibrium.py +107 -0
- k3_node/layers/aggr/fused.py +43 -0
- k3_node/layers/aggr/gmt.py +89 -0
- k3_node/layers/aggr/gru.py +58 -0
- k3_node/layers/aggr/lcm.py +143 -0
- k3_node/layers/aggr/lstm.py +58 -0
- k3_node/layers/aggr/mlp.py +75 -0
- k3_node/layers/aggr/multi.py +154 -0
- k3_node/layers/aggr/patch_transformer.py +137 -0
- k3_node/layers/aggr/quantile.py +125 -0
- k3_node/layers/aggr/resolver.py +68 -0
- k3_node/layers/aggr/scaler.py +133 -0
- k3_node/layers/aggr/set2set.py +87 -0
- k3_node/layers/aggr/set_transformer.py +107 -0
- k3_node/layers/aggr/sort.py +68 -0
- k3_node/layers/aggr/test_aggr.py +337 -0
- k3_node/layers/aggr/utils.py +210 -0
- k3_node/layers/aggr/variance_preserving.py +54 -0
- k3_node/layers/attention/__init__.py +5 -0
- k3_node/layers/attention/pair_attention.py +448 -0
- k3_node/layers/attention/performer.py +187 -0
- k3_node/layers/attention/polynormer.py +160 -0
- k3_node/layers/attention/qformer.py +143 -0
- k3_node/layers/attention/sgformer.py +106 -0
- k3_node/layers/attention/test_attention.py +68 -0
- k3_node/layers/attention/test_pair_attention.py +91 -0
- k3_node/layers/conv/__init__.py +149 -0
- k3_node/layers/conv/agnn_conv.py +120 -0
- k3_node/layers/conv/antisymmetric_conv.py +94 -0
- k3_node/layers/conv/appnp.py +105 -0
- k3_node/layers/conv/appnp_conv.py +157 -0
- k3_node/layers/conv/arma_conv.py +231 -0
- k3_node/layers/conv/cg_conv.py +92 -0
- k3_node/layers/conv/cheb_conv.py +137 -0
- k3_node/layers/conv/cluster_gcn_conv.py +102 -0
- k3_node/layers/conv/conv.py +100 -0
- k3_node/layers/conv/crystal_conv.py +140 -0
- k3_node/layers/conv/cugraph.py +84 -0
- k3_node/layers/conv/diffusion_conv.py +144 -0
- k3_node/layers/conv/dir_gnn_conv.py +93 -0
- k3_node/layers/conv/dna_conv.py +192 -0
- k3_node/layers/conv/edge_conv.py +107 -0
- k3_node/layers/conv/eg_conv.py +155 -0
- k3_node/layers/conv/fa_conv.py +107 -0
- k3_node/layers/conv/feast_conv.py +126 -0
- k3_node/layers/conv/film_conv.py +143 -0
- k3_node/layers/conv/gat_conv.py +244 -0
- k3_node/layers/conv/gated_graph_conv.py +136 -0
- k3_node/layers/conv/gatv2_conv.py +205 -0
- k3_node/layers/conv/gcn.py +144 -0
- k3_node/layers/conv/gcn2_conv.py +126 -0
- k3_node/layers/conv/gcn_conv.py +135 -0
- k3_node/layers/conv/gen_conv.py +163 -0
- k3_node/layers/conv/general_conv.py +218 -0
- k3_node/layers/conv/gin_conv.py +218 -0
- k3_node/layers/conv/gmm_conv.py +172 -0
- k3_node/layers/conv/gps_conv.py +153 -0
- k3_node/layers/conv/graph_attention.py +262 -0
- k3_node/layers/conv/graph_conv.py +84 -0
- k3_node/layers/conv/gravnet_conv.py +93 -0
- k3_node/layers/conv/han_conv.py +175 -0
- k3_node/layers/conv/heat_conv.py +131 -0
- k3_node/layers/conv/hetero_conv.py +128 -0
- k3_node/layers/conv/hgt_conv.py +218 -0
- k3_node/layers/conv/hypergraph_conv.py +182 -0
- k3_node/layers/conv/le_conv.py +81 -0
- k3_node/layers/conv/lg_conv.py +58 -0
- k3_node/layers/conv/meshcnn_conv.py +84 -0
- k3_node/layers/conv/message_passing.py +451 -0
- k3_node/layers/conv/mf_conv.py +95 -0
- k3_node/layers/conv/mixhop_conv.py +108 -0
- k3_node/layers/conv/nn_conv.py +110 -0
- k3_node/layers/conv/pan_conv.py +100 -0
- k3_node/layers/conv/pdn_conv.py +109 -0
- k3_node/layers/conv/pna_conv.py +177 -0
- k3_node/layers/conv/point_conv.py +101 -0
- k3_node/layers/conv/point_gnn_conv.py +90 -0
- k3_node/layers/conv/point_transformer_conv.py +132 -0
- k3_node/layers/conv/ppf_conv.py +135 -0
- k3_node/layers/conv/ppnp.py +89 -0
- k3_node/layers/conv/res_gated_graph_conv.py +126 -0
- k3_node/layers/conv/rgat_conv.py +251 -0
- k3_node/layers/conv/rgcn_conv.py +321 -0
- k3_node/layers/conv/sage_conv.py +154 -0
- k3_node/layers/conv/sg_conv.py +96 -0
- k3_node/layers/conv/signed_conv.py +100 -0
- k3_node/layers/conv/simple_conv.py +75 -0
- k3_node/layers/conv/spline_conv.py +182 -0
- k3_node/layers/conv/ssg_conv.py +101 -0
- k3_node/layers/conv/supergat_conv.py +195 -0
- k3_node/layers/conv/tag_conv.py +98 -0
- k3_node/layers/conv/test_backend_consistency.py +164 -0
- k3_node/layers/conv/test_conv.py +176 -0
- k3_node/layers/conv/test_conv_pyg.py +566 -0
- k3_node/layers/conv/transformer_conv.py +168 -0
- k3_node/layers/conv/utils.py +403 -0
- k3_node/layers/conv/wl_conv.py +151 -0
- k3_node/layers/conv/x_conv.py +187 -0
- k3_node/layers/dense/__init__.py +40 -0
- k3_node/layers/dense/dense_gat_conv.py +149 -0
- k3_node/layers/dense/dense_gcn_conv.py +117 -0
- k3_node/layers/dense/dense_gin_conv.py +88 -0
- k3_node/layers/dense/dense_graph_conv.py +95 -0
- k3_node/layers/dense/dense_sage_conv.py +85 -0
- k3_node/layers/dense/diff_pool.py +76 -0
- k3_node/layers/dense/dmon_pool.py +223 -0
- k3_node/layers/dense/linear.py +327 -0
- k3_node/layers/dense/mincut_pool.py +92 -0
- k3_node/layers/dense/test_dense.py +377 -0
- k3_node/layers/functional/__init__.py +13 -0
- k3_node/layers/functional/bro.py +49 -0
- k3_node/layers/functional/edge_dropout.py +55 -0
- k3_node/layers/functional/gini.py +44 -0
- k3_node/layers/functional/test_functional.py +34 -0
- k3_node/layers/kge/__init__.py +17 -0
- k3_node/layers/kge/base.py +255 -0
- k3_node/layers/kge/complex.py +98 -0
- k3_node/layers/kge/distmult.py +79 -0
- k3_node/layers/kge/loader.py +50 -0
- k3_node/layers/kge/rotate.py +103 -0
- k3_node/layers/kge/test_kge.py +76 -0
- k3_node/layers/kge/transe.py +96 -0
- k3_node/layers/norm/__init__.py +23 -0
- k3_node/layers/norm/batch_norm.py +328 -0
- k3_node/layers/norm/diff_group_norm.py +141 -0
- k3_node/layers/norm/graph_norm.py +105 -0
- k3_node/layers/norm/graph_size_norm.py +57 -0
- k3_node/layers/norm/instance_norm.py +163 -0
- k3_node/layers/norm/layer_norm.py +245 -0
- k3_node/layers/norm/mean_subtraction_norm.py +57 -0
- k3_node/layers/norm/msg_norm.py +58 -0
- k3_node/layers/norm/pair_norm.py +94 -0
- k3_node/layers/norm/test_norm.py +275 -0
- k3_node/layers/pool/__init__.py +83 -0
- k3_node/layers/pool/approx_knn.py +101 -0
- k3_node/layers/pool/asap.py +173 -0
- k3_node/layers/pool/avg_pool.py +165 -0
- k3_node/layers/pool/cluster_pool.py +168 -0
- k3_node/layers/pool/connect/__init__.py +10 -0
- k3_node/layers/pool/connect/base.py +103 -0
- k3_node/layers/pool/connect/filter_edges.py +113 -0
- k3_node/layers/pool/consecutive.py +30 -0
- k3_node/layers/pool/decimation.py +48 -0
- k3_node/layers/pool/edge_pool.py +189 -0
- k3_node/layers/pool/glob.py +139 -0
- k3_node/layers/pool/graclus.py +66 -0
- k3_node/layers/pool/knn.py +253 -0
- k3_node/layers/pool/max_pool.py +159 -0
- k3_node/layers/pool/mem_pool.py +145 -0
- k3_node/layers/pool/pan_pool.py +144 -0
- k3_node/layers/pool/point_cloud.py +212 -0
- k3_node/layers/pool/pool.py +119 -0
- k3_node/layers/pool/sag_pool.py +174 -0
- k3_node/layers/pool/select/__init__.py +10 -0
- k3_node/layers/pool/select/base.py +112 -0
- k3_node/layers/pool/select/topk.py +206 -0
- k3_node/layers/pool/test_pool.py +456 -0
- k3_node/layers/pool/topk_pool.py +103 -0
- k3_node/layers/pool/voxel_grid.py +70 -0
- k3_node/layers/unpool/__init__.py +9 -0
- k3_node/layers/unpool/knn_interpolate.py +57 -0
- k3_node/layers/unpool/test_unpool.py +31 -0
- k3_node/loader/__init__.py +62 -0
- k3_node/loader/base.py +69 -0
- k3_node/loader/cache.py +68 -0
- k3_node/loader/cluster.py +127 -0
- k3_node/loader/data_list_loader.py +45 -0
- k3_node/loader/dataloader.py +117 -0
- k3_node/loader/dense_data_loader.py +62 -0
- k3_node/loader/dynamic_batch_sampler.py +93 -0
- k3_node/loader/graph_saint.py +188 -0
- k3_node/loader/hgt_loader.py +90 -0
- k3_node/loader/imbalanced_sampler.py +87 -0
- k3_node/loader/keras_dataset.py +334 -0
- k3_node/loader/link_loader.py +179 -0
- k3_node/loader/link_neighbor_loader.py +202 -0
- k3_node/loader/mixin.py +190 -0
- k3_node/loader/neighbor_loader.py +159 -0
- k3_node/loader/neighbor_sampler.py +167 -0
- k3_node/loader/node_loader.py +185 -0
- k3_node/loader/prefetch.py +115 -0
- k3_node/loader/random_node_loader.py +89 -0
- k3_node/loader/sampler_utils.py +499 -0
- k3_node/loader/shadow.py +115 -0
- k3_node/loader/temporal_dataloader.py +98 -0
- k3_node/loader/test_dataloader.py +113 -0
- k3_node/loader/test_keras_dataset.py +221 -0
- k3_node/loader/test_neighbor_loader.py +122 -0
- k3_node/loader/test_sampler_utils.py +82 -0
- k3_node/loader/test_samplers.py +96 -0
- k3_node/loader/test_subgraph_loaders.py +89 -0
- k3_node/loader/utils.py +232 -0
- k3_node/loader/zip_loader.py +88 -0
- k3_node/metrics.py +94 -0
- k3_node/models/__init__.py +424 -0
- k3_node/models/attentive_fp.py +232 -0
- k3_node/models/attract_repel.py +108 -0
- k3_node/models/autoencoder.py +318 -0
- k3_node/models/basic_gnn.py +443 -0
- k3_node/models/bio/__init__.py +4 -0
- k3_node/models/captum.py +52 -0
- k3_node/models/chemistry/__init__.py +4 -0
- k3_node/models/correct_and_smooth.py +146 -0
- k3_node/models/deep_graph_infomax.py +113 -0
- k3_node/models/deepgcn.py +121 -0
- k3_node/models/dimenet.py +737 -0
- k3_node/models/dimenet_utils.py +153 -0
- k3_node/models/gnnff.py +263 -0
- k3_node/models/gps_model.py +1122 -0
- k3_node/models/gpse.py +638 -0
- k3_node/models/graph_unet.py +199 -0
- k3_node/models/graphmae2.py +954 -0
- k3_node/models/graphormer.py +1258 -0
- k3_node/models/graphormer_3d.py +868 -0
- k3_node/models/grover.py +1066 -0
- k3_node/models/jumping_knowledge.py +200 -0
- k3_node/models/label_prop.py +110 -0
- k3_node/models/lightgcn.py +171 -0
- k3_node/models/linkx.py +181 -0
- k3_node/models/lpformer.py +404 -0
- k3_node/models/mask_label.py +114 -0
- k3_node/models/materials/__init__.py +33 -0
- k3_node/models/meta.py +133 -0
- k3_node/models/metapath2vec.py +234 -0
- k3_node/models/mlp.py +264 -0
- k3_node/models/mole_bert.py +379 -0
- k3_node/models/neural_fingerprint.py +95 -0
- k3_node/models/node2vec.py +213 -0
- k3_node/models/pmlp.py +157 -0
- k3_node/models/polynormer.py +229 -0
- k3_node/models/rect.py +93 -0
- k3_node/models/renet.py +221 -0
- k3_node/models/rev_gnn.py +128 -0
- k3_node/models/schnet.py +484 -0
- k3_node/models/sgformer.py +195 -0
- k3_node/models/signed_gcn.py +185 -0
- k3_node/models/test_attentive_fp.py +32 -0
- k3_node/models/test_attract_repel.py +33 -0
- k3_node/models/test_autoencoder.py +119 -0
- k3_node/models/test_basic_gnn.py +102 -0
- k3_node/models/test_correct_and_smooth.py +40 -0
- k3_node/models/test_deep_graph_infomax.py +68 -0
- k3_node/models/test_deepgcn.py +21 -0
- k3_node/models/test_dimenet.py +86 -0
- k3_node/models/test_domain_apis.py +138 -0
- k3_node/models/test_gnnff.py +24 -0
- k3_node/models/test_gps_model.py +271 -0
- k3_node/models/test_gpse.py +34 -0
- k3_node/models/test_graph_unet.py +26 -0
- k3_node/models/test_graphmae2.py +226 -0
- k3_node/models/test_graphormer.py +233 -0
- k3_node/models/test_graphormer3d.py +163 -0
- k3_node/models/test_grover.py +287 -0
- k3_node/models/test_jumping_knowledge.py +129 -0
- k3_node/models/test_label_prop.py +37 -0
- k3_node/models/test_lightgcn.py +38 -0
- k3_node/models/test_linkx.py +31 -0
- k3_node/models/test_lpformer.py +22 -0
- k3_node/models/test_mask_label.py +90 -0
- k3_node/models/test_meta.py +159 -0
- k3_node/models/test_metapath2vec.py +45 -0
- k3_node/models/test_mlp.py +62 -0
- k3_node/models/test_mole_bert.py +164 -0
- k3_node/models/test_neural_fingerprint.py +13 -0
- k3_node/models/test_node2vec.py +57 -0
- k3_node/models/test_pmlp.py +81 -0
- k3_node/models/test_polynormer.py +104 -0
- k3_node/models/test_rect.py +23 -0
- k3_node/models/test_renet.py +32 -0
- k3_node/models/test_rev_gnn.py +24 -0
- k3_node/models/test_schnet.py +43 -0
- k3_node/models/test_sgformer.py +48 -0
- k3_node/models/test_signed_gcn.py +28 -0
- k3_node/models/test_tgn.py +77 -0
- k3_node/models/test_unimol.py +179 -0
- k3_node/models/test_unimol2.py +114 -0
- k3_node/models/test_unimol_plus.py +131 -0
- k3_node/models/test_visnet.py +44 -0
- k3_node/models/tgn.py +382 -0
- k3_node/models/unimol.py +1156 -0
- k3_node/models/unimol2.py +616 -0
- k3_node/models/unimol_docking_v2.py +301 -0
- k3_node/models/unimol_plus.py +456 -0
- k3_node/models/utils.py +97 -0
- k3_node/models/visnet.py +759 -0
- k3_node/ops/__init__.py +4 -0
- k3_node/ops/conv.py +56 -0
- k3_node/ops/creation.py +43 -0
- k3_node/ops/graph.py +27 -0
- k3_node/ops/host.py +41 -0
- k3_node/ops/matmul.py +49 -0
- k3_node/ops/numpy.py +24 -0
- k3_node/ops/segment.py +54 -0
- k3_node/ops/sparse.py +51 -0
- k3_node/rag/__init__.py +49 -0
- k3_node/rag/encoders.py +312 -0
- k3_node/rag/pipeline.py +192 -0
- k3_node/rag/projector.py +184 -0
- k3_node/rag/subgraph.py +270 -0
- k3_node/rag/test_rag.py +347 -0
- k3_node/rag/verbalizer.py +162 -0
- k3_node/tasks/__init__.py +19 -0
- k3_node/tasks/backbone_resolver.py +125 -0
- k3_node/tasks/base.py +67 -0
- k3_node/tasks/graph_classification.py +270 -0
- k3_node/tasks/graph_regression.py +228 -0
- k3_node/tasks/link_prediction.py +306 -0
- k3_node/tasks/node_classification.py +194 -0
- k3_node/tasks/node_regression.py +138 -0
- k3_node/tasks/test_tasks.py +319 -0
- k3_node/test_docstring_examples.py +106 -0
- k3_node/test_training_forwarding.py +116 -0
- k3_node/training.py +115 -0
- k3_node/transforms/__init__.py +166 -0
- k3_node/transforms/base_transform.py +32 -0
- k3_node/transforms/compose.py +58 -0
- k3_node/transforms/general.py +676 -0
- k3_node/transforms/graph.py +1070 -0
- k3_node/transforms/spatial.py +797 -0
- k3_node/transforms/test_random_link_split.py +45 -0
- k3_node/transforms/test_spatial_transforms.py +65 -0
- k3_node/transforms/test_transforms.py +253 -0
- k3_node/transforms/utils.py +102 -0
- k3_node/utils/__init__.py +5 -0
- k3_node/utils/backend_import.py +12 -0
- k3_node/utils/graph.py +286 -0
- k3_node/utils/keras.py +94 -0
- k3_node/utils/random.py +103 -0
- k3_node/utils/smiles.py +235 -0
- k3_node-1.0.0.dist-info/METADATA +284 -0
- k3_node-1.0.0.dist-info/RECORD +459 -0
- k3_node-1.0.0.dist-info/WHEEL +5 -0
- k3_node-1.0.0.dist-info/licenses/LICENSE +21 -0
- k3_node-1.0.0.dist-info/top_level.txt +1 -0
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import numpy as np
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import keras
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from keras import ops
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from k3_node.layers.conv.message_passing import MessagePassing
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from k3_node.layers.conv.utils import scatter
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class WLConv(keras.layers.Layer):
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r"""The Weisfeiler Lehman (WL) operator from the `"A Reduction of a Graph
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to a Canonical Form and an Algebra Arising During this Reduction"
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<https://www.iti.zcu.cz/wl2018/pdf/wl_paper_translation.pdf>`_ paper.
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Args:
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**kwargs: Additional layer arguments.
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Example:
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```python
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import numpy as np
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from k3_node.layers import WLConv
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colors = np.array([0, 1, 0, 1]) # discrete node colors (labels)
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edge_index = np.array([[0, 1, 2, 3], [1, 2, 3, 0]])
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layer = WLConv()
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new_colors = layer(colors, edge_index) # one Weisfeiler-Lehman refinement step
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print(tuple(new_colors.shape)) # (4,)
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print(tuple(layer.histogram(new_colors).shape)) # (1, 2): color histogram per graph
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```
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"""
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def __init__(self, **kwargs):
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super().__init__(**kwargs)
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self.hashmap = {}
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def reset_parameters(self):
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self.hashmap = {}
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def build(self, input_shape=None):
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self.built = True
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def call(self, x, edge_index=None, num_nodes=None):
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if edge_index is None:
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if isinstance(x, (tuple, list)) and len(x) >= 2:
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x, edge_index = x[0], x[1]
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elif ops.shape(x)[0] == 2:
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edge_index = x
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if num_nodes is None:
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num_nodes = int(ops.max(edge_index)) + 1
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x = ops.zeros((num_nodes,), dtype="int64")
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if len(ops.shape(x)) > 1:
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x = ops.argmax(x, axis=-1)
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x_np = ops.convert_to_numpy(x)
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edge_index_np = ops.convert_to_numpy(edge_index)
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num_nodes = len(x_np)
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row, col = edge_index_np[0], edge_index_np[1]
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# Group neighbors by target node col
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neighbors_dict = {i: [] for i in range(num_nodes)}
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for src, dst in zip(row, col):
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neighbors_dict[int(dst)].append(int(x_np[src]))
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out = []
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for i in range(num_nodes):
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node_color = int(x_np[i])
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sorted_neighs = sorted(neighbors_dict[i])
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key = hash((node_color, tuple(sorted_neighs)))
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if key not in self.hashmap:
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self.hashmap[key] = len(self.hashmap)
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out.append(self.hashmap[key])
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return ops.convert_to_tensor(np.array(out, dtype=np.int64))
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def histogram(self, x, batch=None, norm: bool = False):
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x_np = ops.convert_to_numpy(x)
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num_nodes = len(x_np)
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if batch is None:
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batch_np = np.zeros(num_nodes, dtype=np.int64)
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else:
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batch_np = ops.convert_to_numpy(batch).astype(np.int64)
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num_colors = len(self.hashmap)
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batch_size = int(np.max(batch_np)) + 1 if len(batch_np) > 0 else 1
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hist = np.zeros((batch_size, num_colors), dtype=np.float32)
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for b, c in zip(batch_np, x_np):
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hist[b, c] += 1.0
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if norm:
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norms = np.linalg.norm(hist, axis=-1, keepdims=True)
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hist = hist / np.maximum(norms, 1e-12)
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return ops.convert_to_tensor(hist)
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class WLConvContinuous(MessagePassing):
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r"""The Weisfeiler Lehman operator from the `"Wasserstein
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Weisfeiler-Lehman Graph Kernels" <https://arxiv.org/abs/1906.01277>`_ paper.
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Args:
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**kwargs: Additional arguments of :class:`MessagePassing`.
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Example:
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```python
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import numpy as np
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from k3_node.layers import WLConvContinuous
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x = np.random.rand(10, 8).astype("float32") # 10 nodes with 8 features each
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edge_index = np.random.randint(0, 10, size=(2, 30)) # 30 random edges
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layer = WLConvContinuous()
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out = layer(x, edge_index)
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print(tuple(out.shape)) # (10, 8)
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```
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"""
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def __init__(self, **kwargs):
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kwargs.setdefault("aggr", "add")
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super().__init__(**kwargs)
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def build(self, input_shape=None):
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self.built = True
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def call(self, x, edge_index, edge_weight=None):
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if isinstance(x, (tuple, list)):
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x_src, x_dst = x[0], x[1]
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else:
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x_src = x_dst = x
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out = self.propagate(edge_index, x=(x_src, x_dst), edge_weight=edge_weight)
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dst_index = edge_index[1]
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if edge_weight is None:
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edge_weight = ops.ones((ops.shape(dst_index)[0],), dtype=out.dtype)
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num_nodes = ops.shape(out)[0]
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deg = scatter(edge_weight, dst_index, dim=0, dim_size=num_nodes, reduce="sum")
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deg_inv = ops.where(ops.equal(deg, 0), 0.0, 1.0 / deg)
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out = ops.expand_dims(deg_inv, axis=-1) * out
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if x_dst is not None:
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out = 0.5 * (x_dst + out)
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return out
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def message(self, x_j, edge_weight=None):
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if edge_weight is not None:
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return ops.expand_dims(edge_weight, axis=-1) * x_j
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return x_j
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from math import ceil
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from typing import Optional
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import keras
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from keras import ops
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from k3_node.layers.conv.message_passing import MessagePassing
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from k3_node.ops.creation import repeat
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class GroupedConv1dFlat(keras.layers.Layer):
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"""A 1D convolution over input of shape (N, C, K) with kernel_size=K and groups=C."""
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def __init__(self, in_channels: int, out_channels: int, kernel_size: int, **kwargs):
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super().__init__(**kwargs)
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self.in_channels = in_channels
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self.out_channels = out_channels
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self.kernel_size = kernel_size
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self.multiplier = out_channels // in_channels
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def build(self, input_shape=None):
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self.kernel = self.add_weight(
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shape=(self.in_channels, self.multiplier, self.kernel_size),
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initializer="glorot_uniform",
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trainable=True,
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name="kernel",
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)
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self.bias = self.add_weight(
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shape=(self.out_channels,),
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initializer="zeros",
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trainable=True,
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name="bias",
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)
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super().build(input_shape)
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def call(self, x):
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# x: (N, C, K)
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out = ops.einsum("nck,cmk->ncm", x, self.kernel)
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out = ops.reshape(out, (-1, self.out_channels)) + self.bias
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return out
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class XConv(keras.layers.Layer):
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r"""The convolutional operator on :math:`\mathcal{X}`-transformed points
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from the `"PointCNN: Convolution On X-Transformed Points"
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<https://arxiv.org/abs/1801.07791>`_ paper.
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Args:
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in_channels (int): Size of each input sample.
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out_channels (int): Size of each output sample.
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dim (int): Point cloud dimensionality.
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kernel_size (int): Size of the convolving kernel.
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hidden_channels (int, optional): Dimensionality of lifted points.
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dilation (int, optional): Dilation factor. (default: :obj:`1`)
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bias (bool, optional): Whether to learn an additive bias. (default: :obj:`True`)
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num_workers (int, optional): Kept for PyG compatibility.
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Example:
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```python
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import numpy as np
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from k3_node.layers import XConv
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x = np.random.rand(10, 8).astype("float32") # 10 nodes with 8 features each
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edge_index = np.random.randint(0, 10, size=(2, 30)) # 30 random edges
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pos = np.random.rand(10, 3).astype("float32") # 3D node positions
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layer = XConv(in_channels=8, out_channels=16, dim=3, kernel_size=2)
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out = layer(x, pos) # neighborhoods are built from `pos`
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print(tuple(out.shape)) # (10, 16)
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```
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"""
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def __init__(
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self,
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in_channels: int,
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out_channels: int,
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dim: int,
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kernel_size: int,
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hidden_channels: Optional[int] = None,
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dilation: int = 1,
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bias: bool = True,
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num_workers: int = 1,
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**kwargs,
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):
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super().__init__(**kwargs)
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self.in_channels = in_channels
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86
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if hidden_channels is None:
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hidden_channels = in_channels // 4
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88
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+
assert hidden_channels > 0
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self.hidden_channels = hidden_channels
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90
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+
self.out_channels = out_channels
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91
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+
self.dim = dim
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92
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self.kernel_size = kernel_size
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93
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+
self.dilation = dilation
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94
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+
self.use_bias = bias
|
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95
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+
|
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96
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+
C_in, C_delta, C_out = in_channels, hidden_channels, out_channels
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97
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+
D, K = dim, kernel_size
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98
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+
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99
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+
# mlp1
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100
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+
self.mlp1_l1 = keras.layers.Dense(C_delta)
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101
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+
self.mlp1_bn1 = keras.layers.BatchNormalization(axis=-1, momentum=0.9, epsilon=1e-5)
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102
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+
self.mlp1_l2 = keras.layers.Dense(C_delta)
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103
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+
self.mlp1_bn2 = keras.layers.BatchNormalization(axis=-1, momentum=0.9, epsilon=1e-5)
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104
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+
|
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105
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+
# mlp2
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|
106
|
+
self.mlp2_l1 = keras.layers.Dense(K * K)
|
|
107
|
+
self.mlp2_bn1 = keras.layers.BatchNormalization(axis=-1, momentum=0.9, epsilon=1e-5)
|
|
108
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+
self.mlp2_conv1 = GroupedConv1dFlat(K, K * K, K)
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109
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self.mlp2_bn2 = keras.layers.BatchNormalization(axis=-1, momentum=0.9, epsilon=1e-5)
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self.mlp2_conv2 = GroupedConv1dFlat(K, K * K, K)
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self.mlp2_bn3 = keras.layers.BatchNormalization(axis=-1, momentum=0.9, epsilon=1e-5)
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depth_multiplier = int(ceil(C_out / C_total))
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self.conv_op = GroupedConv1dFlat(C_total, C_total * depth_multiplier, K)
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self.conv_lin = keras.layers.Dense(C_out, use_bias=bias)
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def _mlp1(self, pos, training=None):
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return h
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def _mlp2(self, pos_flat, training=None):
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K = self.kernel_size
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h = ops.reshape(h, (-1, K, K))
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h = ops.reshape(h, (-1, K, K))
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return ops.reshape(h, (-1, K, K))
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def call(self, x, pos, batch=None, training=None):
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# Pairwise distance KNN
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mask = ops.equal(ops.expand_dims(batch, axis=1), ops.expand_dims(batch, axis=0))
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dist = ops.where(mask, dist, 1e10)
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if self.dilation > 1:
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top_k = top_k[:, ::self.dilation]
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row = repeat(ops.arange(N), K)
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col = ops.reshape(top_k, (-1,))
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x_star = self._mlp1(pos_diff, training=training)
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x_star = ops.reshape(x_star, (N, K, self.hidden_channels))
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if x is not None:
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if len(ops.shape(x)) == 1:
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x = ops.expand_dims(x, axis=-1)
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x_col = ops.take(x, col, axis=0)
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x_col = ops.reshape(x_col, (N, K, self.in_channels))
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x_star = ops.concatenate([x_star, x_col], axis=-1)
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x_star = ops.transpose(x_star, (0, 2, 1)) # (N, C_total, K)
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transform_matrix = self._mlp2(ops.reshape(pos_diff, (N, K * D)), training=training) # (N, K, K)
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x_transformed = ops.matmul(x_star, transform_matrix) # (N, C_total, K)
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out = self._conv(x_transformed)
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return out
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@@ -0,0 +1,40 @@
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r"""Dense neural network module package.
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+
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3
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This package provides modules applicable for operating on dense tensor
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representations.
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"""
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from .linear import Linear, HeteroLinear, HeteroDictLinear
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from .dense_gat_conv import DenseGATConv
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from .dense_sage_conv import DenseSAGEConv
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from .dense_gcn_conv import DenseGCNConv
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+
from .dense_graph_conv import DenseGraphConv
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+
from .dense_gin_conv import DenseGINConv
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+
from .diff_pool import dense_diff_pool
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+
diff_pool = dense_diff_pool
|
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15
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+
from .mincut_pool import dense_mincut_pool
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+
mincut_pool = dense_mincut_pool
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+
from .dmon_pool import DMoNPooling, dense_dmon_pool, dmon_pool
|
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+
|
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19
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+
__all__ = [
|
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"Linear",
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21
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+
"HeteroLinear",
|
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22
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+
"HeteroDictLinear",
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23
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+
"DenseGCNConv",
|
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24
|
+
"DenseGINConv",
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|
+
"DenseGraphConv",
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26
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+
"DenseSAGEConv",
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+
"DenseGATConv",
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+
"dense_diff_pool",
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|
+
"diff_pool",
|
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+
"dense_mincut_pool",
|
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31
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+
"mincut_pool",
|
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32
|
+
"DMoNPooling",
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33
|
+
"dense_dmon_pool",
|
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34
|
+
"dmon_pool",
|
|
35
|
+
]
|
|
36
|
+
|
|
37
|
+
lin_classes = __all__[:3]
|
|
38
|
+
conv_classes = __all__[3:8]
|
|
39
|
+
pool_classes = __all__[8:]
|
|
40
|
+
|
|
@@ -0,0 +1,149 @@
|
|
|
1
|
+
from typing import Optional
|
|
2
|
+
from keras import initializers, layers, ops
|
|
3
|
+
from .linear import Linear
|
|
4
|
+
|
|
5
|
+
|
|
6
|
+
class DenseGATConv(layers.Layer):
|
|
7
|
+
r"""See :class:`torch_geometric.nn.conv.GATConv`.
|
|
8
|
+
|
|
9
|
+
Example:
|
|
10
|
+
```python
|
|
11
|
+
import numpy as np
|
|
12
|
+
from k3_node.layers import DenseGATConv
|
|
13
|
+
|
|
14
|
+
x = np.random.rand(2, 10, 8).astype("float32") # batch of 2 graphs, 10 nodes, 8 features
|
|
15
|
+
adj = (np.random.rand(2, 10, 10) > 0.7).astype("float32") # dense adjacency matrices
|
|
16
|
+
|
|
17
|
+
layer = DenseGATConv(in_channels=8, out_channels=16, heads=2)
|
|
18
|
+
out = layer(x, adj)
|
|
19
|
+
print(tuple(out.shape)) # (2, 10, 32)
|
|
20
|
+
```
|
|
21
|
+
"""
|
|
22
|
+
def __init__(
|
|
23
|
+
self,
|
|
24
|
+
in_channels: int,
|
|
25
|
+
out_channels: int,
|
|
26
|
+
heads: int = 1,
|
|
27
|
+
concat: bool = True,
|
|
28
|
+
negative_slope: float = 0.2,
|
|
29
|
+
dropout: float = 0.0,
|
|
30
|
+
bias: bool = True,
|
|
31
|
+
**kwargs
|
|
32
|
+
):
|
|
33
|
+
super().__init__(**kwargs)
|
|
34
|
+
self.in_channels = in_channels
|
|
35
|
+
self.out_channels = out_channels
|
|
36
|
+
self.heads = heads
|
|
37
|
+
self.concat = concat
|
|
38
|
+
self.negative_slope = negative_slope
|
|
39
|
+
self.dropout = dropout
|
|
40
|
+
self.use_bias = bias
|
|
41
|
+
|
|
42
|
+
self.lin = Linear(in_channels, heads * out_channels, bias=False,
|
|
43
|
+
weight_initializer='glorot', name="lin")
|
|
44
|
+
|
|
45
|
+
self.att_src = self.add_weight(
|
|
46
|
+
shape=(1, 1, heads, out_channels),
|
|
47
|
+
initializer="glorot_uniform",
|
|
48
|
+
trainable=True,
|
|
49
|
+
name="att_src",
|
|
50
|
+
)
|
|
51
|
+
self.att_dst = self.add_weight(
|
|
52
|
+
shape=(1, 1, heads, out_channels),
|
|
53
|
+
initializer="glorot_uniform",
|
|
54
|
+
trainable=True,
|
|
55
|
+
name="att_dst",
|
|
56
|
+
)
|
|
57
|
+
|
|
58
|
+
if bias and concat:
|
|
59
|
+
self.bias = self.add_weight(
|
|
60
|
+
shape=(heads * out_channels,),
|
|
61
|
+
initializer="zeros",
|
|
62
|
+
trainable=True,
|
|
63
|
+
name="bias",
|
|
64
|
+
)
|
|
65
|
+
elif bias and not concat:
|
|
66
|
+
self.bias = self.add_weight(
|
|
67
|
+
shape=(out_channels,),
|
|
68
|
+
initializer="zeros",
|
|
69
|
+
trainable=True,
|
|
70
|
+
name="bias",
|
|
71
|
+
)
|
|
72
|
+
else:
|
|
73
|
+
self.bias = None
|
|
74
|
+
|
|
75
|
+
def reset_parameters(self):
|
|
76
|
+
self.lin.reset_parameters()
|
|
77
|
+
# A new initializer per tensor: a reused unseeded Keras 3 initializer returns the same values on every call.
|
|
78
|
+
glorot = lambda shape, dtype=None: initializers.GlorotUniform()(shape, dtype=dtype)
|
|
79
|
+
self.att_src.assign(glorot(self.att_src.shape, dtype=self.att_src.dtype))
|
|
80
|
+
self.att_dst.assign(glorot(self.att_dst.shape, dtype=self.att_dst.dtype))
|
|
81
|
+
if self.bias is not None:
|
|
82
|
+
self.bias.assign(ops.zeros(self.bias.shape, dtype=self.bias.dtype))
|
|
83
|
+
|
|
84
|
+
def build(self, input_shape):
|
|
85
|
+
if isinstance(input_shape, (tuple, list)):
|
|
86
|
+
x_shape = input_shape[0]
|
|
87
|
+
else:
|
|
88
|
+
x_shape = input_shape
|
|
89
|
+
self.lin.build(x_shape)
|
|
90
|
+
super().build(input_shape)
|
|
91
|
+
|
|
92
|
+
def call(self, x, adj, mask: Optional[any] = None, add_loop: bool = True, training=None):
|
|
93
|
+
is_2d_x = (len(ops.shape(x)) == 2)
|
|
94
|
+
if is_2d_x:
|
|
95
|
+
x = ops.expand_dims(x, axis=0)
|
|
96
|
+
if len(ops.shape(adj)) == 2:
|
|
97
|
+
adj = ops.expand_dims(adj, axis=0)
|
|
98
|
+
|
|
99
|
+
H, C = self.heads, self.out_channels
|
|
100
|
+
B = ops.shape(x)[0]
|
|
101
|
+
N = ops.shape(x)[1]
|
|
102
|
+
|
|
103
|
+
if add_loop:
|
|
104
|
+
eye = ops.expand_dims(ops.eye(N, dtype=adj.dtype), axis=0)
|
|
105
|
+
adj = adj * (1.0 - eye) + eye
|
|
106
|
+
|
|
107
|
+
x_proj = ops.reshape(self.lin(x), (B, N, H, C))
|
|
108
|
+
|
|
109
|
+
alpha_src = ops.sum(x_proj * self.att_src, axis=-1) # [B, N, H]
|
|
110
|
+
alpha_dst = ops.sum(x_proj * self.att_dst, axis=-1) # [B, N, H]
|
|
111
|
+
|
|
112
|
+
alpha = ops.expand_dims(alpha_src, axis=1) + ops.expand_dims(alpha_dst, axis=2) # [B, N, N, H]
|
|
113
|
+
alpha = ops.leaky_relu(alpha, negative_slope=self.negative_slope)
|
|
114
|
+
alpha = ops.where(ops.expand_dims(adj, axis=-1) != 0, alpha, -1e9)
|
|
115
|
+
alpha = ops.softmax(alpha, axis=2)
|
|
116
|
+
|
|
117
|
+
# Transpose to [B, H, N, N] and [B, H, N, C]
|
|
118
|
+
alpha_perm = ops.transpose(alpha, (0, 3, 1, 2))
|
|
119
|
+
x_perm = ops.transpose(x_proj, (0, 2, 1, 3))
|
|
120
|
+
out = ops.matmul(alpha_perm, x_perm) # [B, H, N, C]
|
|
121
|
+
out = ops.transpose(out, (0, 2, 1, 3)) # [B, N, H, C]
|
|
122
|
+
|
|
123
|
+
if self.concat:
|
|
124
|
+
out = ops.reshape(out, (B, N, H * C))
|
|
125
|
+
else:
|
|
126
|
+
out = ops.mean(out, axis=2)
|
|
127
|
+
|
|
128
|
+
if self.bias is not None:
|
|
129
|
+
out = out + self.bias
|
|
130
|
+
|
|
131
|
+
if mask is not None:
|
|
132
|
+
out = out * ops.cast(ops.reshape(mask, (-1, N, 1)), x.dtype)
|
|
133
|
+
|
|
134
|
+
if is_2d_x and ops.shape(out)[0] == 1:
|
|
135
|
+
out = ops.squeeze(out, axis=0)
|
|
136
|
+
|
|
137
|
+
return out
|
|
138
|
+
|
|
139
|
+
def compute_output_shape(self, input_shape):
|
|
140
|
+
if isinstance(input_shape, (tuple, list)):
|
|
141
|
+
x_shape = input_shape[0]
|
|
142
|
+
else:
|
|
143
|
+
x_shape = input_shape
|
|
144
|
+
out_dim = self.heads * self.out_channels if self.concat else self.out_channels
|
|
145
|
+
return (*x_shape[:-1], out_dim)
|
|
146
|
+
|
|
147
|
+
def __repr__(self) -> str:
|
|
148
|
+
return (f'{self.__class__.__name__}({self.in_channels}, '
|
|
149
|
+
f'{self.out_channels}, heads={self.heads})')
|
|
@@ -0,0 +1,117 @@
|
|
|
1
|
+
from keras import layers, ops
|
|
2
|
+
from .linear import Linear
|
|
3
|
+
|
|
4
|
+
|
|
5
|
+
class DenseGCNConv(layers.Layer):
|
|
6
|
+
r"""Applies the dense convolutional operator from the `"Semi-supervised
|
|
7
|
+
Classification with Graph Convolutional Networks"
|
|
8
|
+
<https://arxiv.org/abs/1609.02907>`_ paper.
|
|
9
|
+
|
|
10
|
+
.. math::
|
|
11
|
+
\mathbf{X}^{\prime} = \mathbf{\tilde{D}}^{-1/2} \mathbf{\tilde{A}}
|
|
12
|
+
\mathbf{\tilde{D}}^{-1/2} \mathbf{X} \mathbf{\Theta}
|
|
13
|
+
|
|
14
|
+
Args:
|
|
15
|
+
in_channels (int): Size of each input sample.
|
|
16
|
+
out_channels (int): Size of each output sample.
|
|
17
|
+
improved (bool, optional): If set to :obj:`True`, the layer computes
|
|
18
|
+
:math:`\mathbf{\tilde{A}} = \mathbf{A} + 2 \mathbf{I}`.
|
|
19
|
+
(default: :obj:`False`)
|
|
20
|
+
bias (bool, optional): If set to :obj:`False`, the layer will not learn
|
|
21
|
+
an additive bias. (default: :obj:`True`)
|
|
22
|
+
|
|
23
|
+
Example:
|
|
24
|
+
```python
|
|
25
|
+
import numpy as np
|
|
26
|
+
from k3_node.layers import DenseGCNConv
|
|
27
|
+
|
|
28
|
+
x = np.random.rand(2, 10, 8).astype("float32") # batch of 2 graphs, 10 nodes, 8 features
|
|
29
|
+
adj = (np.random.rand(2, 10, 10) > 0.7).astype("float32") # dense adjacency matrices
|
|
30
|
+
|
|
31
|
+
layer = DenseGCNConv(in_channels=8, out_channels=16)
|
|
32
|
+
out = layer(x, adj)
|
|
33
|
+
print(tuple(out.shape)) # (2, 10, 16)
|
|
34
|
+
```
|
|
35
|
+
"""
|
|
36
|
+
def __init__(
|
|
37
|
+
self,
|
|
38
|
+
in_channels: int,
|
|
39
|
+
out_channels: int,
|
|
40
|
+
improved: bool = False,
|
|
41
|
+
bias: bool = True,
|
|
42
|
+
**kwargs
|
|
43
|
+
):
|
|
44
|
+
super().__init__(**kwargs)
|
|
45
|
+
self.in_channels = in_channels
|
|
46
|
+
self.out_channels = out_channels
|
|
47
|
+
self.improved = improved
|
|
48
|
+
self.use_bias = bias
|
|
49
|
+
|
|
50
|
+
self.lin = Linear(in_channels, out_channels, bias=False,
|
|
51
|
+
weight_initializer='glorot', name="lin")
|
|
52
|
+
|
|
53
|
+
if bias:
|
|
54
|
+
self.bias = self.add_weight(
|
|
55
|
+
shape=(out_channels,),
|
|
56
|
+
initializer="zeros",
|
|
57
|
+
trainable=True,
|
|
58
|
+
name="bias",
|
|
59
|
+
)
|
|
60
|
+
else:
|
|
61
|
+
self.bias = None
|
|
62
|
+
|
|
63
|
+
def reset_parameters(self):
|
|
64
|
+
self.lin.reset_parameters()
|
|
65
|
+
if self.bias is not None:
|
|
66
|
+
self.bias.assign(ops.zeros(self.bias.shape, dtype=self.bias.dtype))
|
|
67
|
+
|
|
68
|
+
def build(self, input_shape):
|
|
69
|
+
if isinstance(input_shape, (tuple, list)):
|
|
70
|
+
x_shape = input_shape[0]
|
|
71
|
+
else:
|
|
72
|
+
x_shape = input_shape
|
|
73
|
+
self.lin.build(x_shape)
|
|
74
|
+
super().build(input_shape)
|
|
75
|
+
|
|
76
|
+
def call(self, x, adj, mask=None, add_loop: bool = True):
|
|
77
|
+
is_2d_x = (len(ops.shape(x)) == 2)
|
|
78
|
+
if is_2d_x:
|
|
79
|
+
x = ops.expand_dims(x, axis=0)
|
|
80
|
+
if len(ops.shape(adj)) == 2:
|
|
81
|
+
adj = ops.expand_dims(adj, axis=0)
|
|
82
|
+
|
|
83
|
+
N = ops.shape(adj)[1]
|
|
84
|
+
|
|
85
|
+
if add_loop:
|
|
86
|
+
diag_val = 2.0 if self.improved else 1.0
|
|
87
|
+
eye = ops.expand_dims(ops.eye(N, dtype=adj.dtype), axis=0)
|
|
88
|
+
adj = adj * (1.0 - eye) + diag_val * eye
|
|
89
|
+
|
|
90
|
+
out = self.lin(x)
|
|
91
|
+
deg = ops.maximum(ops.sum(adj, axis=-1), 1.0)
|
|
92
|
+
deg_inv_sqrt = ops.power(deg, -0.5)
|
|
93
|
+
|
|
94
|
+
adj_norm = ops.expand_dims(deg_inv_sqrt, axis=-1) * adj * ops.expand_dims(deg_inv_sqrt, axis=-2)
|
|
95
|
+
out = ops.matmul(adj_norm, out)
|
|
96
|
+
|
|
97
|
+
if self.bias is not None:
|
|
98
|
+
out = out + self.bias
|
|
99
|
+
|
|
100
|
+
if mask is not None:
|
|
101
|
+
out = out * ops.cast(ops.reshape(mask, (-1, N, 1)), x.dtype)
|
|
102
|
+
|
|
103
|
+
if is_2d_x and ops.shape(out)[0] == 1:
|
|
104
|
+
out = ops.squeeze(out, axis=0)
|
|
105
|
+
|
|
106
|
+
return out
|
|
107
|
+
|
|
108
|
+
def compute_output_shape(self, input_shape):
|
|
109
|
+
if isinstance(input_shape, (tuple, list)):
|
|
110
|
+
x_shape = input_shape[0]
|
|
111
|
+
else:
|
|
112
|
+
x_shape = input_shape
|
|
113
|
+
return (*x_shape[:-1], self.out_channels)
|
|
114
|
+
|
|
115
|
+
def __repr__(self) -> str:
|
|
116
|
+
return (f'{self.__class__.__name__}({self.in_channels}, '
|
|
117
|
+
f'{self.out_channels})')
|