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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from typing import Optional
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from keras import ops
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import numpy as np
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from .base import Aggregation
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from k3_node.ops.creation import repeat
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class SortAggregation(Aggregation):
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r"""The pooling operator from the `"An End-to-End Deep Learning
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Architecture for Graph Classification"
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<https://www.cse.wustl.edu/~muhan/papers/AAAI_2018_DGCNN.pdf>`_ paper,
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where node features are sorted in descending order based on their last
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feature channel. The first :math:`k` nodes form the output of the layer.
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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 SortAggregation
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x = np.random.rand(10, 8).astype("float32") # 10 nodes with 8 features each
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index = np.repeat([0, 1], 5) # aggregate nodes 0-4 into set 0 and nodes 5-9 into set 1
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aggr = SortAggregation(k=2)
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out = aggr(x, index=index, dim_size=2)
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print(tuple(out.shape)) # (2, 16)
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```
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"""
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def __init__(self, k: int, **kwargs):
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super().__init__(**kwargs)
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self.k = k
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def call(
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self,
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x,
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index: Optional[any] = None,
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ptr: Optional[any] = None,
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dim_size: Optional[int] = None,
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dim: int = -2,
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max_num_elements: Optional[int] = None,
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**kwargs,
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):
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fill_value = -1e9
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batch_x, mask = self.to_dense_batch(
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x, index=index, ptr=ptr, dim_size=dim_size, dim=dim,
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fill_value=fill_value, max_num_elements=max_num_elements,
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)
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B = ops.shape(batch_x)[0]
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N = ops.shape(batch_x)[1]
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D = ops.shape(batch_x)[2]
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scores = batch_x[:, :, -1] # [B, N]
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k = self.k
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k_val = min(k, int(scores.shape[1])) if hasattr(scores, "shape") and isinstance(scores.shape[1], int) else k
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_, perm = ops.top_k(scores, k=k_val, sorted=True) # [B, k]
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perm_expanded = repeat(ops.expand_dims(perm, -1), D, axis=-1)
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out_x = ops.take_along_axis(batch_x, perm_expanded, axis=1)
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out_x = ops.where(ops.equal(out_x, fill_value), ops.zeros_like(out_x), out_x)
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static_d = x.shape[-1]
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out_x = ops.reshape(out_x, (-1, k_val * static_d) if isinstance(static_d, int) else (B, -1))
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return out_x
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def __repr__(self) -> str:
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return f"{self.__class__.__name__}(k={self.k})"
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import numpy as np
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import pytest
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from keras import layers, ops
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from k3_node.layers.aggr import (
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Aggregation,
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AttentionalAggregation,
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DeepSetsAggregation,
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DegreeScalerAggregation,
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EquilibriumAggregation,
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FusedAggregation,
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GRUAggregation,
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GraphMultisetTransformer,
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LCMAggregation,
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LSTMAggregation,
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MLPAggregation,
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MaxAggregation,
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MeanAggregation,
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MedianAggregation,
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MinAggregation,
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MulAggregation,
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MultiAggregation,
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PatchTransformerAggregation,
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PowerMeanAggregation,
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QuantileAggregation,
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Set2Set,
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SetTransformerAggregation,
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SoftmaxAggregation,
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SortAggregation,
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StdAggregation,
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SumAggregation,
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VarAggregation,
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VariancePreservingAggregation,
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aggregation_resolver,
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ptr2index,
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to_dense_batch,
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)
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def test_ptr2index_and_to_dense_batch():
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ptr = ops.convert_to_tensor([0, 2, 5, 6], dtype="int32")
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index = ptr2index(ptr)
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assert np.array_equal(ops.convert_to_numpy(index), [0, 0, 1, 1, 1, 2])
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x = ops.convert_to_tensor([
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[1.0, 2.0],
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[3.0, 4.0],
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[5.0, 6.0],
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[7.0, 8.0],
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[9.0, 10.0],
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[11.0, 12.0],
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], dtype="float32")
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dense_x, mask = to_dense_batch(x, index)
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assert ops.shape(dense_x) == (3, 3, 2)
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assert ops.shape(mask) == (3, 3)
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assert np.array_equal(ops.convert_to_numpy(mask), [
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[True, True, False],
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[True, True, True],
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[True, False, False],
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])
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@pytest.mark.parametrize(
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"AggrClass,expected",
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[
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(SumAggregation, [[4.0, 6.0], [21.0, 24.0], [11.0, 12.0]]),
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(MeanAggregation, [[2.0, 3.0], [7.0, 8.0], [11.0, 12.0]]),
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(MaxAggregation, [[3.0, 4.0], [9.0, 10.0], [11.0, 12.0]]),
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(MinAggregation, [[1.0, 2.0], [5.0, 6.0], [11.0, 12.0]]),
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(MulAggregation, [[3.0, 8.0], [315.0, 480.0], [11.0, 12.0]]),
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],
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)
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def test_basic_reductions(AggrClass, expected):
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x = ops.convert_to_tensor([
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[1.0, 2.0],
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[3.0, 4.0],
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[5.0, 6.0],
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[7.0, 8.0],
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[9.0, 10.0],
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[11.0, 12.0],
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], dtype="float32")
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index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
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aggr = AggrClass()
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out = aggr(x, index)
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assert np.allclose(ops.convert_to_numpy(out), expected)
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# Test with ptr
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ptr = ops.convert_to_tensor([0, 2, 5, 6], dtype="int32")
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out_ptr = aggr(x, ptr=ptr)
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assert np.allclose(ops.convert_to_numpy(out_ptr), expected)
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def test_var_and_std_aggregation():
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x = ops.convert_to_tensor([
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[1.0, 2.0],
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[3.0, 4.0],
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[5.0, 6.0],
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[7.0, 8.0],
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[9.0, 10.0],
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[11.0, 12.0],
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], dtype="float32")
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index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
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var_aggr = VarAggregation()
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var_out = var_aggr(x, index)
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assert ops.shape(var_out) == (3, 2)
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assert np.all(ops.convert_to_numpy(var_out) >= 0.0)
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std_aggr = StdAggregation()
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std_out = std_aggr(x, index)
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assert ops.shape(std_out) == (3, 2)
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assert np.all(ops.convert_to_numpy(std_out) >= 0.0)
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def test_softmax_aggregation():
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x = ops.convert_to_tensor([
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[1.0, 2.0],
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[3.0, 4.0],
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[5.0, 6.0],
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[7.0, 8.0],
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[9.0, 10.0],
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[11.0, 12.0],
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], dtype="float32")
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index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
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# Fixed temperature
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aggr = SoftmaxAggregation(t=1.0)
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out = aggr(x, index)
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assert ops.shape(out) == (3, 2)
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# Learnable multi-channel temperature
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learnable_aggr = SoftmaxAggregation(t=1.0, learn=True, channels=2)
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out_learn = learnable_aggr(x, index)
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assert ops.shape(out_learn) == (3, 2)
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def test_powermean_aggregation():
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x = ops.convert_to_tensor([
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[1.0, 2.0],
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[3.0, 4.0],
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[5.0, 6.0],
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[7.0, 8.0],
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[9.0, 10.0],
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[11.0, 12.0],
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], dtype="float32")
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index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
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# Fixed p
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aggr = PowerMeanAggregation(p=2.0)
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out = aggr(x, index)
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assert ops.shape(out) == (3, 2)
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# Learnable p
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learnable_aggr = PowerMeanAggregation(p=1.0, learn=True, channels=2)
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out_learn = learnable_aggr(x, index)
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assert ops.shape(out_learn) == (3, 2)
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def test_quantile_and_median_aggregation():
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x = ops.convert_to_tensor([
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[1.0, 2.0],
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[3.0, 4.0],
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[5.0, 6.0],
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[7.0, 8.0],
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[9.0, 10.0],
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[11.0, 12.0],
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], dtype="float32")
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index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
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171
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+
|
|
172
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# Median
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173
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med_aggr = MedianAggregation()
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174
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med_out = med_aggr(x, index)
|
|
175
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+
assert ops.shape(med_out) == (3, 2)
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176
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+
|
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177
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+
# Quantile with multiple q
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178
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+
q_aggr = QuantileAggregation(q=[0.25, 0.75], interpolation="linear")
|
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179
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+
q_out = q_aggr(x, index)
|
|
180
|
+
assert ops.shape(q_out) == (3, 4)
|
|
181
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+
|
|
182
|
+
# Interpolations
|
|
183
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+
for interp in ["lower", "higher", "nearest", "midpoint"]:
|
|
184
|
+
q_interp = QuantileAggregation(q=0.5, interpolation=interp)
|
|
185
|
+
res = q_interp(x, index)
|
|
186
|
+
assert ops.shape(res) == (3, 2)
|
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187
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+
|
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188
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+
|
|
189
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def test_attentional_aggregation():
|
|
190
|
+
x = ops.convert_to_tensor([
|
|
191
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+
[1.0, 2.0],
|
|
192
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+
[3.0, 4.0],
|
|
193
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+
[5.0, 6.0],
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194
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+
[7.0, 8.0],
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195
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[9.0, 10.0],
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196
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[11.0, 12.0],
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197
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+
], dtype="float32")
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198
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+
index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
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199
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+
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200
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+
gate_nn = layers.Dense(1)
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+
nn = layers.Dense(8)
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aggr = AttentionalAggregation(gate_nn=gate_nn, nn=nn)
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+
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204
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out = aggr(x, index)
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+
assert ops.shape(out) == (3, 8)
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+
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207
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+
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208
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+
def test_set2set_aggregation():
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+
in_channels = 4
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210
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+
x = ops.ones((6, in_channels), dtype="float32")
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211
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+
index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
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212
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+
|
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213
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+
s2s = Set2Set(in_channels=in_channels, processing_steps=2)
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+
out = s2s(x, index)
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+
assert ops.shape(out) == (3, 2 * in_channels)
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216
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+
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217
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+
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218
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+
def test_degree_scaler_aggregation():
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+
x = ops.ones((6, 4), dtype="float32")
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220
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+
index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
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221
|
+
deg = ops.convert_to_tensor([0.0, 1.0, 2.0, 3.0], dtype="float32")
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222
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+
|
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223
|
+
scalers = ["identity", "amplification", "attenuation", "linear", "inverse_linear"]
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224
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+
aggr = DegreeScalerAggregation(aggr="mean", scaler=scalers, deg=deg)
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+
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226
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+
out = aggr(x, index)
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+
assert ops.shape(out) == (3, 4 * len(scalers))
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|
+
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+
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+
def test_sort_aggregation():
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+
x = ops.convert_to_tensor([
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|
+
[1.0, 2.0],
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233
|
+
[3.0, 1.0],
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234
|
+
[5.0, 9.0],
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+
[7.0, 8.0],
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236
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+
[9.0, 10.0],
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|
+
[11.0, 5.0],
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238
|
+
], dtype="float32")
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+
index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
|
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240
|
+
|
|
241
|
+
aggr = SortAggregation(k=2)
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|
+
out = aggr(x, index)
|
|
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|
+
assert ops.shape(out) == (3, 2 * 2)
|
|
244
|
+
|
|
245
|
+
|
|
246
|
+
def test_multi_aggregation():
|
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|
+
x = ops.ones((6, 4), dtype="float32")
|
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248
|
+
index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
|
|
249
|
+
|
|
250
|
+
# Cat mode
|
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251
|
+
aggr_cat = MultiAggregation(["mean", "max"], mode="cat")
|
|
252
|
+
assert ops.shape(aggr_cat(x, index)) == (3, 8)
|
|
253
|
+
|
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254
|
+
# Proj mode
|
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255
|
+
aggr_proj = MultiAggregation(["mean", "max"], mode="proj", mode_kwargs={"in_channels": 4, "out_channels": 16})
|
|
256
|
+
assert ops.shape(aggr_proj(x, index)) == (3, 16)
|
|
257
|
+
|
|
258
|
+
# Elementwise modes
|
|
259
|
+
for m in ["sum", "mean", "max", "min", "var", "std"]:
|
|
260
|
+
aggr_m = MultiAggregation(["sum", "mean"], mode=m)
|
|
261
|
+
assert ops.shape(aggr_m(x, index)) == (3, 4)
|
|
262
|
+
|
|
263
|
+
|
|
264
|
+
def test_deep_sets_and_mlp_aggregation():
|
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265
|
+
x = ops.ones((6, 4), dtype="float32")
|
|
266
|
+
index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
|
|
267
|
+
|
|
268
|
+
# DeepSets
|
|
269
|
+
ds = DeepSetsAggregation(local_nn=layers.Dense(8), global_nn=layers.Dense(16))
|
|
270
|
+
assert ops.shape(ds(x, index)) == (3, 16)
|
|
271
|
+
|
|
272
|
+
# MLP
|
|
273
|
+
mlp_aggr = MLPAggregation(in_channels=4, out_channels=16, max_num_elements=3)
|
|
274
|
+
assert ops.shape(mlp_aggr(x, index)) == (3, 16)
|
|
275
|
+
|
|
276
|
+
|
|
277
|
+
def test_lstm_and_gru_aggregation():
|
|
278
|
+
x = ops.ones((6, 4), dtype="float32")
|
|
279
|
+
index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
|
|
280
|
+
|
|
281
|
+
lstm_aggr = LSTMAggregation(in_channels=4, out_channels=8)
|
|
282
|
+
assert ops.shape(lstm_aggr(x, index)) == (3, 8)
|
|
283
|
+
|
|
284
|
+
gru_aggr = GRUAggregation(in_channels=4, out_channels=8)
|
|
285
|
+
assert ops.shape(gru_aggr(x, index)) == (3, 8)
|
|
286
|
+
|
|
287
|
+
|
|
288
|
+
def test_set_transformer_and_gmt():
|
|
289
|
+
x = ops.ones((6, 4), dtype="float32")
|
|
290
|
+
index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
|
|
291
|
+
|
|
292
|
+
st = SetTransformerAggregation(channels=4, num_seed_points=2, heads=1, concat=True)
|
|
293
|
+
out_st = st(x, index)
|
|
294
|
+
assert ops.shape(out_st) == (3, 8)
|
|
295
|
+
|
|
296
|
+
gmt = GraphMultisetTransformer(channels=4, k=2, heads=1)
|
|
297
|
+
out_gmt = gmt(x, index)
|
|
298
|
+
assert ops.shape(out_gmt) == (3, 4)
|
|
299
|
+
|
|
300
|
+
|
|
301
|
+
def test_variance_preserving_and_patch_transformer():
|
|
302
|
+
x = ops.ones((6, 4), dtype="float32")
|
|
303
|
+
index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
|
|
304
|
+
|
|
305
|
+
vpa = VariancePreservingAggregation()
|
|
306
|
+
assert ops.shape(vpa(x, index)) == (3, 4)
|
|
307
|
+
|
|
308
|
+
pt = PatchTransformerAggregation(in_channels=4, out_channels=8, patch_size=2, hidden_channels=4)
|
|
309
|
+
assert ops.shape(pt(x, index)) == (3, 8)
|
|
310
|
+
|
|
311
|
+
|
|
312
|
+
def test_lcm_and_equilibrium_aggregation():
|
|
313
|
+
x = ops.ones((6, 4), dtype="float32")
|
|
314
|
+
index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
|
|
315
|
+
|
|
316
|
+
lcm = LCMAggregation(in_channels=4, out_channels=4, project=False)
|
|
317
|
+
assert ops.shape(lcm(x, index)) == (3, 4)
|
|
318
|
+
|
|
319
|
+
eq = EquilibriumAggregation(in_channels=4, out_channels=4, num_layers=[8])
|
|
320
|
+
assert ops.shape(eq(x, index)) == (3, 4)
|
|
321
|
+
|
|
322
|
+
|
|
323
|
+
def test_fused_and_resolver():
|
|
324
|
+
x = ops.ones((6, 4), dtype="float32")
|
|
325
|
+
index = ops.convert_to_tensor([0, 0, 1, 1, 1, 2], dtype="int32")
|
|
326
|
+
|
|
327
|
+
fused = FusedAggregation(["sum", "mean", "max"])
|
|
328
|
+
outs = fused(x, index)
|
|
329
|
+
assert len(outs) == 3
|
|
330
|
+
for o in outs:
|
|
331
|
+
assert ops.shape(o) == (3, 4)
|
|
332
|
+
|
|
333
|
+
# Resolver
|
|
334
|
+
res_sum = aggregation_resolver("sum")
|
|
335
|
+
assert isinstance(res_sum, SumAggregation)
|
|
336
|
+
res_mean = aggregation_resolver("mean")
|
|
337
|
+
assert isinstance(res_mean, MeanAggregation)
|
|
@@ -0,0 +1,210 @@
|
|
|
1
|
+
from typing import Optional
|
|
2
|
+
from keras import initializers, layers, ops
|
|
3
|
+
|
|
4
|
+
|
|
5
|
+
class MultiheadAttentionBlock(layers.Layer):
|
|
6
|
+
r"""The Multihead Attention Block (MAB) from the `"Set Transformer: A
|
|
7
|
+
Framework for Attention-based Permutation-Invariant Neural Networks"
|
|
8
|
+
<https://arxiv.org/abs/1810.00825>`_ paper.
|
|
9
|
+
"""
|
|
10
|
+
|
|
11
|
+
def __init__(
|
|
12
|
+
self,
|
|
13
|
+
channels: int,
|
|
14
|
+
heads: int = 1,
|
|
15
|
+
layer_norm: bool = True,
|
|
16
|
+
dropout: float = 0.0,
|
|
17
|
+
**kwargs,
|
|
18
|
+
):
|
|
19
|
+
super().__init__(**kwargs)
|
|
20
|
+
self.supports_masking = True
|
|
21
|
+
self.channels = channels
|
|
22
|
+
self.heads = heads
|
|
23
|
+
self.dropout = dropout
|
|
24
|
+
|
|
25
|
+
key_dim = max(channels // heads, 1)
|
|
26
|
+
self.attn = layers.MultiHeadAttention(
|
|
27
|
+
num_heads=heads,
|
|
28
|
+
key_dim=key_dim,
|
|
29
|
+
dropout=dropout,
|
|
30
|
+
)
|
|
31
|
+
self.lin = layers.Dense(channels)
|
|
32
|
+
self.layer_norm1 = layers.LayerNormalization() if layer_norm else None
|
|
33
|
+
self.layer_norm2 = layers.LayerNormalization() if layer_norm else None
|
|
34
|
+
|
|
35
|
+
def compute_mask(self, inputs, mask=None):
|
|
36
|
+
return mask
|
|
37
|
+
|
|
38
|
+
def reset_parameters(self):
|
|
39
|
+
pass
|
|
40
|
+
|
|
41
|
+
def call(
|
|
42
|
+
self,
|
|
43
|
+
x,
|
|
44
|
+
y,
|
|
45
|
+
x_mask: Optional[any] = None,
|
|
46
|
+
y_mask: Optional[any] = None,
|
|
47
|
+
training: bool = False,
|
|
48
|
+
):
|
|
49
|
+
attn_mask = None
|
|
50
|
+
if y_mask is not None:
|
|
51
|
+
# y_mask shape: [B, S], expand to [B, 1, S]
|
|
52
|
+
attn_mask = ops.expand_dims(ops.cast(y_mask, "bool"), axis=1)
|
|
53
|
+
|
|
54
|
+
out = self.attn(
|
|
55
|
+
query=x,
|
|
56
|
+
value=y,
|
|
57
|
+
key=y,
|
|
58
|
+
attention_mask=attn_mask,
|
|
59
|
+
training=training,
|
|
60
|
+
)
|
|
61
|
+
|
|
62
|
+
if x_mask is not None:
|
|
63
|
+
out = out * ops.cast(ops.expand_dims(x_mask, axis=-1), out.dtype)
|
|
64
|
+
|
|
65
|
+
out = out + x
|
|
66
|
+
if self.layer_norm1 is not None:
|
|
67
|
+
out = self.layer_norm1(out)
|
|
68
|
+
|
|
69
|
+
out = out + ops.relu(self.lin(out))
|
|
70
|
+
if self.layer_norm2 is not None:
|
|
71
|
+
out = self.layer_norm2(out)
|
|
72
|
+
|
|
73
|
+
return out
|
|
74
|
+
|
|
75
|
+
def __repr__(self) -> str:
|
|
76
|
+
return (
|
|
77
|
+
f"{self.__class__.__name__}({self.channels}, "
|
|
78
|
+
f"heads={self.heads}, layer_norm={self.layer_norm1 is not None}, "
|
|
79
|
+
f"dropout={self.dropout})"
|
|
80
|
+
)
|
|
81
|
+
|
|
82
|
+
|
|
83
|
+
class SetAttentionBlock(layers.Layer):
|
|
84
|
+
r"""The Set Attention Block (SAB) from the `"Set Transformer"` paper."""
|
|
85
|
+
|
|
86
|
+
def __init__(
|
|
87
|
+
self,
|
|
88
|
+
channels: int,
|
|
89
|
+
heads: int = 1,
|
|
90
|
+
layer_norm: bool = True,
|
|
91
|
+
dropout: float = 0.0,
|
|
92
|
+
**kwargs,
|
|
93
|
+
):
|
|
94
|
+
super().__init__(**kwargs)
|
|
95
|
+
self.supports_masking = True
|
|
96
|
+
self.mab = MultiheadAttentionBlock(channels, heads, layer_norm, dropout)
|
|
97
|
+
|
|
98
|
+
def compute_mask(self, inputs, mask=None):
|
|
99
|
+
return mask
|
|
100
|
+
|
|
101
|
+
def reset_parameters(self):
|
|
102
|
+
self.mab.reset_parameters()
|
|
103
|
+
|
|
104
|
+
def call(self, x, mask: Optional[any] = None, training: bool = False):
|
|
105
|
+
return self.mab(x, x, x_mask=mask, y_mask=mask, training=training)
|
|
106
|
+
|
|
107
|
+
def __repr__(self) -> str:
|
|
108
|
+
return (
|
|
109
|
+
f"{self.__class__.__name__}({self.mab.channels}, "
|
|
110
|
+
f"heads={self.mab.heads}, layer_norm={self.mab.layer_norm1 is not None}, "
|
|
111
|
+
f"dropout={self.mab.dropout})"
|
|
112
|
+
)
|
|
113
|
+
|
|
114
|
+
|
|
115
|
+
class InducedSetAttentionBlock(layers.Layer):
|
|
116
|
+
r"""The Induced Set Attention Block (ISAB) from the `"Set Transformer"` paper."""
|
|
117
|
+
|
|
118
|
+
def __init__(
|
|
119
|
+
self,
|
|
120
|
+
channels: int,
|
|
121
|
+
num_induced_points: int,
|
|
122
|
+
heads: int = 1,
|
|
123
|
+
layer_norm: bool = True,
|
|
124
|
+
dropout: float = 0.0,
|
|
125
|
+
**kwargs,
|
|
126
|
+
):
|
|
127
|
+
super().__init__(**kwargs)
|
|
128
|
+
self.supports_masking = True
|
|
129
|
+
self.channels = channels
|
|
130
|
+
self.num_induced_points = num_induced_points
|
|
131
|
+
|
|
132
|
+
self.ind = self.add_weight(
|
|
133
|
+
shape=(1, num_induced_points, channels),
|
|
134
|
+
initializer=initializers.GlorotUniform(),
|
|
135
|
+
trainable=True,
|
|
136
|
+
name="ind",
|
|
137
|
+
)
|
|
138
|
+
self.mab1 = MultiheadAttentionBlock(channels, heads, layer_norm, dropout)
|
|
139
|
+
self.mab2 = MultiheadAttentionBlock(channels, heads, layer_norm, dropout)
|
|
140
|
+
|
|
141
|
+
def compute_mask(self, inputs, mask=None):
|
|
142
|
+
return mask
|
|
143
|
+
|
|
144
|
+
def reset_parameters(self):
|
|
145
|
+
init = initializers.GlorotUniform()
|
|
146
|
+
self.ind.assign(init(self.ind.shape, dtype=self.ind.dtype))
|
|
147
|
+
self.mab1.reset_parameters()
|
|
148
|
+
self.mab2.reset_parameters()
|
|
149
|
+
|
|
150
|
+
def call(self, x, mask: Optional[any] = None, training: bool = False):
|
|
151
|
+
B = ops.shape(x)[0]
|
|
152
|
+
ind_expanded = ops.broadcast_to(self.ind, (B, self.num_induced_points, self.channels))
|
|
153
|
+
h = self.mab1(ind_expanded, x, y_mask=mask, training=training)
|
|
154
|
+
return self.mab2(x, h, x_mask=mask, training=training)
|
|
155
|
+
|
|
156
|
+
def __repr__(self) -> str:
|
|
157
|
+
return (
|
|
158
|
+
f"{self.__class__.__name__}({self.channels}, "
|
|
159
|
+
f"num_induced_points={self.num_induced_points}, "
|
|
160
|
+
f"heads={self.mab1.heads})"
|
|
161
|
+
)
|
|
162
|
+
|
|
163
|
+
|
|
164
|
+
class PoolingByMultiheadAttention(layers.Layer):
|
|
165
|
+
r"""The Pooling by Multihead Attention (PMA) layer from the `"Set Transformer"` paper."""
|
|
166
|
+
|
|
167
|
+
def __init__(
|
|
168
|
+
self,
|
|
169
|
+
channels: int,
|
|
170
|
+
num_seed_points: int = 1,
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171
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+
heads: int = 1,
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172
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+
layer_norm: bool = True,
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173
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+
dropout: float = 0.0,
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174
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+
**kwargs,
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175
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+
):
|
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176
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+
super().__init__(**kwargs)
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177
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+
self.supports_masking = True
|
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178
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+
self.channels = channels
|
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179
|
+
self.num_seed_points = num_seed_points
|
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180
|
+
self.lin = layers.Dense(channels)
|
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181
|
+
self.seed = self.add_weight(
|
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182
|
+
shape=(1, num_seed_points, channels),
|
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183
|
+
initializer=initializers.GlorotUniform(),
|
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184
|
+
trainable=True,
|
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185
|
+
name="seed",
|
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186
|
+
)
|
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187
|
+
self.mab = MultiheadAttentionBlock(channels, heads, layer_norm, dropout)
|
|
188
|
+
|
|
189
|
+
def compute_mask(self, inputs, mask=None):
|
|
190
|
+
return None
|
|
191
|
+
|
|
192
|
+
def reset_parameters(self):
|
|
193
|
+
self.lin.reset_parameters()
|
|
194
|
+
init = initializers.GlorotUniform()
|
|
195
|
+
self.seed.assign(init(self.seed.shape, dtype=self.seed.dtype))
|
|
196
|
+
self.mab.reset_parameters()
|
|
197
|
+
|
|
198
|
+
def call(self, x, mask: Optional[any] = None, training: bool = False):
|
|
199
|
+
B = ops.shape(x)[0]
|
|
200
|
+
x_proj = ops.relu(self.lin(x))
|
|
201
|
+
seed_expanded = ops.broadcast_to(self.seed, (B, self.num_seed_points, self.channels))
|
|
202
|
+
return self.mab(seed_expanded, x_proj, y_mask=mask, training=training)
|
|
203
|
+
|
|
204
|
+
def __repr__(self) -> str:
|
|
205
|
+
return (
|
|
206
|
+
f"{self.__class__.__name__}({self.channels}, "
|
|
207
|
+
f"num_seed_points={self.num_seed_points}, "
|
|
208
|
+
f"heads={self.mab.heads})"
|
|
209
|
+
)
|
|
210
|
+
|
|
@@ -0,0 +1,54 @@
|
|
|
1
|
+
from typing import Optional
|
|
2
|
+
from keras import ops
|
|
3
|
+
|
|
4
|
+
from .base import Aggregation
|
|
5
|
+
from k3_node.ops.segment import segment_sum
|
|
6
|
+
|
|
7
|
+
|
|
8
|
+
class VariancePreservingAggregation(Aggregation):
|
|
9
|
+
r"""Performs the Variance Preserving Aggregation (VPA) from the `"GNN-VPA:
|
|
10
|
+
A Variance-Preserving Aggregation Strategy for Graph Neural Networks"
|
|
11
|
+
<https://arxiv.org/abs/2403.04747>`_ paper.
|
|
12
|
+
|
|
13
|
+
Example:
|
|
14
|
+
```python
|
|
15
|
+
import numpy as np
|
|
16
|
+
from k3_node.layers import VariancePreservingAggregation
|
|
17
|
+
|
|
18
|
+
x = np.random.rand(10, 8).astype("float32") # 10 nodes with 8 features each
|
|
19
|
+
index = np.repeat([0, 1], 5) # aggregate nodes 0-4 into set 0 and nodes 5-9 into set 1
|
|
20
|
+
|
|
21
|
+
aggr = VariancePreservingAggregation()
|
|
22
|
+
out = aggr(x, index=index, dim_size=2)
|
|
23
|
+
print(tuple(out.shape)) # (2, 8)
|
|
24
|
+
```
|
|
25
|
+
"""
|
|
26
|
+
|
|
27
|
+
def call(
|
|
28
|
+
self,
|
|
29
|
+
x,
|
|
30
|
+
index: Optional[any] = None,
|
|
31
|
+
ptr: Optional[any] = None,
|
|
32
|
+
dim_size: Optional[int] = None,
|
|
33
|
+
dim: int = -2,
|
|
34
|
+
**kwargs,
|
|
35
|
+
):
|
|
36
|
+
out = self.reduce(x, index, ptr, dim_size, dim, reduce="sum")
|
|
37
|
+
|
|
38
|
+
if ptr is not None and index is None:
|
|
39
|
+
from .base import ptr2index
|
|
40
|
+
index = ptr2index(ptr)
|
|
41
|
+
|
|
42
|
+
index = ops.cast(index, dtype="int32")
|
|
43
|
+
if dim_size is None: # a tensor while tracing; don't test its truth value
|
|
44
|
+
dim_size = int(ops.max(index)) + 1 if ops.shape(index)[0] > 0 else 0
|
|
45
|
+
|
|
46
|
+
ones = ops.ones((ops.shape(index)[0], 1), dtype=out.dtype)
|
|
47
|
+
count = segment_sum(ones, index, num_segments=dim_size)
|
|
48
|
+
count = ops.maximum(ops.sqrt(count), 1.0)
|
|
49
|
+
|
|
50
|
+
return out / count
|
|
51
|
+
|
|
52
|
+
def __repr__(self) -> str:
|
|
53
|
+
return f"{self.__class__.__name__}()"
|
|
54
|
+
|