model: graph_conv-relation_attention_mlp_h128_l3_edge_prediction | (graph_conv-relation_attention_mlp_h128_l3) | WandB: 63xqckzk

config.json

@@ -0,0 +1,104 @@
+{
+  "name": null,
+  "seed": 42,
+  "deterministic": true,
+  "output_dir": "relation_prediction_relationattnmlp_128e_transfer_v1",
+  "model": {
+    "encoder": "graph_conv",
+    "hidden_channels": 128,
+    "num_layers": 3,
+    "dropout": 0.2,
+    "head": "relation_attention_mlp",
+    "init_head_as_identity": false,
+    "gat_heads": 4,
+    "gat_concat": true,
+    "graph_conv_aggregator": "mean",
+    "sage_aggregator": "mean",
+    "mlp_hidden_dim": 128,
+    "mlp_num_layers": 2,
+    "mlp_dropout": 0.1,
+    "nc_dropout": 0.1,
+    "rotate_margin": 0.1,
+    "transe_margin": 0.1,
+    "relation_emb_dim": 64,
+    "relation_attention_heads": 4,
+    "use_edge_encoder": true,
+    "edge_encoder_dim": 32,
+    "edge_encoder_dropout": 0.1,
+    "edge_encoder_init_bias": 0.0,
+    "use_pretrained_model": true,
+    "pretrained_model_source": "huggingface",
+    "pretrained_model_path": "seanhacks/edge_prediction_dotprod_128e",
+    "pretrained_model_revision": null,
+    "pretrained_model_load_head": false,
+    "pretrained_model_freeze_encoder_weights": false,
+    "pretrained_model_freeze_head_weights": false
+  },
+  "data": {
+    "store_dir": "[REDACTED]",
+    "sbml_dfs_path": "[REDACTED]",
+    "napistu_graph_path": "[REDACTED]",
+    "copy_to_store": false,
+    "overwrite": false,
+    "napistu_data_name": "relation_prediction",
+    "other_artifacts": [
+      "comprehensive_pathway_memberships",
+      "edge_strata_by_node_species_type"
+    ]
+  },
+  "task": {
+    "task": "edge_prediction",
+    "metrics": [
+      "auc",
+      "ap"
+    ],
+    "edge_prediction_neg_sampling_ratio": 1.0,
+    "edge_prediction_neg_sampling_stratify_by": "edge_sbo_terms",
+    "edge_prediction_neg_sampling_strategy": "degree_weighted",
+    "weight_loss_by_relation_frequency": true,
+    "loss_weight_alpha": 0.5
+  },
+  "training": {
+    "lr": 0.0005,
+    "weight_decay": 0.0001,
+    "optimizer": "adamw",
+    "scheduler": "onecycle",
+    "gradient_clip_val": null,
+    "epochs": 500,
+    "batches_per_epoch": 20,
+    "accelerator": "auto",
+    "devices": 1,
+    "precision": 32,
+    "early_stopping": true,
+    "early_stopping_patience": 20,
+    "early_stopping_metric": "val_relation_weighted_auc",
+    "save_checkpoints": true,
+    "checkpoint_subdir": "checkpoints",
+    "checkpoint_metric": "val_relation_weighted_auc",
+    "score_distribution_monitoring": true,
+    "score_distribution_monitoring_log_every_n_epochs": 10,
+    "embedding_norm_monitoring": true,
+    "embedding_norm_monitoring_log_every_n_epochs": 10,
+    "weight_monitoring": true
+  },
+  "wandb": {
+    "project": "napistu-experiments",
+    "entity": "napistu",
+    "group": "baseline",
+    "tags": [
+      "relation_prediction",
+      "graph_conv",
+      "edge_prediction",
+      "hidden_128",
+      "layers_3",
+      "lr_0.0005",
+      "epochs_500"
+    ],
+    "log_model": false,
+    "mode": "online",
+    "wandb_subdir": "logs"
+  },
+  "fast_dev_run": false,
+  "limit_train_batches": 1.0,
+  "limit_val_batches": 1.0
+}