config.json

{
  "name": null,
  "seed": 42,
  "deterministic": true,
  "output_dir": "relation_prediction_relationgatedmlp_128e_transfer_v1",
  "model": {
    "encoder": "graph_conv",
    "hidden_channels": 128,
    "num_layers": 3,
    "dropout": 0.2,
    "head": "relation_gated_mlp",
    "init_head_as_identity": false,
    "gat_heads": 4,
    "gat_concat": true,
    "graph_conv_aggregator": "mean",
    "sage_aggregator": "mean",
    "mlp_hidden_dim": 64,
    "mlp_num_layers": 2,
    "mlp_dropout": 0.1,
    "nc_dropout": 0.1,
    "rotate_margin": 9.0,
    "transe_margin": 1.0,
    "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
}