{
  "data_cfg": {
    "dataset_path": "../dataset/data/processed/peptides_bbb_with_augmentation.parquet",
    "fold_col": "fold_id",
    "id_col": "peptide_id",
    "label_col": "bbb_label",
    "random_state": 42,
    "sequence_col": "sequence",
    "struct_manifest_path": "../dataset/data/processed/peptides_struct_manifest.parquet",
    "tabular_exclude": [
      "peptide_id",
      "sequence",
      "bbb_label",
      "split",
      "source_split",
      "source_db",
      "label_tier",
      "is_gold",
      "cluster_id",
      "external_test",
      "source_id",
      "assay_method",
      "reference",
      "organism",
      "fold_id",
      "is_augmented",
      "parent_peptide_id",
      "sample_weight"
    ],
    "test_size": 0.2,
    "three_d_columns": []
  },
  "exp_cfg": {
    "esm": {
      "cache_dir": "artifacts/cache/esm2"
    },
    "features": {
      "use_3d": false,
      "use_esm": true,
      "use_gnn": false,
      "use_tabular": true
    },
    "mixup": {
      "alpha": 0.2,
      "enabled": true,
      "prob": 0.5
    },
    "model": {
      "dropout": 0.2,
      "esm_dim": 128,
      "hidden_dim": 256
    },
    "model_type": "esm_tab_mlp",
    "name": "exp06_esm_tab_mlp_aug"
  },
  "tab_cols": [
    "length",
    "mw",
    "ext_coef_reduced",
    "ext_coef_oxidized",
    "hydrophobic_ratio_pct",
    "pi",
    "net_charge_ph7",
    "total_charge",
    "mean_hydrophobicity",
    "hydrophobicity_ph7",
    "hydrophilic_ratio",
    "aliphatic_index",
    "boman_index",
    "aromaticity",
    "instability_index",
    "gravy",
    "charge_density",
    "aa_basic_pct",
    "aa_acidic_pct",
    "aa_aromatic_pct",
    "aa_hydrophobic_pct",
    "aa_polar_pct",
    "hydrophobic_moment",
    "mw_pyteomics",
    "mw_delta_abs"
  ],
  "train_cfg": {
    "calibration": {
      "enabled": true,
      "method": "isotonic"
    },
    "maximize_metric": true,
    "output": {
      "keep_top_k": 1,
      "root": "artifacts",
      "save_periodic_every": 5
    },
    "primary_metric": "pr_auc",
    "run_name": "default",
    "secondary_metric": "mcc",
    "seed": 42,
    "tracking": {
      "mlflow": true,
      "mlflow_experiment": "bbb_classifier",
      "tensorboard": true
    },
    "training": {
      "batch_size": 128,
      "epochs": 50,
      "eval_every": 1,
      "grad_clip": 1.0,
      "log_every": 5,
      "lr": 0.001,
      "num_workers": 4,
      "patience": 8,
      "weight_decay": 0.0001
    }
  }
}