{
  "format_version": 1,
  "architecture": "SimpleP2G",
  "setting": "single-patch",
  "dataset": "prad",
  "panel": "hvg",
  "fold": 0,
  "seed": 42,
  "model_config": {
    "decoder_depth": 12,
    "num_genes": 200,
    "hidden_size": 384,
    "cond_size": 2560,
    "num_cond_tokens": 4,
    "num_heads": 6,
    "loss_name": "gaussian_nll",
    "dropout": 0.1
  },
  "input": {
    "representation": "frozen Virchow2 CLS token concatenated with mean patch tokens",
    "embedding_dimension": 2560,
    "image_encoder_weights_included": false
  },
  "output": {
    "num_genes": 200,
    "gene_order": "genes.json",
    "expression_scale": "log2(raw_count + 1)",
    "returns": [
      "expression_mean",
      "log_variance"
    ]
  },
  "checkpoint": {
    "epoch": 12,
    "weights": "ema",
    "selection": "highest validation-slide PCC-200; earliest epoch breaks ties"
  },
  "training": {
    "epochs": 100,
    "batch_size": 256,
    "optimizer": {
      "name": "adamw",
      "lr": 3e-05,
      "weight_decay": 0.1,
      "betas": [
        0.9,
        0.999
      ]
    },
    "loss": "gaussian_nll",
    "precision": "fp16",
    "ema_decay": 0.999,
    "sampling": "pooled spots"
  },
  "split": {
    "training_slides": [
      "MEND139",
      "MEND140",
      "MEND141",
      "MEND143",
      "MEND144",
      "MEND146",
      "MEND147",
      "MEND148",
      "MEND149",
      "MEND150",
      "MEND151",
      "MEND152",
      "MEND153",
      "MEND154",
      "MEND156",
      "MEND157",
      "MEND158",
      "MEND159",
      "MEND160",
      "MEND161",
      "MEND162"
    ],
    "validation_slide": "MEND142",
    "test_slide": "MEND145"
  },
  "validation_metrics": {
    "PCC10": 0.7139566340145835,
    "PCC50": 0.5177275273410492,
    "PCC200": 0.20855663886632447,
    "MSE": 0.4681999087333679,
    "MAE": 0.32622313499450684
  },
  "test_metrics": {
    "PCC10": 0.6859417787277124,
    "PCC50": 0.4673065945925007,
    "PCC200": 0.2199021112938024,
    "MSE": 0.29881447553634644,
    "MAE": 0.22787906229496002
  }
}