{
  "format_version": 1,
  "architecture": "SimpleP2G",
  "setting": "single-patch",
  "dataset": "her2st",
  "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": 0.0
  },
  "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": 37,
    "weights": "ema",
    "selection": "highest validation-slide PCC-200; earliest epoch breaks ties"
  },
  "training": {
    "epochs": 100,
    "batch_size": 256,
    "optimizer": {
      "name": "adamw",
      "lr": 0.0001,
      "weight_decay": 0.05,
      "betas": [
        0.9,
        0.999
      ]
    },
    "loss": "gaussian_nll",
    "precision": "fp16",
    "ema_decay": 0.999,
    "sampling": "pooled spots"
  },
  "split": {
    "training_slides": [
      "SPA119",
      "SPA120",
      "SPA121",
      "SPA122",
      "SPA123",
      "SPA124",
      "SPA125",
      "SPA126",
      "SPA128",
      "SPA129",
      "SPA130",
      "SPA131",
      "SPA132",
      "SPA133",
      "SPA134",
      "SPA135",
      "SPA136",
      "SPA137",
      "SPA138",
      "SPA139",
      "SPA140",
      "SPA141",
      "SPA142",
      "SPA143",
      "SPA144",
      "SPA145",
      "SPA146",
      "SPA147",
      "SPA149",
      "SPA150",
      "SPA151",
      "SPA152",
      "SPA153",
      "SPA154"
    ],
    "validation_slide": "SPA127",
    "test_slide": "SPA148"
  },
  "validation_metrics": {
    "PCC10": 0.43139689241917323,
    "PCC50": 0.20696065692979265,
    "PCC200": 0.0662583081649352,
    "MSE": 0.2628522515296936,
    "MAE": 0.31125587224960327
  },
  "test_metrics": {
    "PCC10": 0.751352123780151,
    "PCC50": 0.6407706227872064,
    "PCC200": 0.3798230854871934,
    "MSE": 0.3085944652557373,
    "MAE": 0.2869880795478821
  }
}