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SimpleP2G

PyTorch
Safetensors
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biology
spatial-transcriptomics
computational-pathology
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SimpleP2G
File size: 1,996 Bytes
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{
  "format_version": 1,
  "architecture": "SimpleP2G",
  "setting": "single-patch",
  "dataset": "lung",
  "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": 8,
    "weights": "ema",
    "selection": "highest validation-slide PCC-200; earliest epoch breaks ties"
  },
  "training": {
    "epochs": 100,
    "batch_size": 256,
    "optimizer": {
      "name": "adamw",
      "lr": 5e-05,
      "weight_decay": 0.05,
      "betas": [
        0.9,
        0.999
      ]
    },
    "loss": "gaussian_nll",
    "precision": "fp16",
    "ema_decay": 0.999,
    "sampling": "pooled spots"
  },
  "split": {
    "training_slides": [
      "NCBI857",
      "NCBI858",
      "NCBI859",
      "NCBI861",
      "NCBI864",
      "NCBI865",
      "NCBI866",
      "NCBI867",
      "NCBI870",
      "NCBI873",
      "NCBI875",
      "NCBI876",
      "NCBI879",
      "NCBI880",
      "NCBI881",
      "NCBI882",
      "NCBI883",
      "NCBI884"
    ],
    "validation_slide": "NCBI860",
    "test_slide": "NCBI856"
  },
  "validation_metrics": {
    "PCC10": 0.9030630133389671,
    "PCC50": 0.8287717950429099,
    "PCC200": 0.4339199710155945,
    "MSE": 0.606461763381958,
    "MAE": 0.42725834250450134
  },
  "test_metrics": {
    "PCC10": 0.9472604745563193,
    "PCC50": 0.8581366731430391,
    "PCC200": 0.4954411997870103,
    "MSE": 0.7060865759849548,
    "MAE": 0.4992806017398834
  }
}