| { |
| "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 |
| } |
| } |
|
|
