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