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