| { |
| "format_version": 1, |
| "architecture": "SimpleP2G", |
| "setting": "single-patch", |
| "dataset": "brain", |
| "panel": "hmhvg", |
| "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": 0.05 |
| }, |
| "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": 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": [ |
| "NCBI658", |
| "NCBI659", |
| "NCBI660", |
| "NCBI661", |
| "NCBI662", |
| "NCBI663", |
| "NCBI664", |
| "NCBI665", |
| "NCBI666", |
| "NCBI668", |
| "NCBI669", |
| "NCBI670" |
| ], |
| "validation_slide": "NCBI671", |
| "test_slide": "NCBI667" |
| }, |
| "validation_metrics": { |
| "PCC10": 0.6837345136688756, |
| "PCC50": 0.5748279101783605, |
| "PCC200": 0.4576825647353083, |
| "MSE": 0.7553753852844238, |
| "MAE": 0.6992919445037842 |
| }, |
| "test_metrics": { |
| "PCC10": 0.5845393964585056, |
| "PCC50": 0.5154498406392661, |
| "PCC200": 0.3803240847090443, |
| "MSE": 0.9970911145210266, |
| "MAE": 0.7918735146522522 |
| } |
| } |
|
|
