| { |
| "format_version": 1, |
| "architecture": "SimpleP2G", |
| "setting": "single-patch", |
| "dataset": "ccrcc", |
| "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": 0.1 |
| }, |
| "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": 19, |
| "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": [ |
| "INT1", |
| "INT10", |
| "INT11", |
| "INT12", |
| "INT13", |
| "INT14", |
| "INT15", |
| "INT16", |
| "INT17", |
| "INT18", |
| "INT19", |
| "INT20", |
| "INT21", |
| "INT22", |
| "INT23", |
| "INT24", |
| "INT3", |
| "INT4", |
| "INT5", |
| "INT6", |
| "INT7", |
| "INT8" |
| ], |
| "validation_slide": "INT9", |
| "test_slide": "INT2" |
| }, |
| "validation_metrics": { |
| "PCC10": 0.6926724980557916, |
| "PCC50": 0.6391818018883983, |
| "PCC200": 0.42965969649900465, |
| "MSE": 2.185840368270874, |
| "MAE": 1.17231023311615 |
| }, |
| "test_metrics": { |
| "PCC10": 0.502469291003792, |
| "PCC50": 0.4121004550758145, |
| "PCC200": 0.27036171397452496, |
| "MSE": 1.6523619890213013, |
| "MAE": 0.9979413747787476 |
| } |
| } |
|
|
