brats_example_config.json

{
  "model_config": {
    "architecture": "u_net",
    "optimizer": "adam",
    "loss_config": {
      "type": "cross_entropy",
      "weight_pseudo_labels_start": 0.9,
      "weight_pseudo_labels_end": 0.1,
      "weight_pseudo_labels_scheduler": "linear"
    },
    "learning_rate": 0.0001,
    "num_levels": 4,
    "dim": 2,
    "model_selection_criterion": "mean_dice_score",
    "train_metrics": ["dice_score"],
    "train_metric_confidence_levels": [0.5],
    "test_metrics": ["dice_score", "sensitivity", "specificity", "hausdorff95"],
    "test_metric_confidence_levels": [0.5]
  },
  "dataset_config": {
    "dataset": "brats",
    "data_dir": "/dhc/groups/mpws2021cl1/Data/BraTS",
    "cache_size": 250,
    "pin_memory": true
  },
  "active_learning_config": {
    "active_learning_mode": true,
    "reset_weights": false,
    "initial_training_set_size": 752,
    "iterations": null,
    "items_to_label": 128,
    "batch_size_unlabeled_set": 128,
    "heatmaps_per_iteration": 5
  },
  "strategy_config": {
    "type": "uncertainty",
    "description": "uncertainty-distance",
    "calculation_method": "distance",
    "exclude_background": true,
    "prefer_unique_scans": true
  },
  "wandb_project_name": "active-segmentation-tests",
  "checkpoint_dir": "/dhc/groups/mpws2021cl1/Models",
  "experiment_name": "test-experiment",
  "experiment_tags": [],
  "batch_size": 32,
  "epochs": 5,
  "num_workers": 8,
  "gpus": 1,
  "prediction_count": 5,
  "prediction_dir": "/dhc/groups/mpws2021cl1/Predictions",
  "early_stopping": false,
  "random_state": 42
}