docs/configuration.md

Configuration

YAML values always override CLI defaults (args.__dict__.update(config)). To override a YAML value, edit the YAML file or omit the key so the CLI default is used.

python run_pirads.py --mode train --config config/config_pirads_train.yaml

PI-RADS Training Parameters

Parameter	Default	Description
mode	—	train or test (required)
config	—	Path to YAML config file
data_root	—	Root folder of T2W images
dataset_json	—	Path to dataset JSON file. Format should be as specified in Getting Started
num_classes	4	Number of output classes (PI-RADS 2–5)
mil_mode	att_trans	MIL algorithm (mean, max, att, att_trans, att_trans_pyramid)
tile_count	24	Number of patches per scan
tile_size	64	Patch spatial size in pixels
depth	3	Number of slices per patch
use_heatmap	True	Enable heatmap-guided patch sampling
workers	2	DataLoader workers
checkpoint	None	Path to resume from checkpoint
epochs	50	Max training epochs
early_stop	40	Epochs without improvement before stopping
batch_size	4	Scans per batch
optim_lr	3e-5	Base learning rate
weight_decay	0	Optimizer weight decay
amp	False	Enable automatic mixed precision
val_every	1	Validation frequency (epochs)
wandb	False	Enable Weights & Biases logging
project_name	Classification_prostate	W&B project name
run_name	train_pirads	Run name for logging. If using SLURM, takes SLURM JOB_ID

csPCa Training Parameters

Parameter	Default	Description
mode	—	train or test (required)
config	—	Path to YAML config file
data_root	—	Root folder of images
dataset_json	—	Path to dataset JSON file
checkpoint_pirads	—	Path to pre-trained PI-RADS model (required for train)
checkpoint_cspca	—	Path to csPCa checkpoint (required for test)
epochs	30	Max training epochs
batch_size	32	Scans per batch
optim_lr	2e-4	Learning rate
num_seeds	20	Number of random seeds for CI

Shared parameters (num_classes, mil_mode, tile_count, tile_size, depth, use_heatmap, workers, val_every) have the same defaults as PI-RADS.

Preprocessing Parameters

Parameter	Default	Description
config	—	Path to YAML config file
steps	—	Steps to execute (required, one or more)
t2_dir	—	Directory of T2W images
dwi_dir	—	Directory of DWI images
adc_dir	—	Directory of ADC images
seg_dir	—	Directory of segmentation masks
output_dir	—	Output directory
margin	0.2	Center-crop margin fraction

Example YAML

=== "PI-RADS Training"

```yaml
data_root: /path/to/registered/t2_hist_matched
dataset_json: /path/to/PI-RADS_data.json
num_classes: 4
mil_mode: att_trans
tile_count: 24
tile_size: 64
depth: 3
use_heatmap: true
workers: 4
epochs: 100
batch_size: 8
optim_lr: 2e-4
weight_decay: 1e-5
amp: true
wandb: true
```

=== "csPCa Training"

```yaml
data_root: /path/to/registered/t2_hist_matched
dataset_json: /path/to/csPCa_data.json
num_classes: 4
mil_mode: att_trans
tile_count: 24
tile_size: 64
depth: 3
use_heatmap: true
workers: 6
checkpoint_pirads: /path/to/models/pirads.pt
epochs: 80
batch_size: 8
optim_lr: 2e-4
```

=== "Preprocessing"

```yaml
t2_dir: /path/to/raw/t2
dwi_dir: /path/to/raw/dwi
adc_dir: /path/to/raw/adc
output_dir: /path/to/processed
```