Run workflows

Run the different workflows using

python3 workflows/{file}.py

from the root of the project directory.

Workflows

Workflow	Description
create_dataset.py	Create the dataset from the slides and annotations. Creates a patch level dataset from the slides and performs Stratified k-fold at the patch level. Mainly uses the dataset key in config.yaml.
create_dataset-MIL.py	Creates an MIL dataset from the slides.
model_train.py	Trains the model on the patch level dataset using the selected model. The trainer key in config.yaml is used for training configurations, while the model key is utilised for selecting models and specifying their parameters.
model_train-MIL.py	Train on an MIL dataset.
generate_heatmaps.py	Generate heatmaps for the slides using the predictions of the trained model.
exp_summary.py	Generate a summary of the experiment over the different folds. Also packs the results (metrics, plots and heatmaps) in an exportable ZIP file.