fl-prog

Federated disease progression modelling.

Setup

Check pyproject.toml for supported Python version(s).

In a Python environment managed by uv:

uv sync

In other types of Python environments (venv, conda, etc.):

pip install -e .

Sample commands

Generate synthetic data:

# iid case
./scripts/simulate_data.py ./data --tag iid

# non-iid cases
./scripts/simulate_data.py ./data --t0-min 0 --t0-max 0.32 --t0-min 0.33 --t0-max 0.65 --t0-min 0.66 --t0-max 1 --tag non_overlapping_t0

Merge data for centralized case:

./scripts/merge_data.py ./data --tag iid
./scripts/merge_data.py ./data --tag non_overlapping_t0

Create Fed-BioMed nodes:

# TODO

Add data to nodes:

./scripts/add_datasets_to_nodes.py ./data --tag iid
./scripts/add_datasets_to_nodes.py ./data --tag non_overlapping_t0

Run model fitting:

./scripts/run_fedbiomed.py ./data --tag iid
./scripts/run_fedbiomed.py ./data --tag non_overlapping_t0

Plot: run cells in ./notebooks/figs.ipynb