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 .

Steps

These scripts should be done sequentially.

Generate synthetic data

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

# non-iid cases
./scripts/simulate_data.py --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
./scripts/simulate_data.py --sigma 0.05 --sigma 0.1 --sigma 0.15 --tag unequal_sigma

Merge data for centralized case

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

Create Fed-BioMed nodes and update their config.ini

./scripts/create_nodes.py --tag iid
./scripts/create_nodes.py --tag non_overlapping_t0
./scripts/create_nodes.py --tag unequal_sigma

Add data to nodes

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

Start the nodes in separate processes

• For each node, make sure you are in the node directory, e.g. ./fedbiomed/node-1
• Then run fedbiomed node -p . start

Run model fitting

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

Plot

Run cells in ./notebooks/figs.ipynb