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 run sequentially.

Get data

Synthetic

# 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

ADNI

./scripts/get_fs_data.py --tag adni_iid --iid
./scripts/get_fs_data.py --tag adni_noniid --non-iid

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

./scripts/merge_data.py --tag adni_iid
./scripts/merge_data.py --tag adni_noniid

Create Fed-BioMed nodes and update their config.ini

This only needs to be run if some of the nodes haven't been created yet.

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

./scripts/create_nodes.py --tag adni_iid
./scripts/create_nodes.py --tag adni_noniid

Add data to nodes

If needed, use --wipe to clear existing datasets from each node.

./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

./scripts/add_datasets_to_nodes.py --tag adni_iid
./scripts/add_datasets_to_nodes.py --tag adni_noniid

Start the nodes in separate processes

Start each node in a separate Terminal. These need to be running for the next script (run_fedbiomed.py) to work. Use Ctrl+C to stop a node when done.

# replace <NODE_ID> by '1', '2', '3', ..., or 'centralized'
fedbiomed node -p ./fedbiomed/node-<NODE_ID> start

Run model fitting

./scripts/run_fedbiomed.py --tag iid --n-rounds 5 --n-updates 100 --learning-rate 0.05 --time-shift-range 0 1
./scripts/run_fedbiomed.py --tag non_overlapping_t0 --n-rounds 5 --n-updates 100 --learning-rate 0.05 --time-shift-range 0 1
./scripts/run_fedbiomed.py --tag unequal_sigma --n-rounds 5 --n-updates 100 --learning-rate 0.05 --time-shift-range 0 1

./scripts/run_fedbiomed.py --tag adni_iid --learning-rate 0.05 --n-rounds 6 --n-updates 25 --time-shift-range 0 3 --lambda 10 --training-replies --aggregated-params
./scripts/run_fedbiomed.py --tag adni_noniid --learning-rate 0.05 --n-rounds 6 --n-updates 25 --time-shift-range 0 3 --lambda 10 --training-replies --aggregated-params

Plot

Synthetic data experiments

Run cells in ./notebooks/model_fits_synthetic.ipynb

ADNI data experiments

Run cells in ./notebooks/model_fits_adni.ipynb