Flower Example using KaplanMeierFitter#

This is an introductory example on federated survival analysis using Flower and lifelines library.

The aim of this example is to estimate the survival function using the Kaplan-Meier Estimate implemented in lifelines library (see KaplanMeierFitter). The distributed/federated aspect of this example is the data sending to the server. You can think of it as a federated analytics example. However, it’s worth noting that this procedure violates privacy since the raw data is exchanged.

Finally, many other estimators beyond KaplanMeierFitter can be used with the provided strategy: AalenJohansenFitter, GeneralizedGammaFitter, LogLogisticFitter, SplineFitter, and WeibullFitter.

We also use the NatualPartitioner from Flower Datasets to divide the data according to the group it comes from therefore to simulate the division that might occur.

Survival Function

Project Setup#

Start by cloning the example project. We prepared a single-line command that you can copy into your shell which will checkout the example for you:

$ git clone --depth=1 https://github.com/adap/flower.git _tmp && mv _tmp/examples/federated-kaplan-meier-fitter . && rm -rf _tmp && cd federated-kaplan-meier-fitter

This will create a new directory called federated-kaplan-meier-fitter containing the following files:

-- pyproject.toml
-- requirements.txt
-- client.py
-- server.py
-- centralized.py
-- README.md

Installing Dependencies#

Project dependencies (such as lifelines and flwr) are defined in pyproject.toml and requirements.txt. We recommend Poetry to install those dependencies and manage your virtual environment (Poetry installation) or pip, but feel free to use a different way of installing dependencies and managing virtual environments if you have other preferences.

Poetry#

poetry install
poetry shell

Poetry will install all your dependencies in a newly created virtual environment. To verify that everything works correctly you can run the following command:

poetry run python3 -c "import flwr"

If you don’t see any errors you’re good to go!

pip#

Write the command below in your terminal to install the dependencies according to the configuration file requirements.txt.

pip install -r requirements.txt

Run Federated Survival Analysis with Flower and lifelines’s KaplanMeierFitter#

Start the long-running Flower server (SuperLink)#

flower-superlink --insecure

Start the long-running Flower client (SuperNode)#

In a new terminal window, start the first long-running Flower client:

flower-client-app client:node_1_app --insecure

In yet another new terminal window, start the second long-running Flower client:

flower-client-app client:node_2_app --insecure

Run the Flower App#

With both the long-running server (SuperLink) and two clients (SuperNode) up and running, we can now run the actual Flower App:

flower-server-app server:app --insecure

You will see that the server is printing survival function, median survival time and saves the plot with the survival function.

You can also check that the results match the centralized version.

$ python3 centralized.py