.. FLamby documentation master file, created by
   sphinx-quickstart on Wed May 11 17:24:35 2022.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to FLamby's documentation!
==================================

FLamby
######


.. image:: logo.png
   :scale: 50 %
   :align: center
  



`FLamby <https://github.com/owkin/FLamby>`_ [#flamby_meaning]_ is a repository regrouping several distributed datasets
with natural splits whose aim is to facilitate benchmarking new cross-silo FL strategies on realistic problems.

You can find a link to the companion paper published at NeurIPS 2022 in the 
Dataset and Benchmark track `here <https://arxiv.org/abs/2210.04620>`_

If you use FLamby please consider citing it::

      @inproceedings{NEURIPS2022_232eee8e,
       author = {Ogier du Terrail, Jean and Ayed, Samy-Safwan and Cyffers, Edwige and Grimberg, Felix and He, Chaoyang and Loeb, Regis and Mangold, Paul and Marchand, Tanguy and Marfoq, Othmane and Mushtaq, Erum and Muzellec, Boris and Philippenko, Constantin and Silva, Santiago and Tele\'{n}czuk, Maria and Albarqouni, Shadi and Avestimehr, Salman and Bellet, Aur\'{e}lien and Dieuleveut, Aymeric and Jaggi, Martin and Karimireddy, Sai Praneeth and Lorenzi, Marco and Neglia, Giovanni and Tommasi, Marc and Andreux, Mathieu},
       booktitle = {Advances in Neural Information Processing Systems},
       editor = {S. Koyejo and S. Mohamed and A. Agarwal and D. Belgrave and K. Cho and A. Oh},
       pages = {5315--5334},
       publisher = {Curran Associates, Inc.},
       title = {FLamby: Datasets and Benchmarks for Cross-Silo Federated Learning in Realistic Healthcare Settings},
       url = {https://proceedings.neurips.cc/paper_files/paper/2022/file/232eee8ef411a0a316efa298d7be3c2b-Paper-Datasets_and_Benchmarks.pdf},
       volume = {35},
       year = {2022}
      }


FLamby is more a dataset suite than a pure code repository. Mainly we provide code to easily access datasets stored in other
repositories and make them FL-ready. In particular, we do not distribute datasets in this repository, and we do not own
copyrights on any of the datasets.

The use of any of the datasets included in FLamby requires accepting its corresponding license on the original website. 
We refer to each corresponding dataset's sections for more informations on its terms of use.

For any problem or question with respect to any license related matters, please open `a github issue <https://github.com/owkin/FLamby/issues>`_ 
on this repository.  

Before jumping to the :any:`quickstart` , make sure FLamby is properly installed following the steps highlighted in 
:any:`installation`

Team
----

This repository was created thanks to the contributions of many researchers and engineers. 
We list them in the order of the companion article, following the `CREDIT
framework <https://credit.niso.org/>`__: `Jean Ogier du
Terrail <https://github.com/jeandut>`__, `Samy-Safwan
Ayed <https://github.com/AyedSamy>`__, `Edwige
Cyffers <https://github.com/totilas>`__, `Felix
Grimberg <https://github.com/Grim-bot>`__, `Chaoyang
He <https://github.com/chaoyanghe>`__, `Régis
Loeb <https://github.com/regloeb>`__, `Paul
Mangold <https://github.com/pmangold>`__, `Tanguy
Marchand <https://github.com/tanguy-marchand>`__, `Othmane
Marfoq <https://github.com/omarfoq/>`__, `Erum
Mushtaq <https://github.com/ErumMushtaq>`__, `Boris
Muzellec <https://github.com/BorisMuzellec>`__, `Constantin
Philippenko <https://github.com/philipco>`__, `Santiago
Silva <https://github.com/sssilvar>`__, `Maria
Telenczuk <https://github.com/maikia>`__, `Shadi
Albarqouni <https://albarqouni.github.io/>`__, `Salman
Avestimehr <https://www.avestimehr.com/>`__, `Aurélien
Bellet <http://researchers.lille.inria.fr/abellet/>`__, `Aymeric
Dieuleveut <http://www.cmap.polytechnique.fr/~aymeric.dieuleveut/>`__,
`Martin Jaggi <https://people.epfl.ch/martin.jaggi>`__, `Sai Praneeth
Karimireddy <https://github.com/Saipraneet>`__, `Marco
Lorenzi <https://marcolorenzi.github.io/publications.html>`__, `Giovanni
Neglia <http://www-sop.inria.fr/members/Giovanni.Neglia/publications.htm>`__,
`Marc
Tommasi <http://researchers.lille.inria.fr/tommasi/#publications>`__,
`Mathieu Andreux <https://github.com/mandreux-owkin>`__.

Acknowledgements
----------------

FLamby's initiative was made possible thanks to the support of the following
institutions: - `Owkin <https://www.owkin.com>`__ -
`Inria <https://www.inria.fr>`__ - `Ecole
polytechnique <https://www.polytechnique.edu>`__ - `University of
California - Berkeley <https://www.berkeley.edu/>`__ - `University of
Southern California (USC) <https://www.usc.edu/>`__ -
`EPFL <https://www.epfl.ch>`__ - `Universitätsklinikum
Bonn <https://www.ukbonn.de/patient_innen/international/english/>`__

.. rubric:: Footnotes

.. [#flamby_meaning] `Federated Learning AMple Benchmark of Your cross-silo strategies`



.. toctree::
   :maxdepth: 0
   :caption: Installation
   
   installation


.. toctree::
   :maxdepth: 0
   :caption: Getting Started Instructions
   
   quickstart


.. toctree::
   :maxdepth: 0
   :caption: Datasets informations
   
   fed_tcga_brca
   fed_heart
   fed_ixi
   fed_isic
   fed_camelyon
   fed_lidc
   fed_kits19

.. toctree::
   :maxdepth: 0
   :caption: Integration with FL-frameworks
   
   substra
   fedbiomed
   fedml

.. toctree::
   :maxdepth: 0
   :caption: Reproducible results with docker
   
   docker

.. toctree::
   :maxdepth: 0
   :caption: Reproducing results
   
   reproducing

.. toctree::
   :maxdepth: 0
   :caption: FAQ

   faq


.. toctree::
   :maxdepth: 0
   :caption: Extending FLamby

   contributing


.. toctree::
   :maxdepth: 0
   :caption: Code Documentation

   strategies
   datasets





Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`