PyVertical

A project developing privacy-preserving,
vertical federated learning,
using syft.

• Private entity resolution

     using Private Set Intersection (PSI)

• Trains a model on vertically partitioned data

    using SplitNNs,
    so only data holders can access data

Vertically-partitioned data is data
in which
fields relating to a single record
are distributed across multiple datasets.
For example,
multiple hospitals may have admissions data on the same patients,
or retailers have transaction data on the same shoppers.
Vertically-partitioned data could be applied to solve vital problems,
but data holders can’t combine their datasets
by simply comparing notes with other data holders
unless they want to break user privacy.
PyVertical uses PSI
to link datasets in a privacy-preserving way.
We train SplitNNs on the partitioned data
to ensure the data remains separate throughout the entire process.

See the changelog
for information
on the current status of PyVertical.

NOTE: PyVertical does not currently work with syft 0.3.0

The Process

PyVertical process:

1. Create partitioned dataset
   • Simulate real-world partitioned dataset by splitting MNIST into a dataset of images and a dataset of labels
   • Give each data point (image + label) a unique ID
   • Randomly shuffle each dataset
   • Randomly remove some elements from each dataset
2. Link datasets using PSI
   • Use PSI to link indices in each dataset using unique IDs
   • Reorder datasets using linked indices
3. Train a split neural network
   • Hold both datasets in a dataloader
   • Send images to first part of split network
   • Send labels to second part of split network
   • Train the network

Requirements

OS

Windows	Linux	MacOS

The Windows PyTorch version 1.4.0 is experiencing issues.
It cannot be updated on a working version, until Syft will be updated, too.

Python

3.6	3.7	3.8	3.9

syft and PSI
upstream dependencies do not have Python 3.9
packages.

PyTorch Environment

To install the dependencies,
we recommend using Conda:

1. Clone this repository
2. In the command line, navigate to your local copy of the repository
3. Run conda env create -f environment.yml
   • This creates an environment pyvertical-dev
   • Comes with most dependencies you will need
4. Activate the environment with conda activate pyvertical-dev
5. Run conda install notebook

N.b. Installing the dependencies takes several steps to circumvent versioning incompatibility between
syft and jupyter.
In the future,
all packages will be moved into the environment.yml.

Tensorflow Environment

To install the dependencies,
we recommend using Conda:

1. Clone this repository
2. In the command line, navigate to your local copy of the repository
3. Run conda env create -f tf_environment.yml
   • This creates an environment pyvertical-dev-tf
   • Comes with most dependencies you will need
4. Activate the environment with conda activate pyvertical-dev-tf
5. Run conda install notebook

Docker

You can instead opt to use Docker.

To run:

1. Build the image with docker build -t pyvertical:latest .
2. Launch a container with docker run -it -p 8888:8888 pyvertical:latest
   • Defaults to launching jupyter lab

Synthea

PyVertical is applying fake medical data
generated by synthea
to demonstrate multi-party,
vertical federated learning.
Read the synthea docs
for requirements to generate the data.
With those pre-requisites installed,
run the scripts/download_synthea.sh
bash script
from the root directory
of this project,
which generates a deterministic dataset
and stores it in data/synthea.

Usage

Check out
examples/PyVertical Example.ipynb
to see PyVertical in action.

Goals

• [X] MVP
  • Simple example on MNIST dataset
  • One data holder has images, the other has labels
• Extension demonstration
  • Apply process to electronic health records (EHR) dataset
  • Dual-headed SplitNN: input data is split amongst several data holders
• Integrate with syft

Contributing

Pull requests are welcome.
For major changes,
please open an issue first to discuss what you would like to change.

Read the OpenMined
contributing guidelines
and styleguide
for more information.

Contributors

TTitcombe	Pavlos-p	H4LL	rsandmann	daler3

Testing

We use pytest to test the source code.
To run the tests manually:

1. In the command line, navigate to the root of this repository
2. Run python -m pytest

CI also checks the code is formatting according to contributing guidelines.

Publications

Romanini, D., Hall, A. J., Papadopoulos, P., Titcombe, T., Ismail, A., Cebere, T., Sandmann, R., Roehm, R. & Hoeh, M. A. (2021). PyVertical: A Vertical Federated Learning Framework for Multi-headed SplitNN. arXiv preprint arXiv:2104.00489. (link)

Angelou, N., Benaissa, A., Cebere, B., Clark, W., Hall, A. J., Hoeh, M. A., Liu, D., Papadopoulos, P., Roehm, R., Sandmann, R., Schoppmann, P. & Titcombe, T. (2020). Asymmetric Private Set Intersection with Applications to Contact Tracing and Private Vertical Federated Machine Learning. arXiv preprint arXiv:2011.09350. (link)

You can cite this work using:

@article{romanini2021pyvertical,
    title={PyVertical: A Vertical Federated Learning Framework for Multi-headed SplitNN},
    author={Romanini, Daniele and Hall, Adam James and Papadopoulos, Pavlos and Titcombe, Tom and Ismail, Abbas and Cebere, Tudor and Sandmann, Robert and Roehm, Robin and Hoeh, Michael A},
    journal={arXiv preprint arXiv:2104.00489},
    year={2021}
}
@article{angelou2020asymmetric,
    title={Asymmetric Private Set Intersection with Applications to Contact Tracing and Private Vertical Federated Machine Learning},
    author={Angelou, Nick and Benaissa, Ayoub and Cebere, Bogdan and Clark, William and Hall, Adam James and Hoeh, Michael A and Liu, Daniel and Papadopoulos, Pavlos and Roehm, Robin and Sandmann, Robert and others},
    journal={arXiv preprint arXiv:2011.09350},
    year={2020}
}

License

Apache License 2.0