README.md

Mnist

This example is a Substra implementation of on the MNIST example from Keras, inspired from Substra's Titanic Example

In this example, we'll see how to setup an objective and how to train algorithms on the MNIST dataset.

You can run this example in Google Colab or JupyterLab with this Notebook.

Prerequisites

In order to run this example, you'll need to:

• use Python 3

• have Docker installed

• install the substra cli (supported version: 0.6.0)

• install the substratools library (supported version: 0.6.0)

• pull the substra-tools docker images

• have access to a Substra installation (configure your host to a public node ip or install Substra on your machine). Check that this installation is compatible with your CLI version.

• create a substra profile to define the substra network to target, for instance:

  substra config --profile node-1 http://substra-backend.node-1.com
  substra login --profile node-1 --username node-1 --password 'p@$swr0d44'

• checkout this repository

All commands in this example are run from the mnist folder.

Data preparation

The first step will be to generate train and test data from keras.datasets.mnist

To generate the data, run:

pip install --upgrade pip
pip install -r scripts/requirements.txt
python scripts/generate_data.py

This will create two sub-folders in the assets folder:

• train_data contains train data features and labels as numpy array files
• test_data contains test data features and labels as numpy array files

Writing the objective and data manager

Both objective and data manager will need a proper markdown description, you can check them out in their respective folders. Notice that the data manager's description includes a formal description of the data structure.

Notice also that the metrics.py and opener.py module both rely on classes imported from the substratools module. These classes provide a simple yet rigid structure that will make algorithms pretty easy to write.

Writing a simple algorithm

You'll find under assets/algo_cnn an implementation of the cnn model in the Keras example. Like the metrics and opener scripts, it relies on a class imported from substratools that greatly simplifies the writing process. You'll notice that it handles not only the train and predict tasks but also a lot of data preprocessing.

Testing our assets

Using asset command line interfaces

You can first test each assets with the substratools CLI, by running specific ML tasks in your local Python environment.

Training task

# train your model with the train_data
python assets/algo_cnn/algo.py train \
  --debug \
  --opener-path assets/dataset/opener.py \
  --data-samples-path assets/train_data \
  --output-model-path assets/model/model \
  --log-path assets/logs/train.log

# predict the labels of train_data with your previously trained model
python assets/algo_cnn/algo.py predict \
  --debug \
  --opener-path assets/dataset/opener.py \
  --data-samples-path assets/train_data \
  --output-predictions-path assets/pred-train.npy \
  --models-path assets/model/ \
  --log-path assets/logs/train_predict.log \
  model

# calculate the score of your model on train_data predictions
python assets/objective/metrics.py \
  --debug \
  --opener-path assets/dataset/opener.py \
  --data-samples-path assets/train_data \
  --input-predictions-path assets/pred-train.npy \
  --output-perf-path assets/perf-train.json \
  --log-path assets/logs/train_metrics.log

Testing task

# predict the labels of test_data with your previously trained model
python assets/algo_cnn/algo.py predict \
  --debug \
  --opener-path assets/dataset/opener.py \
  --data-samples-path assets/test_data \
  --output-predictions-path assets/pred-test.npy \
  --models-path assets/model/ \
  --log-path assets/logs/test_predict.log \
  model

# calculate the score of your model on test_data predictions
python assets/objective/metrics.py \
  --debug \
  --opener-path assets/dataset/opener.py \
  --data-samples-path assets/test_data \
  --input-predictions-path assets/pred-test.npy \
  --output-perf-path assets/perf-test.json \
  --log-path assets/logs/test_metrics.log

Using substra cli

Before pushing our assets to the platform, we need to make sure they work well. To do so, we can run them locally in a Docker container. This way, if the training fails, we can access the logs and debug our code.

To test the assets, we'll use substra run-local, passing it paths to our algorithm of course, but also the opener, the metrics and to the data samples we want to use. It will launch a training task on the train data, a prediction task on the test data and return the accuracy score.

substra run-local assets/algo_cnn \
  --train-opener=assets/dataset/opener.py \
  --test-opener=assets/dataset/opener.py \
  --metrics=assets/objective/ \
  --train-data-samples=assets/train_data \
  --test-data-samples=assets/test_data

At the end of this step, you'll find in the newly created sandbox/model folder a model file that contains your trained model. There is also a sandbox/pred_train folder that contains both the predictions made by the model on train data and the associated performance.

Debugging

It's more than probable that your code won't run perfectly the first time. Since runs happen in dockers, you can't debug using prints. Instead, you should use the logging module from python. All logs can then be consulted at the end of the run in sandbox/model/log_model.log.

Adding the assets to substra

Adding the objective, dataset and data samples to substra

A script has been written that adds objective, data manager and data samples to substra. It uses the substra python sdk to perform actions. It's main goal is to create assets, get their keys and use these keys in the creation of other assets.

To run it:

pip install -r scripts/requirements.txt
python scripts/add_dataset_objective.py

This script just generated an assets_keys.json file in the mnist folder. This file contains the keys of all assets we've just created and organizes the keys of the train data samples in folds. This file will be used as input when adding an algorithm so that we can automatically launch all training and testing tasks.

Adding the algorithm and training it

The script add_train_algo_cnn.py pushes our simple algo to substra and then uses the assets_keys.json file we just generated to train it against the dataset and objective we previously set up. It will then update the assets_keys.json file with the newly created assets keys (algo, traintuple and testtuple)

To run it:

python scripts/add_train_algo_cnn.py

It will end by providing a couple of commands you can use to track the progress of the train and test tuples as well as the associated scores. Alternatively, you can browse the frontend to look up progress and scores.