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SOM-VAE model

This repository contains a TensorFlow implementation of the self-organizing map variational autoencoder as described in the paper SOM-VAE: Interpretable Discrete Representation Learning on Time Series.

If you like the SOM-VAE, you should also check out the DPSOM (paper, code), which yields better performance on many tasks.

Getting Started

These instructions will get you a copy of the project up and running on your local machine for development and testing purposes.

Prerequisites

In order to install and run the model, you will need a working Python 3 distribution as well as a NVIDIA GPU with CUDA and cuDNN installed.

Installing

In order to install the model and run it, you have to follow these steps:

  • Clone the repository, i.e. run git clone https://github.com/ratschlab/SOM-VAE
  • Change into the directory, i.e. run cd SOM-VAE
  • Install the requirements, i.e. run pip install -r requirements.txt
  • Install the package itself, i.e. run pip install .
  • Change into the code directory, i.e. cd som_vae

Now you should be able to run the code, e.g. do python somvae_train.py.

Training the model

The SOM-VAE model is defined in somvae_model.py. The training script is somvae_train.py.

If you just want to train the model with default parameter settings, you can run

python somvae_train.py

This will download the MNIST data set into data/MNIST_data/ and train on it. Afterwards, it will evaluate the trained model in terms of different clustering performance measures.

The parameters are handled using sacred. That means that if you want to run the model with a different parameter setting, e.g. a latent space dimensionality of 32, you can just call the training script like

python somvae_train.py with latent_dim=32

Per default, the script will generate time courses of linearly interpolated MNIST digits. To train on normal MNIST instead, run

python somvae_train.py with time_series=False

Note that for non-time-series training, you should also set the loss parameters gamma and tau to 0. If you want to save the model for later use, run

python somvae_train.py with save_model=True

If you want to train on Fashion-MNIST istead of normal MNIST, download the data set into data/fashion/ and run

python somvae_train.py with data_set="fashion"

For more details regarding the different model parameters and how to set them, please look at the documentation in the code and at the sacred documentation.

Hyperparameter optimization

If you want to optimize the models hyperparameters, you have to additionally install labwatch and SMAC and comment the commented out lines in somvae_train.py in. Note that you also have to run a local distribution of the MongoDB.

Train on other kinds of data

If you want to train on other types of data, you have to run the training with

python somvae_train.py with mnist=False

Moreover, you have to define the correct dimensionality in the respective input_length and input_channels parameters of the model, provide a suitable data generator in somvae_train.py and potentially change the dimensionality of the layers in somvae_model.py.

To reproduce the experiments on eICU data, please use the preprocessing pipeline from this repository: https://github.com/ratschlab/variational-psom

Authors

See also the list of contributors who participated in this project.

License

This project is licensed under the MIT License - see the LICENSE file for details