Section: New Software and Platforms


Multi Channel Variational Autoencoder

Keywords: Machine learning - Artificial intelligence - Medical applications - Dimensionality reduction - High Dimensional Data - Unsupervised learning - Heterogeneity

Scientific Description: Interpretable modeling of heterogeneous data channels is essential in medical applications, for example when jointly analyzing clinical scores and medical images. Variational Autoencoders (VAE) are powerful generative models that learn representations of complex data. The flexibility of VAE may come at the expense of lack of interpretability in describing the joint relationship between heterogeneous data. To tackle this problem, in this work we extend the variational framework of VAE to bring parsimony and interpretability when jointly account for latent relationships across multiple channels. In the latent space, this is achieved by constraining the variational distribution of each channel to a common target prior. Parsimonious latent representations are enforced by variational dropout. Experiments on synthetic data show that our model correctly identifies the prescribed latent dimensions and data relationships across multiple testing scenarios. When applied to imaging and clinical data, our method allows to identify the joint effect of age and pathology in describing clinical condition in a large scale clinical cohort.

Functional Description: This software implements the work published in the paper "Sparse Multi-Channel Variational Autoencoder for the Joint Analysis of Heterogeneous Data" presented at the conference ICML 2019 (Long Beach, California, USA).

The software extends classical variational autoencoders by identifying a joint latent code associated to heterogeneous data represented in different channels. The software is implemented in python and is based on pytorch. It can be applied to any kind of data arrays, and provides functions for optimisation, visualisation and writing of the modelling results.

Release Functional Description: First release

News Of The Year: Method presented in the International Conference on Machine Learning (ICML 2019).