GP-VAE: Deep Probabilistic Time Series Imputation

Vincent Fortuin, Dmitry Baranchuk, Gunnar Raetsch, Stephan Mandt
Proceedings of the Twenty Third International Conference on Artificial Intelligence and Statistics, PMLR 108:1651-1661, 2020.

Abstract

Multivariate time series with missing values are common in areas such as healthcare and finance, and have grown in number and complexity over the years. This raises the question whether deep learning methodologies can outperform classical data imputation methods in this domain. However, naive applications of deep learning fall short in giving reliable confidence estimates and lack interpretability.We propose a new deep sequential latent variable model for dimensionality reduction and data imputation. Our modeling assumption is simple and interpretable: the high dimensional time series has a lower-dimensional representation which evolves smoothly in time according to a Gaussian process. The non-linear dimensionality reduction in the presence of missing data is achieved using a VAE approach with a novel structured variational approximation. We demonstrate that our approach outperforms both classical and recent deep learning-based data imputation methods on high dimensional data from the domains of computer vision and healthcare.

Cite this Paper

BibTeX
@InProceedings{pmlr-v108-fortuin20a, title = {GP-VAE: Deep Probabilistic Time Series Imputation}, author = {Fortuin, Vincent and Baranchuk, Dmitry and Raetsch, Gunnar and Mandt, Stephan}, booktitle = {Proceedings of the Twenty Third International Conference on Artificial Intelligence and Statistics}, pages = {1651--1661}, year = {2020}, editor = {Chiappa, Silvia and Calandra, Roberto}, volume = {108}, series = {Proceedings of Machine Learning Research}, month = {26--28 Aug}, publisher = {PMLR}, pdf = {http://proceedings.mlr.press/v108/fortuin20a/fortuin20a.pdf}, url = {https://proceedings.mlr.press/v108/fortuin20a.html}, abstract = {Multivariate time series with missing values are common in areas such as healthcare and finance, and have grown in number and complexity over the years. This raises the question whether deep learning methodologies can outperform classical data imputation methods in this domain. However, naive applications of deep learning fall short in giving reliable confidence estimates and lack interpretability.We propose a new deep sequential latent variable model for dimensionality reduction and data imputation. Our modeling assumption is simple and interpretable: the high dimensional time series has a lower-dimensional representation which evolves smoothly in time according to a Gaussian process. The non-linear dimensionality reduction in the presence of missing data is achieved using a VAE approach with a novel structured variational approximation. We demonstrate that our approach outperforms both classical and recent deep learning-based data imputation methods on high dimensional data from the domains of computer vision and healthcare.} }
Endnote
%0 Conference Paper %T GP-VAE: Deep Probabilistic Time Series Imputation %A Vincent Fortuin %A Dmitry Baranchuk %A Gunnar Raetsch %A Stephan Mandt %B Proceedings of the Twenty Third International Conference on Artificial Intelligence and Statistics %C Proceedings of Machine Learning Research %D 2020 %E Silvia Chiappa %E Roberto Calandra %F pmlr-v108-fortuin20a %I PMLR %P 1651--1661 %U https://proceedings.mlr.press/v108/fortuin20a.html %V 108 %X Multivariate time series with missing values are common in areas such as healthcare and finance, and have grown in number and complexity over the years. This raises the question whether deep learning methodologies can outperform classical data imputation methods in this domain. However, naive applications of deep learning fall short in giving reliable confidence estimates and lack interpretability.We propose a new deep sequential latent variable model for dimensionality reduction and data imputation. Our modeling assumption is simple and interpretable: the high dimensional time series has a lower-dimensional representation which evolves smoothly in time according to a Gaussian process. The non-linear dimensionality reduction in the presence of missing data is achieved using a VAE approach with a novel structured variational approximation. We demonstrate that our approach outperforms both classical and recent deep learning-based data imputation methods on high dimensional data from the domains of computer vision and healthcare.
APA
Fortuin, V., Baranchuk, D., Raetsch, G. & Mandt, S.. (2020). GP-VAE: Deep Probabilistic Time Series Imputation. Proceedings of the Twenty Third International Conference on Artificial Intelligence and Statistics, in Proceedings of Machine Learning Research 108:1651-1661 Available from https://proceedings.mlr.press/v108/fortuin20a.html.

Related Material