BasisVAE: Translation-invariant feature-level clustering with Variational Autoencoders

Kaspar Märtens, Christopher Yau
Proceedings of the Twenty Third International Conference on Artificial Intelligence and Statistics, PMLR 108:2928-2937, 2020.

Abstract

Variational Autoencoders (VAEs) provide a flexible and scalable framework for non-linear dimensionality reduction. However, in application domains such as genomics where data sets are typically tabular and high-dimensional, a black-box approach to dimensionality reduction does not provide sufficient insights. Common data analysis workflows additionally use clustering techniques to identify groups of similar features. This usually leads to a two-stage process, however, it would be desirable to construct a joint modelling framework for simultaneous dimensionality reduction and clustering of features. In this paper, we propose to achieve this through the BasisVAE: a combination of the VAE and a probabilistic clustering prior, which lets us learn a one-hot basis function representation as part of the decoder network. Furthermore, for scenarios where not all features are aligned, we develop an extension to handle translation-invariant basis functions. We show how a collapsed variational inference scheme leads to scalable and efficient inference for BasisVAE, demonstrated on various toy examples as well as on single-cell gene expression data.

Cite this Paper


BibTeX
@InProceedings{pmlr-v108-martens20b, title = {BasisVAE: Translation-invariant feature-level clustering with Variational Autoencoders}, author = {M\"artens, Kaspar and Yau, Christopher}, booktitle = {Proceedings of the Twenty Third International Conference on Artificial Intelligence and Statistics}, pages = {2928--2937}, year = {2020}, editor = {Silvia Chiappa and Roberto Calandra}, volume = {108}, series = {Proceedings of Machine Learning Research}, month = {26--28 Aug}, publisher = {PMLR}, pdf = {http://proceedings.mlr.press/v108/martens20b/martens20b.pdf}, url = { http://proceedings.mlr.press/v108/martens20b.html }, abstract = {Variational Autoencoders (VAEs) provide a flexible and scalable framework for non-linear dimensionality reduction. However, in application domains such as genomics where data sets are typically tabular and high-dimensional, a black-box approach to dimensionality reduction does not provide sufficient insights. Common data analysis workflows additionally use clustering techniques to identify groups of similar features. This usually leads to a two-stage process, however, it would be desirable to construct a joint modelling framework for simultaneous dimensionality reduction and clustering of features. In this paper, we propose to achieve this through the BasisVAE: a combination of the VAE and a probabilistic clustering prior, which lets us learn a one-hot basis function representation as part of the decoder network. Furthermore, for scenarios where not all features are aligned, we develop an extension to handle translation-invariant basis functions. We show how a collapsed variational inference scheme leads to scalable and efficient inference for BasisVAE, demonstrated on various toy examples as well as on single-cell gene expression data. } }
Endnote
%0 Conference Paper %T BasisVAE: Translation-invariant feature-level clustering with Variational Autoencoders %A Kaspar Märtens %A Christopher Yau %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-martens20b %I PMLR %P 2928--2937 %U http://proceedings.mlr.press/v108/martens20b.html %V 108 %X Variational Autoencoders (VAEs) provide a flexible and scalable framework for non-linear dimensionality reduction. However, in application domains such as genomics where data sets are typically tabular and high-dimensional, a black-box approach to dimensionality reduction does not provide sufficient insights. Common data analysis workflows additionally use clustering techniques to identify groups of similar features. This usually leads to a two-stage process, however, it would be desirable to construct a joint modelling framework for simultaneous dimensionality reduction and clustering of features. In this paper, we propose to achieve this through the BasisVAE: a combination of the VAE and a probabilistic clustering prior, which lets us learn a one-hot basis function representation as part of the decoder network. Furthermore, for scenarios where not all features are aligned, we develop an extension to handle translation-invariant basis functions. We show how a collapsed variational inference scheme leads to scalable and efficient inference for BasisVAE, demonstrated on various toy examples as well as on single-cell gene expression data.
APA
Märtens, K. & Yau, C.. (2020). BasisVAE: Translation-invariant feature-level clustering with Variational Autoencoders. Proceedings of the Twenty Third International Conference on Artificial Intelligence and Statistics, in Proceedings of Machine Learning Research 108:2928-2937 Available from http://proceedings.mlr.press/v108/martens20b.html .

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