Concrete Autoencoders: Differentiable Feature Selection and Reconstruction
Muhammed Fatih Balın, Abubakar Abid, James Zou
Abstract
We introduce the concrete autoencoder, an end-to-end differentiable method for global feature selection, which efficiently identifies a subset of the most informative features and simultaneously learns a neural network to reconstruct the input data from the selected features. Our method is unsupervised, and is based on using a concrete selector layer as the encoder and using a standard neural network as the decoder. During the training phase, the temperature of the concrete selector layer is gradually decreased, which encourages a user-specified number of discrete features to be learned; during test time, the selected features can be used with the decoder network to reconstruct the remaining input features. We evaluate concrete autoencoders on a variety of datasets, where they significantly outperform state-of-the-art methods for feature selection and data reconstruction. In particular, on a large-scale gene expression dataset, the concrete autoencoder selects a small subset of genes whose expression levels can be used to impute the expression levels of the remaining genes; in doing so, it improves on the current widely-used expert-curated L1000 landmark genes, potentially reducing measurement costs by 20%. The concrete autoencoder can be implemented by adding just a few lines of code to a standard autoencoder, and the code for the algorithm and experiments is publicly available.
BibTeX
@InProceedings{pmlr-v97-balin19a,
title = {Concrete Autoencoders: Differentiable Feature Selection and Reconstruction},
author = {Bal{\i}n, Muhammed Fatih and Abid, Abubakar and Zou, James},
booktitle = {Proceedings of the 36th International Conference on Machine Learning},
pages = {444--453},
year = {2019},
editor = {Chaudhuri, Kamalika and Salakhutdinov, Ruslan},
volume = {97},
series = {Proceedings of Machine Learning Research},
month = {09--15 Jun},
publisher = {PMLR},
pdf = {http://proceedings.mlr.press/v97/balin19a/balin19a.pdf},
url = {https://proceedings.mlr.press/v97/balin19a.html},
abstract = {We introduce the concrete autoencoder, an end-to-end differentiable method for global feature selection, which efficiently identifies a subset of the most informative features and simultaneously learns a neural network to reconstruct the input data from the selected features. Our method is unsupervised, and is based on using a concrete selector layer as the encoder and using a standard neural network as the decoder. During the training phase, the temperature of the concrete selector layer is gradually decreased, which encourages a user-specified number of discrete features to be learned; during test time, the selected features can be used with the decoder network to reconstruct the remaining input features. We evaluate concrete autoencoders on a variety of datasets, where they significantly outperform state-of-the-art methods for feature selection and data reconstruction. In particular, on a large-scale gene expression dataset, the concrete autoencoder selects a small subset of genes whose expression levels can be used to impute the expression levels of the remaining genes; in doing so, it improves on the current widely-used expert-curated L1000 landmark genes, potentially reducing measurement costs by 20%. The concrete autoencoder can be implemented by adding just a few lines of code to a standard autoencoder, and the code for the algorithm and experiments is publicly available.}
}