Fast and Scalable Spike and Slab Variable Selection in High-Dimensional Gaussian Processes

Hugh Dance, Brooks Paige
Proceedings of The 25th International Conference on Artificial Intelligence and Statistics, PMLR 151:7976-8002, 2022.

Abstract

Variable selection in Gaussian processes (GPs) is typically undertaken by thresholding the inverse lengthscales of automatic relevance determination kernels, but in high-dimensional datasets this approach can be unreliable. A more probabilistically principled alternative is to use spike and slab priors and infer a posterior probability of variable inclusion. However, existing implementations in GPs are very costly to run in both high-dimensional and large-n datasets, or are only suitable for unsupervised settings with specific kernels. As such, we develop a fast and scalable variational inference algorithm for the spike and slab GP that is tractable with arbitrary differentiable kernels. We improve our algorithm’s ability to adapt to the sparsity of relevant variables by Bayesian model averaging over hyperparameters, and achieve substantial speed ups using zero temperature posterior restrictions, dropout pruning and nearest neighbour minibatching. In experiments our method consistently outperforms vanilla and sparse variational GPs whilst retaining similar runtimes (even when n=10^6) and performs competitively with a spike and slab GP using MCMC but runs up to 1000 times faster.

Cite this Paper

BibTeX
@InProceedings{pmlr-v151-dance22a, title = { Fast and Scalable Spike and Slab Variable Selection in High-Dimensional Gaussian Processes }, author = {Dance, Hugh and Paige, Brooks}, booktitle = {Proceedings of The 25th International Conference on Artificial Intelligence and Statistics}, pages = {7976--8002}, year = {2022}, editor = {Camps-Valls, Gustau and Ruiz, Francisco J. R. and Valera, Isabel}, volume = {151}, series = {Proceedings of Machine Learning Research}, month = {28--30 Mar}, publisher = {PMLR}, pdf = {https://proceedings.mlr.press/v151/dance22a/dance22a.pdf}, url = {https://proceedings.mlr.press/v151/dance22a.html}, abstract = { Variable selection in Gaussian processes (GPs) is typically undertaken by thresholding the inverse lengthscales of automatic relevance determination kernels, but in high-dimensional datasets this approach can be unreliable. A more probabilistically principled alternative is to use spike and slab priors and infer a posterior probability of variable inclusion. However, existing implementations in GPs are very costly to run in both high-dimensional and large-n datasets, or are only suitable for unsupervised settings with specific kernels. As such, we develop a fast and scalable variational inference algorithm for the spike and slab GP that is tractable with arbitrary differentiable kernels. We improve our algorithm’s ability to adapt to the sparsity of relevant variables by Bayesian model averaging over hyperparameters, and achieve substantial speed ups using zero temperature posterior restrictions, dropout pruning and nearest neighbour minibatching. In experiments our method consistently outperforms vanilla and sparse variational GPs whilst retaining similar runtimes (even when n=10^6) and performs competitively with a spike and slab GP using MCMC but runs up to 1000 times faster. } }
Endnote
%0 Conference Paper %T Fast and Scalable Spike and Slab Variable Selection in High-Dimensional Gaussian Processes %A Hugh Dance %A Brooks Paige %B Proceedings of The 25th International Conference on Artificial Intelligence and Statistics %C Proceedings of Machine Learning Research %D 2022 %E Gustau Camps-Valls %E Francisco J. R. Ruiz %E Isabel Valera %F pmlr-v151-dance22a %I PMLR %P 7976--8002 %U https://proceedings.mlr.press/v151/dance22a.html %V 151 %X Variable selection in Gaussian processes (GPs) is typically undertaken by thresholding the inverse lengthscales of automatic relevance determination kernels, but in high-dimensional datasets this approach can be unreliable. A more probabilistically principled alternative is to use spike and slab priors and infer a posterior probability of variable inclusion. However, existing implementations in GPs are very costly to run in both high-dimensional and large-n datasets, or are only suitable for unsupervised settings with specific kernels. As such, we develop a fast and scalable variational inference algorithm for the spike and slab GP that is tractable with arbitrary differentiable kernels. We improve our algorithm’s ability to adapt to the sparsity of relevant variables by Bayesian model averaging over hyperparameters, and achieve substantial speed ups using zero temperature posterior restrictions, dropout pruning and nearest neighbour minibatching. In experiments our method consistently outperforms vanilla and sparse variational GPs whilst retaining similar runtimes (even when n=10^6) and performs competitively with a spike and slab GP using MCMC but runs up to 1000 times faster.
APA
Dance, H. & Paige, B.. (2022). Fast and Scalable Spike and Slab Variable Selection in High-Dimensional Gaussian Processes . Proceedings of The 25th International Conference on Artificial Intelligence and Statistics, in Proceedings of Machine Learning Research 151:7976-8002 Available from https://proceedings.mlr.press/v151/dance22a.html.

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