deepgp-package: Package deepgp

deepgp-packageR Documentation

Package deepgp


Performs posterior inference for deep Gaussian processes following Sauer, Gramacy, and Higdon (2020) <arXiv:2012.08015>. Models are trained through MCMC including elliptical slice sampling of latent Gaussian layers and Metropolis-Hastings sampling of kernel hyperparameters. Vecchia-approximation for faster computation is implemented following Sauer, Cooper, and Gramacy (2022) <arXiv:2204.02904>. Downstream tasks include sequential design through active learning Cohn/integrated mean squared error (ALC/IMSE; Sauer, Gramacy, and Higdon, 2020) and optimization through expected improvement (EI; Gramacy, Sauer, and Wycoff, 2021 <arXiv:2112.07457>). Models extend up to three layers deep; a one layer model is equivalent to typical Gaussian process regression. Covariance kernel options are matern (default) and squared exponential. Applicable to both noisy and deterministic functions. Incorporates SNOW parallelization and utilizes C and C++ under the hood.

Important Functions

  • fit_one_layer: conducts MCMC sampling of hyperparameters for a one layer GP

  • fit_two_layer: conducts MCMC sampling of hyperparameters and hidden layer for a two layer deep GP

  • fit_three_layer: conducts MCMC sampling of hyperparameters and hidden layers for a three layer deep GP

  • continue: collects additional MCMC samples

  • trim: cuts off burn-in and optionally thins samples

  • predict: calculates posterior mean and variance over a set of input locations (optionally calculates EI)

  • plot: produces trace plots, hidden layer plots, and posterior plots

  • ALC: calculates active learning Cohn over set of input locations using reference grid

  • IMSE: calculates integrated mean-squared error over set of input locations


Annie Sauer


Sauer, A, RB Gramacy, and D Higdon. 2021. "Active Learning for Deep Gaussian Process Surrogates." Technometrics, (just-accepted), 1-39.

Sauer, A, A Cooper, and RB Gramacy. 2022. "Vecchia-approximated Deep Gaussian Processes for Computer Experiments." pre-print on arXiv:2204.02904

Katzfuss, M, J Guinness, W Gong, and D Zilber. 2020. "Vecchia aproximations of Gaussian-process predictions." Journal of Agricultural, Biological, and Environmental Statistics 25, 383-414.

Binois, M, J Huang, RB Gramacy, and M Ludkovski. 2019. Replication or Exploration? Sequential Design for Stochastic Simulation Experiments. Technometrics 61, 7-23. Taylor & Francis. doi:10.1080/00401706.2018.1469433.

Gramacy, RB. Surrogates: Gaussian Process Modeling, Design, and Optimization for the Applied Sciences. Chapman Hall, 2020.

Jones, DR, M Schonlau, and WJ Welch. 1998. "Efficient Global Optimization of Expensive Black-Box Functions." Journal of Global Optimization 13, 455-492. doi:10.1023/A:1008306431147.

Murray, I, RP Adams, and D MacKay. 2010. "Elliptical slice sampling." Journal of Machine Learning Research 9, 541-548.

Seo, S, M Wallat, T Graepel, and K Obermayer. 2000. Gaussian Process Regression: Active Data Selection and Test Point Rejection. In Mustererkennung 2000, 27-34. New York, NY: Springer Verlag.


# See "fit_one_layer", "fit_two_layer", "fit_three_layer", 
# "ALC", or "IMSE" for examples
# Examples of real-world implementations are available at: 

deepgp documentation built on Dec. 28, 2022, 1:32 a.m.