Comparison of Gaussian process software

This is a comparison of statistical analysis software that allows doing inference with Gaussian processes often using approximations.

This article is written from the point of view of Bayesian statistics, which may use a terminology different from the one commonly used in kriging. The next section should clarify the mathematical/computational meaning of the information provided in the table independently of contextual terminology.

Description of columns

This section details the meaning of the columns in the table below.

Solvers

These columns are about the algorithms used to solve the linear system defined by the prior covariance matrix, i.e., the matrix built by evaluating the kernel.

Input

These columns are about the points on which the Gaussian process is evaluated, i.e. if the process is .

Output

These columns are about the values yielded by the process, and how they are connected to the data used in the fit.

Hyperparameters

These columns are about finding values of variables which enter somehow in the definition of the specific problem but that can not be inferred by the Gaussian process fit, for example parameters in the formula of the kernel.

If both the "Prior" and "Posterior" cells contain "Manually", the software provides an interface for computing the marginal likelihood and its gradient w.r.t. hyperparameters, which can be feed into an optimization/sampling algorithm, e.g., gradient descent or Markov chain Monte Carlo.

Linear transformations

These columns are about the possibility of fitting datapoints simultaneously to a process and to linear transformations of it.

Comparison table

Name License Language Solvers Input Output Hyperparameters Linear transformations Name
Exact
Specialized
Approxi­mate
ND
Non-real
Likelihood Errors Prior Posterior
Derivative
Finite Sum
PyMC Apache Python Yes Kronecker Sparse ND No Any Correlated Yes Yes No Yes Yes PyMC
Stan BSD, GPL custom Yes No No ND No Any Correlated Yes Yes No Yes Yes Stan
scikit-learn BSD Python Yes No No ND Yes Bernoulli Uncorrelated Manually Manually No No No scikit-learn
fbm
Free C Yes No No ND No Bernoulli, Poisson Uncorrelated, Stationary Many Yes No No Yes fbm
GPML
BSD MATLAB Yes No Sparse ND No Many i.i.d. Manually Manually No No No GPML
GPstuff
GNU GPL MATLAB, R Yes Markov Sparse ND No Many Correlated Many Yes First RBF No Yes GPstuff
GPy
BSD Python Yes No Sparse ND No Many Uncorrelated Yes Yes No No No GPy
GPflow
Apache Python Yes No Sparse ND No Many Uncorrelated Yes Yes No No No GPflow
GPyTorch
MIT Python Yes Toeplitz, Kronecker Sparse ND No Many Uncorrelated Yes Yes First RBF Manually Manually GPyTorch
GPvecchia
GNU GPL R Yes No Sparse, Hierarch­ical ND No Exponential family Uncorrelated No No No No No GPvecchia
pyGPs
BSD Python Yes No Sparse ND Graphs, Manually Bernoulli i.i.d. Manually Manually No No No pyGPs
gptk
BSD R Yes Block? Sparse ND No Gaussian No Manually Manually No No No gptk
celerite
MIT Python, Julia, C++ No Semisep. No 1D No Gaussian Uncorrelated Manually Manually No No No celerite
george
MIT Python, C++ Yes No Hierarch­ical ND No Gaussian Uncorrelated Manually Manually No No Manually george
neural-tangents
Apache Python Yes Block, Kronecker No ND No Gaussian No No No No No No neural-tangents
DiceKriging
GNU GPL R Yes No No ND No? Gaussian Uncorrelated SCAD RBF MAP No No No DiceKriging
OpenTURNS
GNU LGPL Python, C++ Yes No No ND No Gaussian Uncorrelated Manually (no grad.) MAP No No No OpenTURNS
UQLab
Proprietary MATLAB Yes No No ND No Gaussian Correlated No MAP No No No UQLab
ooDACE Proprietary MATLAB Yes No No ND No Gaussian Correlated No MAP No No No ooDACE
DACE Proprietary MATLAB Yes No No ND No Gaussian No No MAP No No No DACE
GpGp MIT R No No Sparse ND No Gaussian i.i.d. Manually Manually No No No GpGp
SuperGauss GNU GPL R, C++ No Toeplitz No 1D No Gaussian No Manually Manually No No No SuperGauss
STK GNU GPL MATLAB Yes No No ND No Gaussian Uncorrelated Manually Manually No No Manually STK
GSTools GNU LGPL Python Yes No No ND No Gaussian Yes Yes Yes Yes No No GSTools
PyKrige BSD Python Yes No No 2D,3D No Gaussian i.i.d. No No No No No PyKrige
GPR Apache C++ Yes No Sparse ND No Gaussian i.i.d. Some, Manually Manually First No No GPR
celerite2 MIT Python No Semisep. No 1D No Gaussian Uncorrelated Manually Manually No No Yes celerite2
SMT
BSD Python Yes No Sparse, PODI, other ND No Gaussian i.i.d. Some Some First No No SMT
GPJax Apache Python Yes No Sparse ND Graphs Bernoulli No Yes Yes No No No GPJax
Stheno MIT Python Yes Low rank Sparse ND No Gaussian i.i.d. Manually Manually Approxi­mate No Yes Stheno
Egobox-gp
Apache Rust Yes No Sparse ND No Gaussian i.i.d. No MAP First No No Egobox-gp
Name License Language Exact
Specialized
Approxi­mate
ND
Non-real
Likelihood Errors Prior Posterior
Derivative
Finite Sum Name
Solvers Input Output Hyperparameters Linear transformations

Notes

  1. 1 2 celerite implements only a specific subalgebra of kernels which can be solved in .
  2. ↑ neural-tangents is a specialized package for infinitely wide neural networks.
  3. ↑ SuperGauss implements a superfast Toeplitz solver with computational complexity .
  4. ↑ celerite2 has a PyMC3 interface.
  5. ↑ PODI (Proper Orthogonal Decomposition + Interpolation) is an approximation for high-dimensional multioutput regressions. The regression function is lower-dimensional than the outcomes, and the subspace is chosen with the PCA of the (outcome, dependent variable) data. Each principal component is modeled with an a priori independent Gaussian process.

References

  1. ↑ P. Cunningham, John; Gilboa, Elad; Saatçi, Yunus (Feb 2015). "Scaling Multidimensional Inference for Structured Gaussian Processes". IEEE Transactions on Pattern Analysis and Machine Intelligence. 37 (2): 424–436. arXiv:1209.4120. Bibcode:2015ITPAM..37..424G. doi:10.1109/TPAMI.2013.192. PMID 26353252. S2CID 6878550.
  2. ↑ Leith, D. J.; Zhang, Yunong; Leithead, W. E. (2005). "Time-series Gaussian Process Regression Based on Toeplitz Computation of O(N²) Operations and O(N)-level Storage". Proceedings of the 44th IEEE Conference on Decision and Control. pp. 3711–3716. doi:10.1109/CDC.2005.1582739. ISBN 0-7803-9567-0. S2CID 13627455.
  3. 1 2 3 Foreman-Mackey, Daniel; Angus, Ruth; Agol, Eric; Ambikasaran, Sivaram (9 November 2017). "Fast and Scalable Gaussian Process Modeling with Applications to Astronomical Time Series". The Astronomical Journal. 154 (6): 220. arXiv:1703.09710. Bibcode:2017AJ....154..220F. doi:10.3847/1538-3881/aa9332. S2CID 88521913.
  4. ↑ Sarkka, Simo; Solin, Arno; Hartikainen, Jouni (2013). "Spatiotemporal Learning via Infinite-Dimensional Bayesian Filtering and Smoothing: A Look at Gaussian Process Regression Through Kalman Filtering". IEEE Signal Processing Magazine. 30 (4): 51–61. doi:10.1109/MSP.2013.2246292. S2CID 7485363.
  5. ↑ Quiñonero-Candela, Joaquin; Rasmussen, Carl Edward (5 December 2005). "A Unifying View of Sparse Approximate Gaussian Process Regression". Journal of Machine Learning Research. 6: 1939–1959. Retrieved 23 May 2020.
  6. 1 2 Ambikasaran, S.; Foreman-Mackey, D.; Greengard, L.; Hogg, D. W.; O'Neil, M. (1 Feb 2016). "Fast Direct Methods for Gaussian Processes". IEEE Transactions on Pattern Analysis and Machine Intelligence. 38 (2): 252–265. arXiv:1403.6015. doi:10.1109/TPAMI.2015.2448083. PMID 26761732. S2CID 15206293.
  7. 1 2 3 Vanhatalo, Jarno; Riihimäki, Jaakko; Hartikainen, Jouni; Jylänki, Pasi; Tolvanen, Ville; Vehtari, Aki (Apr 2013). "GPstuff: Bayesian Modeling with Gaussian Processes". Journal of Machine Learning Research. 14: 1175−1179. Retrieved 23 May 2020.
  8. ↑ Rasmussen, Carl Edward; Nickisch, Hannes (Nov 2010). "Gaussian processes for machine learning (GPML) toolbox". Journal of Machine Learning Research. 11 (2): 3011–3015. doi:10.1016/0002-9610(74)90157-3. PMID 4204594.
  9. 1 2 Matthews, Alexander G. de G.; van der Wilk, Mark; Nickson, Tom; Fujii, Keisuke; Boukouvalas, Alexis; León-Villagrá, Pablo; Ghahramani, Zoubin; Hensman, James (April 2017). "GPflow: A Gaussian process library using TensorFlow". Journal of Machine Learning Research. 18 (40): 1–6. arXiv:1610.08733. Retrieved 6 July 2020.
  10. ↑ Gardner, Jacob R; Pleiss, Geoff; Bindel, David; Weinberger, Kilian Q; Wilson, Andrew Gordon (2018). "GPyTorch: Blackbox Matrix-Matrix Gaussian Process Inference with GPU Acceleration" (PDF). Advances in Neural Information Processing Systems. 31: 7576–7586. arXiv:1809.11165. Retrieved 23 May 2020.
  11. ↑ Zilber, Daniel; Katzfuss, Matthias (January 2021). "Vecchia–Laplace approximations of generalized Gaussian processes for big non-Gaussian spatial data". Computational Statistics & Data Analysis. 153 107081. arXiv:1906.07828. doi:10.1016/j.csda.2020.107081. ISSN 0167-9473. S2CID 195068888. Retrieved 1 September 2021.
  12. ↑ Neumann, Marion; Huang, Shan; E. Marthaler, Daniel; Kersting, Kristian (2015). "pyGPs — A Python Library for Gaussian Process Regression and Classification". Journal of Machine Learning Research. 16: 2611–2616.
  13. ↑ Kalaitzis, Alfredo; Lawrence, Neil D. (May 20, 2011). "A Simple Approach to Ranking Differentially Expressed Gene Expression Time Courses through Gaussian Process Regression". BMC Bioinformatics. 12 (1): 180. doi:10.1186/1471-2105-12-180. ISSN 1471-2105. PMC 3116489. PMID 21599902.
  14. ↑ Novak, Roman; Xiao, Lechao; Hron, Jiri; Lee, Jaehoon; Alemi, Alexander A.; Sohl-Dickstein, Jascha; Schoenholz, Samuel S. (2020). "Neural Tangents: Fast and Easy Infinite Neural Networks in Python". International Conference on Learning Representations. arXiv:1912.02803.
  15. ↑ Roustant, Olivier; Ginsbourger, David; Deville, Yves (2012). "DiceKriging, DiceOptim: Two R Packages for the Analysis of Computer Experiments by Kriging-Based Metamodeling and Optimization". Journal of Statistical Software. 51 (1): 1–55. doi:10.18637/jss.v051.i01. S2CID 60672249.
  16. ↑ Baudin, Michaël; Dutfoy, Anne; Iooss, Bertrand; Popelin, Anne-Laure (2015). "OpenTURNS: An Industrial Software for Uncertainty Quantification in Simulation". In Roger Ghanem; David Higdon; Houman Owhadi (eds.). Handbook of Uncertainty Quantification. pp. 1–38. arXiv:1501.05242. doi:10.1007/978-3-319-11259-6_64-1. ISBN 978-3-319-11259-6. S2CID 88513894.
  17. ↑ Marelli, Stefano; Sudret, Bruno (2014). "UQLab: a framework for uncertainty quantification in MATLAB" (PDF). Vulnerability, Uncertainty, and Risk. Quantification, Mitigation, and Management: 2554–2563. doi:10.3929/ethz-a-010238238. ISBN 978-0-7844-1360-9. Retrieved 28 May 2020.{{cite journal}}: CS1 maint: periodical has ISBN (link)
  18. ↑ Couckuyt, Ivo; Dhaene, Tom; Demeester, Piet (2014). "ooDACE toolbox: a flexible object-oriented Kriging implementation" (PDF). Journal of Machine Learning Research. 15: 3183–3186. Retrieved 8 July 2020.
  19. ↑ Bouhlel, Mohamed A.; Hwang, John T.; Bartoli, Nathalie; Lafage, Rémi; Morlier, Joseph; Martins, Joaquim R.R.A. (2019). "A Python surrogate modeling framework with derivatives". Advances in Engineering Software. 135 (1): 102662. doi:10.1016/j.advengsoft.2019.03.005.
  20. ↑ Saves, Paul; Lafage, Rémi; Bartoli, Nathalie; Diouane, Youssef; Bussemaker, Jasper; Lefebvre, Thierry; Hwang, John T.; Morlier, Joseph; Martins, Joaquim R.R.A. (2024). "SMT 2.0: A Surrogate Modeling Toolbox with a focus on hierarchical and mixed variables Gaussian processes". Advances in Engineering Software. 188 (1) 103571. arXiv:2305.13998. doi:10.1016/j.advengsoft.2023.103571.
  21. ↑ Porrello, Christian; Dubreuil, Sylvain; Farhat, Charbel (2024). "Bayesian Framework With Projection-Based Model Order Reduction for Efficient Global Optimization". AIAA Aviation Forum and Ascend 2024. p. 4580. doi:10.2514/6.2024-4580. ISBN 978-1-62410-716-0.
  22. ↑ Lafage, Rémi (2022). "egobox, a Rust toolbox for efficient global optimization" (PDF). Journal of Open Source Software. 7 (78): 4737. Bibcode:2022JOSS....7.4737L. doi:10.21105/joss.04737.