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  • Review Article
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Gaussian processes for autonomous data acquisition at large-scale synchrotron and neutron facilities

Nature Reviews Physics volume 3, pages 685–697 (2021)Cite this article

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Abstract

The execution and analysis of complex experiments are challenged by the vast dimensionality of the underlying parameter spaces. Although an increase in data-acquisition rates should allow broader querying of the parameter space, the complexity of experiments and the subtle dependence of the model function on input parameters remains daunting owing to the sheer number of variables. New strategies for autonomous data acquisition are being developed, with one promising direction being the use of Gaussian process regression (GPR). GPR is a quick, non-parametric and robust approximation and uncertainty quantification method that can be applied directly to autonomous data acquisition. We review GPR-driven autonomous experimentation and illustrate its functionality using real-world examples from large experimental facilities in the USA and France. We introduce the basics of a GPR-driven autonomous loop with a focus on Gaussian processes, and then shift the focus to the infrastructure that needs to be built around GPR to create a closed loop. Finally, the case studies we discuss show that Gaussian-process-based autonomous data acquisition is a widely applicable method that can facilitate the optimal use of instruments and facilities by enabling the efficient acquisition of high-value datasets.

Key points

  • Gaussian process regression (GPR) is a robust statistical, non-parametric technique for uncertainty quantification and function approximation.

  • GPR can directly be applied to autonomous and optimal data acquisition.

  • GPR provides straightforward ways to inject domain knowledge and can easily be customized for feature finding.

  • The gpCAM software tool provides a simple way for practitioners to use GPR for autonomous experimentation.

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Fig. 1: Schematic of an example autonomous experiment at a synchrotron radiation beam line.
Fig. 2: Key elements for a successful application of gpCAM to infrared mapping.
Fig. 3: Autonomous identification of sample phases, and convergence towards the ground-truth for a surrogate sample measurement with ground truth spectrum consisting of 8,000 points acquired on a uniform mesh.
Fig. 4: Commissioning run of gpCAM at the triple-axis spectrometer ThALES57 at the Institut Laue-Langevin in Grenoble, France.

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Code availability

The gpCAM code for autonomous steering associated with this Review is available at https://doi.org/10.11578/dc.20210217.5 and https://bitbucket.org/MarcusMichaelNoack/gpcam and via pip install gpCAM. Any updates will be published in the repository and on the Python package index (PyPi). The Takin software is available at https://doi.org/10.1016/j.softx.2021.100667.

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Acknowledgements

The work was partly funded through the Center for Advanced Mathematics for Energy Research Applications (CAMERA), which is jointly funded by the Advanced Scientific Computing Research (ASCR) and Basic Energy Sciences (BES) within the Department of Energy’s Office of Science, as well as by the Laboratory Directed Research and Development Program of Lawrence Berkeley National Laboratory, under US Department of Energy contract no. DE-AC02-05CH11231. This research used resources of the Center for Functional Nanomaterials and the National Synchrotron Light Source II, which are US DOE Office of Science facilities, at Brookhaven National Laboratory under contract no. DE-SC0012704. This research also used resources of the Berkeley Synchrotron Infrared Structural Biology (BSISB) Imaging Program, funded by the US Department of Energy, Office of Biological and Environmental Research, under contract no. DE-AC02-05CH11231. The Advanced Light Source is supported by the Director, Office of Science, and the Office of Basic Energy Sciences. Both the ALS and BSISB were supported through contract no. DE-AC02-05CH11231. K.C.E. and C.B.M. acknowledge support from the Office of Naval Research Multidisciplinary University Research Initiative Award ONR N00014-18-1-2497. K.C.E. acknowledges support from the NSF Graduate Research Fellowship Program under grant no. DGE-1321851. This work is based on experiments performed at the Institut Laue-Langevin (ILL) in Grenoble, France. The collected datasets have the DOIs 10.5291/ILL-DATA.TEST-3123 and in part 10.5291/ILL-DATA.4-01-1643. The authors thank E. Villard, P. Chevalier and J. Locatelli for technical support at the ThALES spectrometer. C. N. Melton (author of ref.51) performed the K-means cluster-based GP collection simulations.

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Authors and Affiliations

  1. The Center for Advanced Mathematics for Energy Research Applications (CAMERA), Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    Marcus M. Noack, Petrus H. Zwart, Daniela M. Ushizima & James A. Sethian

  2. Molecular Biophysics and Integrated Bioimaging Division (MBIB), Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    Petrus H. Zwart, Hoi-Ying N. Holman, Steven Lee & Liang Chen

  3. Berkeley Synchrotron Infrared Structural Biology Imaging Resource (BSISB), Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    Petrus H. Zwart, Hoi-Ying N. Holman, Steven Lee & Liang Chen

  4. Bakar Institute, University of California, San Francisco, San Francisco, CA, USA

    Daniela M. Ushizima

  5. National Synchrotron Light Source II (NSLS-II), Brookhaven National Laboratory, Upton, NY, USA

    Masafumi Fukuto, Ruipeng Li, Guillaume Freychet & Mikhail Zhernenkov

  6. Center for Functional Nanomaterials (CFN), Brookhaven National Laboratory, Upton, NY, USA

    Kevin G. Yager, Aaron Stein, Gregory S. Doerk & Esther H. R. Tsai

  7. Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA

    Katherine C. Elbert & Christopher B. Murray

  8. Department of Physics, University of California, Berkeley, CA, USA

    Steven Lee

  9. Advanced Light Source (ALS), Lawrence Berkeley National Laboratory, Berkeley, CA, USA

    Eli Rotenberg

  10. Institut Laue-Langevin (ILL), Grenoble, France

    Tobias Weber, Yannick Le Goc, Martin Boehm, Paul Steffens & Paolo Mutti

  11. Department of Mathematics, University of California, Berkeley, CA, USA

    James A. Sethian

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  1. Marcus M. Noack
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Contributions

M.M.N. wrote the initial drafts of the introduction and the technical sections, devised the algorithm used, formulated the required mathematics, and implemented the computer codes (gpCAM). P.H.Z. designed, coordinated and collaborated on the development of basic computational strategies in gpCAM and on its use in SR-FTIR microscopy and ARPES experiments and took part in writing and editing this manuscript. D.M.U. designed, configured and implemented codes associated with convnets for reverse image search and wrote the related section. M.F. and K.G.Y. planned, supervised and coordinated experiments at Brookhaven National Laboratory’s National Synchrotron Light Source II, and wrote the related section. M.F., K.G.Y., E.H.R.T., R.L., G.F. and M.Z. performed X-ray scattering experiments at National Synchrotron Light Source II, including beamline operation and data analytics. K.C.E. and C.B.M. prepared nanoplatelet materials. A.S. and G.S.D. prepared chemical templates and self-assembled films. E.R. planned and led the ARPES measurements at the Advanced Light Source, and wrote the related section. H.-Y.N.H. led the SR-FTIR measurements, coordinated the simulations and wrote the initial draft of the related section, S.L. designed and performed the PCA-based GP collection simulations and wrote the related section. L.C. designed the simulations and wrote the related section. Y.L.G. and T.W. customized gpCAM for use at the ThALES spectrometer. T.W. developed and performed preparatory simulations with gpCAM using theoretical dynamical structure factor models for neutron scattering. T.W. planned and T.W., M.B., P.S. and P.M. performed the first autonomous commissioning experiment at ThALES measuring the magnons in the chiral magnet MnSi. M.B. proposed and M.B., T.W., P.S. and P.M. performed the second autonomous commissioning experiment at ThALES, the results of which are shown in Fig. 4. The sample for the first experiment (MnSi) was provided by A. Bauer, the sample for the second autonomous commissioning experiment was provided by M.B. T.W. analysed the data of the first experiment (MnSi, not shown), M.B. analysed the data of the second experiment (Fig. 4). M.B. and T.W. wrote the text of the corresponding section to equal parts. J.A.S. supervised the development of the mathematics and the implementation of the code, and revised and improved the manuscript. All authors commented on the manuscript and revised it repeatedly.

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Correspondence to Marcus M. Noack.

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Supplementary information

Glossary

Uncertainty quantification

The quantitative characterization of uncertainties in computational and real-world applications.

Himmelblau’s function

A common test function in the optimization community.

Principal component analysis

A dimensionality reduction technique that finds an orthonormal basis; typically retaining only the first few basis vectors preserves the majority of the variance of the dataset while substantially reducing data dimensionality.

Non-negative matrix factorization

A computational linear algebra technique to factorize a matrix into two matrices without negative elements.

Bump function

A function that is both smooth and compactly supported.

Surrogate model

An approximate model when the actual model is difficult or costly to evaluate.

Linear interpolation with Voronoi tessellation

A technique for function approximation and automated data acquisition.

Triple-axis spectrometers

A special spectrometer that selects the wavelengths of neutrons before and after they hit the sample, which directly probes the energy and momentum response of various materials.

Delaunay triangulation

A triangulation technique such that no point in the set is inside the circumcircle of any of the triangles connecting the points.

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Noack, M.M., Zwart, P.H., Ushizima, D.M. et al. Gaussian processes for autonomous data acquisition at large-scale synchrotron and neutron facilities. Nat Rev Phys 3, 685–697 (2021). https://doi.org/10.1038/s42254-021-00345-y

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