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Solving Bayesian Inverse Problems With Expensive Likelihoods Using Constrained Gaussian Processes and Active Learning (2312.08085v1)

Published 13 Dec 2023 in cs.CE

Abstract: Solving inverse problems using Bayesian methods can become prohibitively expensive when likelihood evaluations involve complex and large scale numerical models. A common approach to circumvent this issue is to approximate the forward model or the likelihood function with a surrogate model. But also there, due to limited computational resources, only a few training points are available in many practically relevant cases. Thus, it can be advantageous to model the additional uncertainties of the surrogate in order to incorporate the epistemic uncertainty due to limited data. In this paper, we develop a novel approach to approximate the log likelihood by a constrained Gaussian process based on prior knowledge about its boundedness. This improves the accuracy of the surrogate approximation without increasing the number of training samples. Additionally, we introduce a formulation to integrate the epistemic uncertainty due to limited training points into the posterior density approximation. This is combined with a state of the art active learning strategy for selecting training points, which allows to approximate posterior densities in higher dimensions very efficiently. We demonstrate the fast convergence of our approach for a benchmark problem and infer a random field that is discretized by 30 parameters using only about 1000 model evaluations. In a practically relevant example, the parameters of a reduced lung model are calibrated based on flow observations over time and voltage measurements from a coupled electrical impedance tomography simulation.

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References (59)
  1. S Schoeder, M Kronbichler and W A Wall “Photoacoustic image reconstruction: material detection and acoustical heterogeneities” In Inverse Problems 33.5, 2017, pp. 055010 DOI: 10.1088/1361-6420/aa635b
  2. “Tumour growth: An approach to calibrate parameters of a multiphase porous media model based on in vitro observations of Neuroblastoma spheroid growth in a hydrogel microenvironment” In Computers in Biology and Medicine 159, 2023, pp. 106895 DOI: 10.1016/j.compbiomed.2023.106895
  3. “A novel physics-based and data-supported microstructure model for part-scale simulation of laser powder bed fusion of Ti-6Al-4V” In Advanced Modeling and Simulation in Engineering Sciences 8.1, 2021, pp. 16 DOI: 10.1186/s40323-021-00201-9
  4. Harald Willmann and Wolfgang A. Wall “Inverse analysis of material parameters in coupled multi-physics biofilm models” In Advanced Modeling and Simulation in Engineering Sciences 9.1, 2022, pp. 7 DOI: 10.1186/s40323-022-00220-0
  5. “Numerical Methods for the Solution of Ill-Posed Problems” Dordrecht: Springer Netherlands, 1995 DOI: 10.1007/978-94-015-8480-7
  6. “Statistical and computational inverse problems”, Applied mathematical sciences v. 160 New York: Springer, 2005
  7. “Equation of State Calculations by Fast Computing Machines” _eprint: https://pubs.aip.org/aip/jcp/article-pdf/21/6/1087/8115285/1087_1_online.pdf In The Journal of Chemical Physics 21.6, 2004, pp. 1087–1092 DOI: 10.1063/1.1699114
  8. Radford M. Neal “An Improved Acceptance Procedure for the Hybrid Monte Carlo Algorithm” In Journal of Computational Physics 111.1, 1994, pp. 194–203 DOI: https://doi.org/10.1006/jcph.1994.1054
  9. Matthew D. Hoffman and Andrew Gelman “The No-U-Turn Sampler: Adaptively Setting Path Lengths in Hamiltonian Monte Carlo” In Journal of Machine Learning Research 15.47, 2014, pp. 1593–1623 URL: http://jmlr.org/papers/v15/hoffman14a.html
  10. N. Chopin “A sequential particle filter method for static models” In Biometrika 89.3, 2002, pp. 539–552 DOI: 10.1093/biomet/89.3.539
  11. “An Introduction to Sequential Monte Carlo”, Springer Series in Statistics Cham: Springer International Publishing, 2020 DOI: 10.1007/978-3-030-47845-2
  12. Pierre Del Moral, Arnaud Doucet and Ajay Jasra “Sequential Monte Carlo samplers” In Journal of the Royal Statistical Society: Series B (Statistical Methodology) 68.3, 2006, pp. 411–436 DOI: 10.1111/j.1467-9868.2006.00553.x
  13. Arnaud Doucet, Nando De Freitas and Neil James Gordon “Sequential Monte Carlo methods in practice” Springer, 2001
  14. David M. Blei, Alp Kucukelbir and Jon D. McAuliffe “Variational Inference: A Review for Statisticians” Publisher: Taylor & Francis In Journal of the American Statistical Association 112.518, 2017, pp. 859–877 DOI: 10.1080/01621459.2017.1285773
  15. “Variational Inference with Normalizing Flows” In Proceedings of the 32nd International Conference on Machine Learning 37, Proceedings of Machine Learning Research Lille, France: PMLR, 2015, pp. 1530–1538 URL: https://proceedings.mlr.press/v37/rezende15.html
  16. Durk P Kingma, Tim Salimans and Max Welling “Variational Dropout and the Local Reparameterization Trick” In Advances in Neural Information Processing Systems 28 Curran Associates, Inc., 2015 URL: https://proceedings.neurips.cc/paper_files/paper/2015/file/bc7316929fe1545bf0b98d114ee3ecb8-Paper.pdf
  17. Rajesh Ranganath, Sean Gerrish and David Blei “Black Box Variational Inference” In Proceedings of the Seventeenth International Conference on Artificial Intelligence and Statistics 33, Proceedings of Machine Learning Research Reykjavik, Iceland: PMLR, 2014, pp. 814–822 URL: https://proceedings.mlr.press/v33/ranganath14.html
  18. Youssef M. Marzouk, Habib N. Najm and Larry A. Rahn “Stochastic spectral methods for efficient Bayesian solution of inverse problems” In Journal of Computational Physics 224.2, 2007, pp. 560–586 DOI: 10.1016/j.jcp.2006.10.010
  19. “A Stochastic Collocation Approach to Bayesian Inference in Inverse Problems” In Communications in Computational Physics 6.4, 2009, pp. 826–847 DOI: 10.4208/cicp.2009.v6.p826
  20. “An efficient Bayesian inference approach to inverse problems based on an adaptive sparse grid collocation method” In Inverse Problems 25.3, 2009, pp. 035013 DOI: 10.1088/0266-5611/25/3/035013
  21. David J.C MacKay “Bayesian neural networks and density networks” In Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment 354.1, 1995, pp. 73–80 DOI: 10.1016/0168-9002(94)00931-7
  22. Marc C. Kennedy and Anthony O’Hagan “Bayesian calibration of computer models” _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1111/1467-9868.00294 In Journal of the Royal Statistical Society: Series B (Statistical Methodology) 63.3, 2001, pp. 425–464 DOI: 10.1111/1467-9868.00294
  23. Carl Edward Rasmussen “Gaussian processes to speed up hybrid Monte Carlo for expensive Bayesian integrals” In Seventh Valencia international meeting, dedicated to Dennis V. Lindley Oxford University Press, 2003, pp. 651–659
  24. “Solution of inverse problems with limited forward solver evaluations: a Bayesian perspective” In Inverse Problems 30.1, 2014, pp. 015004 DOI: 10.1088/0266-5611/30/1/015004
  25. “Adaptive Gaussian Process Regression for Efficient Building of Surrogate Models in Inverse Problems” _eprint: 2303.05824 In arXiv e-prints, 2023, pp. arXiv:2303.05824 DOI: 10.48550/arXiv.2303.05824
  26. “Physics-constrained deep learning for high-dimensional surrogate modeling and uncertainty quantification without labeled data” In Journal of Computational Physics 394, 2019, pp. 56–81 DOI: 10.1016/j.jcp.2019.05.024
  27. “A probabilistic generative model for semi-supervised training of coarse-grained surrogates and enforcing physical constraints through virtual observables” In Journal of Computational Physics 434, 2021, pp. 110218 DOI: 10.1016/j.jcp.2021.110218
  28. M. Raissi, P. Perdikaris and G.E. Karniadakis “Physics-informed neural networks: A deep learning framework for solving forward and inverse problems involving nonlinear partial differential equations” In Journal of Computational Physics 378, 2019, pp. 686–707 DOI: 10.1016/j.jcp.2018.10.045
  29. “Surrogate-Based Bayesian Inverse Modeling of the Hydrological System: An Adaptive Approach Considering Surrogate Approximation Error” _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1029/2019WR025721 In Water Resources Research 56.1, 2020, pp. e2019WR025721 DOI: 10.1029/2019WR025721
  30. Kirthevasan Kandasamy, Jeff Schneider and Barnabas Poczos “Bayesian Active Learning for Posterior Estimation” In Proceedings of 24th International Joint Conference on Artificial Intelligence (IJCAI ’15), 2015, pp. 3605–3611
  31. “Adaptive Gaussian Process Approximation for Bayesian Inference with Expensive Likelihood Functions” In Neural Computation 30.11, 2018, pp. 3072–3094 DOI: 10.1162/neco_a_01127
  32. “QUEENS - A software platform for uncertainty quantification, physics-informed machine learning, bayesian optimization, inverse problems and simulation analytics: User guide”, 2019
  33. Carl Edward Rasmussen and Christopher K.I. Williams “Gaussian processes for machine learning” OCLC: ocm61285753, Adaptive computation and machine learning Cambridge, Mass: MIT Press, 2006
  34. Christian Agrell “Gaussian Processes with Linear Operator Inequality Constraints” In Journal of Machine Learning Research 20.135, 2019, pp. 1–36 URL: http://jmlr.org/papers/v20/19-065.html
  35. Robert B. Gramacy and Herbert K.H. Lee “Cases for the nugget in modeling computer experiments” In Statistics and Computing 22.3, 2012, pp. 713–722 DOI: 10.1007/s11222-010-9224-x
  36. “Exact Gaussian Processes on a Million Data Points” In Advances in Neural Information Processing Systems 32 Curran Associates, Inc., 2019 URL: https://proceedings.neurips.cc/paper_files/paper/2019/file/01ce84968c6969bdd5d51c5eeaa3946a-Paper.pdf
  37. Vidhi Lalchand and Carl Edward Rasmussen “Approximate Inference for Fully Bayesian Gaussian Process Regression” In Proceedings of The 2nd Symposium on Advances in Approximate Bayesian Inference 118, Proceedings of Machine Learning Research PMLR, 2020, pp. 1–12 URL: https://proceedings.mlr.press/v118/lalchand20a.html
  38. Jasper Snoek, Hugo Larochelle and Ryan P Adams “Practical Bayesian Optimization of Machine Learning Algorithms” In Advances in Neural Information Processing Systems 25 Curran Associates, Inc., 2012 URL: https://proceedings.neurips.cc/paper_files/paper/2012/file/05311655a15b75fab86956663e1819cd-Paper.pdf
  39. Peter Auer “Using Confidence Bounds for Exploitation-Exploration Trade-Offs” Publisher: JMLR.org In Journal of Machine Learning Research 3, 2003, pp. 397–422
  40. “Gaussian Process Optimization in the Bandit Setting: No Regret and Experimental Design” event-place: Haifa, Israel In Proceedings of the 27th International Conference on International Conference on Machine Learning, ICML’10 Madison, WI, USA: Omnipress, 2010, pp. 1015–1022
  41. Tirupathi R. Chandrupatla “A new hybrid quadratic/bisection algorithm for finding the zero of a nonlinear function without using derivatives” In Advances in Engineering Software 28.3, 1997, pp. 145–149 DOI: https://doi.org/10.1016/S0965-9978(96)00051-8
  42. “Waste-Free Sequential Monte Carlo” _eprint: https://academic.oup.com/jrsssb/article-pdf/84/1/114/49324223/jrsssb_84_1_114.pdf In Journal of the Royal Statistical Society Series B: Statistical Methodology 84.1, 2021, pp. 114–148 DOI: 10.1111/rssb.12475
  43. Andreas Krause, Ajit Singh and Carlos Guestrin “Near-Optimal Sensor Placements in Gaussian Processes: Theory, Efficient Algorithms and Empirical Studies” In Journal of Machine Learning Research 9.8, 2008, pp. 235–284 URL: http://jmlr.org/papers/v9/krause08a.html
  44. “Mercer Kernels and Integrated Variance Experimental Design: Connections Between Gaussian Process Regression and Polynomial Approximation” In SIAM/ASA Journal on Uncertainty Quantification 4.1, 2016, pp. 796–828 DOI: 10.1137/15M1017119
  45. Kittipat Kampa, Erion Hasanbelliu and Jose C. Principe “Closed-form cauchy-schwarz PDF divergence for mixture of Gaussians” ISSN: 2161-4407 In The 2011 International Joint Conference on Neural Networks, 2011, pp. 2578–2585 DOI: 10.1109/IJCNN.2011.6033555
  46. “On Information and Sufficiency” In The Annals of Mathematical Statistics 22.1, 1951, pp. 79–86 DOI: 10.1214/aoms/1177729694
  47. “Basix: a runtime finite element basis evaluation library” In Journal of Open Source Software 7.73, 2022, pp. 3982 DOI: 10.21105/joss.03982
  48. “Unified Form Language: A domain-specific language for weak formulations of partial differential equations” In ACM Transactions on Mathematical Software 40, 2014 DOI: 10.1145/2566630
  49. Roger G Ghanem and Pol D Spanos “Stochastic finite elements: a spectral approach” Courier Corporation, 2003
  50. M. Ismail, A. Comerford and W.A. Wall “Coupled and reduced dimensional modeling of respiratory mechanics during spontaneous breathing” _eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/cnm.2577 In International Journal for Numerical Methods in Biomedical Engineering 29.11, 2013, pp. 1285–1305 DOI: 10.1002/cnm.2577
  51. “Coupling of EIT with computational lung modeling for predicting patient-specific ventilatory responses.” Place: United States In Journal of applied physiology (Bethesda, Md. : 1985) 122.4, 2017, pp. 855–867 DOI: 10.1152/japplphysiol.00236.2016
  52. “BACI: A Comprehensive Multi-Physics Simulation Framework” URL: https://baci.pages.gitlab.lrz.de/website
  53. “An approach to study recruitment/derecruitment dynamics in a patient-specific computational model of an injured human lung” Publisher: John Wiley & Sons, Ltd In International Journal for Numerical Methods in Biomedical Engineering, 2023, pp. e3745 DOI: 10.1002/cnm.3745
  54. Raymond William Ogden and Rodney Hill “Large deformation isotropic elasticity – on the correlation of theory and experiment for incompressible rubberlike solids” _eprint: https://royalsocietypublishing.org/doi/pdf/10.1098/rspa.1972.0026 In Proceedings of the Royal Society of London. A. Mathematical and Physical Sciences 326.1567, 1972, pp. 565–584 DOI: 10.1098/rspa.1972.0026
  55. B.H. Brown “Electrical impedance tomography (EIT): a review” Publisher: Taylor & Francis _eprint: https://doi.org/10.1080/0309190021000059687 In Journal of Medical Engineering & Technology 27.3, 2003, pp. 97–108 DOI: 10.1080/0309190021000059687
  56. “Correlation between alveolar ventilation and electrical properties of lung parenchyma” In Physiological Measurement 36.6, 2015, pp. 1211–1226 DOI: 10.1088/0967-3334/36/6/1211
  57. Andy Adler and William R B Lionheart “Uses and abuses of EIDORS: an extensible software base for EIT” In Physiological Measurement 27.5, 2006, pp. S25–S42 DOI: 10.1088/0967-3334/27/5/S03
  58. “A coupled approach for identification of nonlinear and compressible material models for soft tissue based on different experimental setups – Exemplified and detailed for lung parenchyma” In Journal of the Mechanical Behavior of Biomedical Materials 94, 2019, pp. 126–143 DOI: https://doi.org/10.1016/j.jmbbm.2019.02.019
  59. “Aging and anatomical variations in lung tissue stiffness.” Place: United States In American journal of physiology. Lung cellular and molecular physiology 314.6, 2018, pp. L946–L955 DOI: 10.1152/ajplung.00415.2017
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Authors (5)
  1. Maximilian Dinkel (2 papers)
  2. Carolin M. Geitner (3 papers)
  3. Gil Robalo Rei (2 papers)
  4. Jonas Nitzler (8 papers)
  5. Wolfgang A. Wall (89 papers)
Citations (2)