Likelihood-Free Inference with Deep Gaussian Processes

In recent years, surrogate models have been successfully used in likelihood-free inference to decrease the number of simulator evaluations. The current state-of-the-art performance for this task has been achieved by Bayesian Optimization with Gaussian Processes (GPs). While this combination works well for unimodal target distributions, it is restricting the flexibility and applicability of Bayesian Optimization for accelerating likelihood-free inference more generally. We address this problem by proposing a Deep Gaussian Process (DGP) surrogate model that can handle more irregularly behaved target distributions. Our experiments show how DGPs can outperform GPs on objective functions with multimodal distributions and maintain a comparable performance in unimodal cases. This confirms that DGPs as surrogate models can extend the applicability of Bayesian Optimization for likelihood-free inference (BOLFI), while adding computational overhead that remains negligible for computationally intensive simulators.

[1]  Iain Murray,et al.  Masked Autoregressive Flow for Density Estimation , 2017, NIPS.

[2]  D. Balding,et al.  Approximate Bayesian computation in population genetics. , 2002, Genetics.

[3]  Wittawat Jitkrittum,et al.  K2-ABC: Approximate Bayesian Computation with Kernel Embeddings , 2015, AISTATS.

[4]  Andrew R. Francis,et al.  Using Approximate Bayesian Computation to Estimate Tuberculosis Transmission Parameters From Genotype Data , 2006, Genetics.

[5]  Flora Jay,et al.  Inferring Population Size History from Large Samples of Genome-Wide Molecular Data - An Approximate Bayesian Computation Approach , 2016, bioRxiv.

[6]  G. Schoolnik,et al.  The epidemiology of tuberculosis in San Francisco. A population-based study using conventional and molecular methods. , 1994, The New England journal of medicine.

[7]  Michael L. Littman,et al.  Markov Games as a Framework for Multi-Agent Reinforcement Learning , 1994, ICML.

[8]  M. Gutmann,et al.  Fundamentals and Recent Developments in Approximate Bayesian Computation , 2016, Systematic biology.

[9]  Mark M. Tanaka,et al.  Sequential Monte Carlo without likelihoods , 2007, Proceedings of the National Academy of Sciences.

[10]  Hugo Larochelle,et al.  MADE: Masked Autoencoder for Distribution Estimation , 2015, ICML.

[11]  S. Wood Statistical inference for noisy nonlinear ecological dynamic systems , 2010, Nature.

[12]  M. Feldman,et al.  Population growth of human Y chromosomes: a study of Y chromosome microsatellites. , 1999, Molecular biology and evolution.

[13]  D. Rubin,et al.  Inference from Iterative Simulation Using Multiple Sequences , 1992 .

[14]  Jukka Corander,et al.  Resolving outbreak dynamics using Approximate Bayesian Computation for stochastic birth-death models , 2017 .

[15]  Andreas Huth,et al.  Statistical inference for stochastic simulation models--theory and application. , 2011, Ecology letters.

[16]  Nando de Freitas,et al.  Taking the Human Out of the Loop: A Review of Bayesian Optimization , 2016, Proceedings of the IEEE.

[17]  Neil D. Lawrence,et al.  Deep Gaussian Processes , 2012, AISTATS.

[18]  Andrew M. Stuart,et al.  How Deep Are Deep Gaussian Processes? , 2017, J. Mach. Learn. Res..

[19]  Carl E. Rasmussen,et al.  Gaussian processes for machine learning , 2005, Adaptive computation and machine learning.

[20]  David Welch,et al.  Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems , 2009, Journal of The Royal Society Interface.

[21]  Frank Technow,et al.  Integrating Crop Growth Models with Whole Genome Prediction through Approximate Bayesian Computation , 2015, bioRxiv.

[22]  Aki Vehtari,et al.  ELFI: Engine for Likelihood Free Inference , 2016, J. Mach. Learn. Res..

[23]  Michael U. Gutmann,et al.  Bayesian Optimization for Likelihood-Free Inference of Simulator-Based Statistical Models , 2015, J. Mach. Learn. Res..

[24]  Jimmy Ba,et al.  Adam: A Method for Stochastic Optimization , 2014, ICLR.

[25]  Jakob H. Macke,et al.  Flexible statistical inference for mechanistic models of neural dynamics , 2017, NIPS.

[26]  Juan José Murillo-Fuentes,et al.  Inference in Deep Gaussian Processes using Stochastic Gradient Hamiltonian Monte Carlo , 2018, NeurIPS.

[27]  K. Fukumizu,et al.  Kernel approximate Bayesian computation in population genetic inferences , 2012, Statistical applications in genetics and molecular biology.

[28]  Fabio Tozeto Ramos,et al.  Bayesian Learning of Conditional Kernel Mean Embeddings for Automatic Likelihood-Free Inference , 2019, AISTATS.

[29]  Max Welling,et al.  GPS-ABC: Gaussian Process Surrogate Approximate Bayesian Computation , 2014, UAI.

[30]  Marc Peter Deisenroth,et al.  Doubly Stochastic Variational Inference for Deep Gaussian Processes , 2017, NIPS.

[31]  Aaron Roth,et al.  The Algorithmic Foundations of Differential Privacy , 2014, Found. Trends Theor. Comput. Sci..

[32]  David T. Frazier,et al.  Bayesian Synthetic Likelihood , 2017, 2305.05120.

[33]  Yanan Fan,et al.  Handbook of Approximate Bayesian Computation , 2018 .

[34]  James Hensman,et al.  Deep Gaussian Processes with Importance-Weighted Variational Inference , 2019, ICML.

[35]  Iain Murray,et al.  Sequential Neural Likelihood: Fast Likelihood-free Inference with Autoregressive Flows , 2018, AISTATS.

[36]  D. Dennis,et al.  A statistical method for global optimization , 1992, [Proceedings] 1992 IEEE International Conference on Systems, Man, and Cybernetics.

[37]  Aki Vehtari,et al.  Efficient Acquisition Rules for Model-Based Approximate Bayesian Computation , 2017, Bayesian Analysis.

[38]  David Abel,et al.  simple_rl: Reproducible Reinforcement Learning in Python , 2019, RML@ICLR.

[39]  Alice S.A. Johnston,et al.  Calibration and evaluation of individual-based models using Approximate Bayesian Computation , 2015 .

[40]  Gabriel Peyré,et al.  Stochastic Optimization for Large-scale Optimal Transport , 2016, NIPS.

[41]  Kai Xu,et al.  Inverse Reinforcement Learning Based Human Behavior Modeling for Goal Recognition in Dynamic Local Network Interdiction , 2018, AAAI Workshops.

[42]  P. Diggle,et al.  Monte Carlo Methods of Inference for Implicit Statistical Models , 1984 .

[43]  Alexis Boukouvalas,et al.  GPflow: A Gaussian Process Library using TensorFlow , 2016, J. Mach. Learn. Res..

[44]  Paul Marjoram,et al.  Markov chain Monte Carlo without likelihoods , 2003, Proceedings of the National Academy of Sciences of the United States of America.