Automatic Posterior Transformation for Likelihood-Free Inference

How can one perform Bayesian inference on stochastic simulators with intractable likelihoods? A recent approach is to learn the posterior from adaptively proposed simulations using neural network-based conditional density estimators. However, existing methods are limited to a narrow range of proposal distributions or require importance weighting that can limit performance in practice. Here we present automatic posterior transformation (APT), a new sequential neural posterior estimation method for simulation-based inference. APT can modify the posterior estimate using arbitrary, dynamically updated proposals, and is compatible with powerful flow-based density estimators. It is more flexible, scalable and efficient than previous simulation-based inference techniques. APT can operate directly on high-dimensional time series and image data, opening up new applications for likelihood-free inference.

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

[2]  T. Reichenbach,et al.  Mobility promotes and jeopardizes biodiversity in rock–paper–scissors games , 2007, Nature.

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

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

[5]  Brandon M. Turner,et al.  A generalized, likelihood-free method for posterior estimation , 2014, Psychonomic bulletin & review.

[6]  Dustin Tran,et al.  Hierarchical Implicit Models and Likelihood-Free Variational Inference , 2017, NIPS.

[7]  Prafulla Dhariwal,et al.  Glow: Generative Flow with Invertible 1x1 Convolutions , 2018, NeurIPS.

[8]  Gilles Louppe,et al.  Approximating Likelihood Ratios with Calibrated Discriminative Classifiers , 2015, 1506.02169.

[9]  Christopher C. Drovandi,et al.  Likelihood-free inference in high dimensions with synthetic likelihood , 2018, Comput. Stat. Data Anal..

[10]  A. J. Lotka Analytical Note on Certain Rhythmic Relations in Organic Systems , 1920, Proceedings of the National Academy of Sciences.

[11]  Michael U. Gutmann,et al.  Dynamic Likelihood-free Inference via Ratio Estimation (DIRE) , 2018, ArXiv.

[12]  Paul Fearnhead,et al.  Constructing summary statistics for approximate Bayesian computation: semi‐automatic approximate Bayesian computation , 2012 .

[13]  Arthur Pesah,et al.  Recurrent machines for likelihood-free inference , 2018, ArXiv.

[14]  Ritabrata Dutta,et al.  Likelihood-free inference via classification , 2014, Stat. Comput..

[15]  Frank D. Wood,et al.  Using synthetic data to train neural networks is model-based reasoning , 2017, 2017 International Joint Conference on Neural Networks (IJCNN).

[16]  John P. Cunningham,et al.  Neural data science: accelerating the experiment-analysis-theory cycle in large-scale neuroscience , 2017, Current Opinion in Neurobiology.

[17]  Pushmeet Kohli,et al.  Vision-as-Inverse-Graphics: Obtaining a Rich 3D Explanation of a Scene from a Single Image , 2017, 2017 IEEE International Conference on Computer Vision Workshops (ICCVW).

[18]  Bernhard Schölkopf,et al.  A Kernel Two-Sample Test , 2012, J. Mach. Learn. Res..

[19]  Erwin Frey,et al.  Self-organization of mobile populations in cyclic competition. , 2008, Journal of theoretical biology.

[20]  D. J. Nott,et al.  Approximate Bayesian computation via regression density estimation , 2012, 1212.1479.

[21]  Alexander J. Smola,et al.  Deep Sets , 2017, 1703.06114.

[22]  Bai Jiang,et al.  Learning Summary Statistic for Approximate Bayesian Computation via Deep Neural Network , 2015, 1510.02175.

[23]  Shakir Mohamed,et al.  Variational Inference with Normalizing Flows , 2015, ICML.

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

[25]  Olivier François,et al.  Non-linear regression models for Approximate Bayesian Computation , 2008, Stat. Comput..

[26]  E. Gehan,et al.  The properties of high-dimensional data spaces: implications for exploring gene and protein expression data , 2008, Nature Reviews Cancer.

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

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

[29]  Yee Whye Teh,et al.  Probabilistic symmetry and invariant neural networks , 2019, J. Mach. Learn. Res..

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

[31]  A. Mincholé,et al.  Variational Inference over Non-differentiable Cardiac Simulators using Bayesian Optimization , 2017, 1712.03353.

[32]  Ferenc Huszár,et al.  Variational Inference using Implicit Distributions , 2017, ArXiv.

[33]  Yun S. Song,et al.  A Likelihood-Free Inference Framework for Population Genetic Data using Exchangeable Neural Networks , 2018, bioRxiv.

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

[35]  A. Doucet,et al.  Particle Markov chain Monte Carlo methods , 2010 .

[36]  Yoshua Bengio,et al.  Learning Phrase Representations using RNN Encoder–Decoder for Statistical Machine Translation , 2014, EMNLP.

[37]  Iain Murray,et al.  Fast $\epsilon$-free Inference of Simulation Models with Bayesian Conditional Density Estimation , 2016, 1605.06376.

[38]  Jakob H. Macke,et al.  Likelihood-free inference with emulator networks , 2018, AABI.

[39]  David J. Nott,et al.  Variational Bayes With Intractable Likelihood , 2015, 1503.08621.

[40]  Darren J Wilkinson,et al.  Likelihood free inference for Markov processes: a comparison , 2014, Statistical applications in genetics and molecular biology.

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

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

[43]  S. Sisson,et al.  A comparative review of dimension reduction methods in approximate Bayesian computation , 2012, 1202.3819.

[44]  Jukka Corander,et al.  Likelihood-Free Inference by Ratio Estimation , 2016, Bayesian Analysis.

[45]  Gilles Louppe,et al.  Adversarial Variational Optimization of Non-Differentiable Simulators , 2017, BNAIC/BENELEARN.

[46]  Gilles Louppe,et al.  Mining gold from implicit models to improve likelihood-free inference , 2018, Proceedings of the National Academy of Sciences.

[47]  Iain Murray,et al.  Sequential Neural Methods for Likelihood-free Inference , 2018, ArXiv.

[48]  Shakir Mohamed,et al.  Learning in Implicit Generative Models , 2016, ArXiv.

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

[50]  R. May,et al.  Nonlinear Aspects of Competition Between Three Species , 1975 .