Many statistical models can be simulated forwards but have intractable likelihoods.

Notation details are defined in Section 2.1.

Our method extends recent developments in simulation-based inference (SBI) based on normalizing flows to Bayesian hierarchical models.

The author responses answered my questions as well as points raised by other reviewers, providing additional clarification.] This paper formulates a fully probabilistic model of the vesicle-release dynamics at the sub-cellular biophysical level in the ribbon synapse. The paper then develops a likelihood-free inference method, tests it on a synthetic dataset, and finally infers the parameters of vesicle release in the ribbon synapse from real data. Originality: The paper presents a novel combination of biophysical modeling of ribbon synapse and a likelihood-free inference of the parameters. To my knowledge, the fully stochastic modeling of the vesicle-release dynamics is itself new.

We present a likelihood-free probabilistic inversion method based on normalizing flows for high-dimensional inverse problems. The proposed method is composed of two complementary networks: a summary network for data compression and an inference network for parameter estimation. The summary network encodes raw observations into a fixed-size vector of summary features, while the inference network generates samples of the approximate posterior distribution of the model parameters based on these summary features. The posterior samples are produced in a deep generative fashion by sampling from a latent Gaussian distribution and passing these samples through an invertible transformation. We construct this invertible transformation by sequentially alternating conditional invertible neural network and conditional neural spline flow layers. The summary and inference networks are trained simultaneously. We apply the proposed method to an inversion problem in groundwater hydrology to estimate the posterior distribution of the log-conductivity field conditioned on spatially sparse time-series observations of the system's hydraulic head responses.The conductivity field is represented with 706 degrees of freedom in the considered problem.The comparison with the likelihood-based iterative ensemble smoother PEST-IES method demonstrates that the proposed method accurately estimates the parameter posterior distribution and the observations' predictive posterior distribution at a fraction of the inference time of PEST-IES.

Sequential neural posterior estimation (SNPE) techniques have been recently proposed for dealing with simulation-based models with intractable likelihoods. Unlike approximate Bayesian computation, SNPE techniques learn the posterior from sequential simulation using neural network-based conditional density estimators by minimizing a specific loss function. The SNPE method proposed by Lueckmann et al. (2017) used a calibration kernel to boost the sample weights around the observed data, resulting in a concentrated loss function. However, the use of calibration kernels may increase the variances of both the empirical loss and its gradient, making the training inefficient. To improve the stability of SNPE, this paper proposes to use an adaptive calibration kernel and several variance reduction techniques. The proposed method greatly speeds up the process of training, and provides a better approximation of the posterior than the original SNPE method and some existing competitors as confirmed by numerical experiments.

We introduce a new amortized likelihood ratio estimator for likelihood-free simulation-based inference (SBI). Our estimator is simple to train and estimates the likelihood ratio using a single forward pass of the neural estimator. Our approach directly computes the likelihood ratio between two competing parameter sets which is different from the previous approach of comparing two neural network output values. We refer to our model as the direct neural ratio estimator (DNRE). As part of introducing the DNRE, we derive a corresponding Monte Carlo estimate of the posterior. We benchmark our new ratio estimator and compare to previous ratio estimators in the literature. We show that our new ratio estimator often outperforms these previous approaches. As a further contribution, we introduce a new derivative estimator for likelihood ratio estimators that enables us to compare likelihood-free Hamiltonian Monte Carlo (HMC) with random-walk Metropolis-Hastings (MH). We show that HMC is equally competitive, which has not been previously shown. Finally, we include a novel real-world application of SBI by using our neural ratio estimator to design a quadcopter. Code is available at https://github.com/SRI-CSL/dnre.

We present a framework for the efficient computation of optimal Bayesian decisions under intractable likelihoods, by learning a surrogate model for the expected utility (or its distribution) as a function of the action and data spaces. We leverage recent advances in simulation-based inference and Bayesian optimization to develop active learning schemes to choose where in parameter and action spaces to simulate. This allows us to learn the optimal action in as few simulations as possible. The resulting framework is extremely simulation efficient, typically requiring fewer model calls than the associated posterior inference task alone, and a factor of $100-1000$ more efficient than Monte-Carlo based methods. Our framework opens up new capabilities for performing Bayesian decision making, particularly in the previously challenging regime where likelihoods are intractable, and simulations expensive.

Likelihood-free inference methods typically make use of a distance between simulated and real data. A common example is the maximum mean discrepancy (MMD), which has previously been used for approximate Bayesian computation, minimum distance estimation, generalised Bayesian inference, and within the nonparametric learning framework. The MMD is commonly estimated at a root-$m$ rate, where $m$ is the number of simulated samples. This can lead to significant computational challenges since a large $m$ is required to obtain an accurate estimate, which is crucial for parameter estimation. In this paper, we propose a novel estimator for the MMD with significantly improved sample complexity. The estimator is particularly well suited for computationally expensive smooth simulators with low- to mid-dimensional inputs. This claim is supported through both theoretical results and an extensive simulation study on benchmark simulators.