sbi reloaded: a toolkit for simulation-based inference workflows

Scientists and engineers use simulators to model empirically observed phenomena. However, tuning the parameters of a simulator to ensure its outputs match observed data presents a significant challenge. Simulation-based inference (SBI) addresses this by enabling Bayesian inference for simulators, identifying parameters that match observed data and align with prior knowledge. Unlike traditional Bayesian inference, SBI only needs access to simulations from the model and does not require evaluations of the likelihood-function. In addition, SBI algorithms do not require gradients through the simulator, allow for massive parallelization of simulations, and can perform inference for different observations without further simulations or training, thereby amortizing inference. Over the past years, we have developed, maintained, and extended $\texttt{sbi}$, a PyTorch-based package that implements Bayesian SBI algorithms based on neural networks. The $\texttt{sbi}$ toolkit implements a wide range of inference methods, neural network architectures, sampling methods, and diagnostic tools. In addition, it provides well-tested default settings but also offers flexibility to fully customize every step of the simulation-based inference workflow. Taken together, the $\texttt{sbi}$ toolkit enables scientists and engineers to apply state-of-the-art SBI methods to black-box simulators, opening up new possibilities for aligning simulations with empirically observed data.

Diffusion posterior sampling for simulation-based inference in tall data settings

Determining which parameters of a non-linear model could best describe a set of experimental data is a fundamental problem in science and it has gained much traction lately with the rise of complex large-scale simulators (a.k.a. black-box simulators). The likelihood of such models is typically intractable, which is why classical MCMC methods can not be used. Simulation-based inference (SBI) stands out in this context by only requiring a dataset of simulations to train deep generative models capable of approximating the posterior distribution that relates input parameters to a given observation. In this work, we consider a tall data extension in which multiple observations are available and one wishes to leverage their shared information to better infer the parameters of the model. The method we propose is built upon recent developments from the flourishing score-based diffusion literature and allows us to estimate the tall data posterior distribution simply using information from the score network trained on individual observations. We compare our method to recently proposed competing approaches on various numerical experiments and demonstrate its superiority in terms of numerical stability and computational cost.

L-C2ST: Local Diagnostics for Posterior Approximations in Simulation-Based Inference

Many recent works in simulation-based inference (SBI) rely on deep generative models to approximate complex, high-dimensional posterior distributions. However, evaluating whether or not these approximations can be trusted remains a challenge. Most approaches evaluate the posterior estimator only in expectation over the observation space. This limits their interpretability and is not sufficient to identify for which observations the approximation can be trusted or should be improved. Building upon the well-known classifier two-sample test (C2ST), we introduce L-C2ST, a new method that allows for a local evaluation of the posterior estimator at any given observation. It offers theoretically grounded and easy to interpret - e.g. graphical - diagnostics, and unlike C2ST, does not require access to samples from the true posterior. In the case of normalizing flow-based posterior estimators, L-C2ST can be specialized to offer better statistical power, while being computationally more efficient. On standard SBI benchmarks, L-C2ST provides comparable results to C2ST and outperforms alternative local approaches such as coverage tests based on highest predictive density (HPD). We further highlight the importance of local evaluation and the benefit of interpretability of L-C2ST on a challenging application from computational neuroscience.

Validation Diagnostics for SBI algorithms based on Normalizing Flows

Building on the recent trend of new deep generative models known as Normalizing Flows (NF), simulation-based inference (SBI) algorithms can now efficiently accommodate arbitrary complex and high-dimensional data distributions. The development of appropriate validation methods however has fallen behind. Indeed, most of the existing metrics either require access to the true posterior distribution, or fail to provide theoretical guarantees on the consistency of the inferred approximation beyond the one-dimensional setting. This work proposes easy to interpret validation diagnostics for multi-dimensional conditional (posterior) density estimators based on NF. It also offers theoretical guarantees based on results of local consistency. The proposed workflow can be used to check, analyse and guarantee consistent behavior of the estimator. The method is illustrated with a challenging example that involves tightly coupled parameters in the context of computational neuroscience. This work should help the design of better specified models or drive the development of novel SBI-algorithms, hence allowing to build up trust on their ability to address important questions in experimental science.