Mixed neural posterior estimation for simulators with discrete and continuous parameters
Authors: Jan Boelts, Cornelius Schröder, Jonas Beck, Jakob H. Macke, Michael Deistler, Daniel Gedon
Organizations: appliedAI Institute for Europe · Machine Learning in Science, University of Tübingen · Tübingen AI Center · Hertie Institute for AI in Brain Health, University of Tübingen · Max Planck Institute for Intelligent Systems · Max Planck Institute for Biological Intelligence
Abstract
Neural Posterior Estimation (NPE) enables rapid parameter inference for complex simulators with intractable likelihoods. NPE trains an inference network to estimate a probability density over parameters given data, typically assumed to be \emph{continuous}. However, many scientific models involve parameter spaces that are \emph{mixed}, that is, they contain both discrete and continuous dimensions. We address this limitation by extending NPE to mixed parameter spaces through an inference network that jointly handles discrete and continuous parameters. The inference network factorizes the joint posterior into discrete and continuous components, combining an autoregressive classifier for the discrete parameters with a generative model for the continuous parameters, trained jointly under a single simulation-based objective. In addition, we propose a diagnostic tool to assess the calibration of the mixed posterior approximation. Across tractable toy examples and real-world scientific simulators, our joint inference approach yields accurate and calibrated posteriors. The inference framework is available in the \texttt{sbi} Python package.
Simulation-based inference with neural posterior estimation (NPE) often yields overconfident and unreliable posteriors under limited simulation budgets. To address this, we propose DRO-NPE, a distributionally robust approach that replaces the standard NPE objective with a worst-case loss over a Wasserstein ambiguity set. We introduce KL-based metrics for miscoverage and miscalibration, and use these to show that the DRO-NPE objective controls overfitting and reduces posterior overconfidence. Our method is tractable, parallelisable, and readily integrates with standard normalising flows. Across benchmark SBI tasks, DRO-NPE consistently improves coverage and calibration, while narrowing the gap between empirical and population NPE loss, leading to more reliable inference in low-simulation regimes.
William Laplante, Yuga Hikida, Charita Dellaporta +2
Simulation-based inference (SBI) with machine learning is an increasingly important tool for solving inverse problems in science and engineering, including parameter inference and the inversion of detector effects. We provide an overview of the Bayesian and frequentist statistical frameworks, describe how machine-learning-based SBI methods, such as neural posterior estimation and neural likelihood estimation, can be used for parameter estimation within these frameworks, and show that the same methods can also be applied to Empirical Bayes or unfolding tasks. We also discuss how to validate inference results and the limitations of SBI with machine learning.
Neural simulation-based inference enables parameter estimation for complex models, but typically requires the user to specify a simulator encoding a fixed model structure. We present a framework for joint model selection and parameter estimation that combines large language models for program synthesis with neural simulation-based inference. Given a natural language description of the system and data under investigation, an LLM proposes candidate simulator programs which are iteratively refined via feedback-driven mutation and evaluated using neural density estimation. The approach enables simulation-based inference over a pool of models, not just parameters within a fixed model. On benchmarks spanning deterministic dynamics, stochastic epidemic models, and dark matter substructure inference from gravitational-lensing images, the method identifies plausible model families from open-ended prompts, with accuracy that reflects the information content of the data and identifiability of candidate models.