Simulation-based inference (SBI; Cranmer et al., 2020) is a powerful framework for inferring parameters of scientific models whose likelihood functions are unavailable or computationally prohibitive to evaluate, but for which simulating data is straightforward. The use of flexible neural conditional density estimators has substantially expanded the applicability of SBI to challenging problems, especially in fields such as particle physics (Brehmer, 2021), cognitive neuroscience (Fengler et al., 2021), economics (Dyer et al., 2024) and cosmology (Alsing et al., 2018; Jeffrey et al., 2021). Neural SBI methods rely on simulations from the scientific model to approximate intractable quantities such as the posterior, the likelihood, the likelihood-to-evidence ratio, or the score function; see Zammit-Mangion et al. (2024) for a recent review. In this work, we focus on the widely used neural posterior estimation (NPE) method (Papamakarios and Murray, 2016; Radev et al., 2022). A central practical limitation of NPE is the simulation budget required to train the conditional density estimator. As many scientific simulators are expensive to run, generating a sufficiently large training set is often the main computational bottleneck.

Selection bias arises when the probability that an observation enters a dataset depends on variables related to the quantities of interest, leading to systematic distortions in estimation and uncertainty quantification. For example, in epidemiological or survey settings, individuals with certain outcomes may be more likely to be included, resulting in biased prevalence estimates with potentially substantial downstream impact. Classical corrections, such as inverse-probability weighting or explicit likelihood-based models of the selection process, rely on tractable likelihoods, which limits their applicability in complex stochastic models with latent dynamics or high-dimensional structure. Simulation-based inference enables Bayesian analysis without tractable likelihoods but typically assumes missingness at random and thus fails when selection depends on unobserved outcomes or covariates. Here, we develop a bias-aware simulation-based inference framework that explicitly incorporates selection into neural posterior estimation. By embedding the selection mechanism directly into the generative simulator, the approach enables amortized Bayesian inference without requiring tractable likelihoods. This recasting of selection bias as part of the simulation process allows us to both obtain debiased estimates and explicitly test for the presence of bias. The framework integrates diagnostics to detect discrepancies between simulated and observed data and to assess posterior calibration. The method recovers well-calibrated posterior distributions across three statistical applications with diverse selection mechanisms, including settings in which likelihood-based approaches yield biased estimates. These results recast the correction of selection bias as a simulation problem and establish simulation-based inference as a practical and testable strategy for parameter estimation under selection bias.

Figure 1: Comparison of network architectures (left) and flow trajectories (right). Discrete flows (NPE, top) require a specialized architecture for the density estimator. Continuous flows (FMPE, bottom) are based on a vector field parametrized with an unconstrained architecture.

Figure 1: Comparison of network architectures (left) and flow trajectories (right). Discrete flows (NPE, top) require a specialized architecture for the density estimator. Continuous flows (FMPE, bottom) are based on a vector field parametrized with an unconstrained architecture.

Figure 1: Comparison of network architectures (left) and flow trajectories (right). Discrete flows (NPE, top) require a specialized architecture for the density estimator. Continuous flows (FMPE, bottom) are based on a vector field parametrized with an unconstrained architecture.

Figure 1: Comparison of network architectures (left) and flow trajectories (right). Discrete flows (NPE, top) require a specialized architecture for the density estimator. Continuous flows (FMPE, bottom) are based on a vector field parametrized with an unconstrained architecture.

Amortized Bayesian model comparison (BMC) enables fast probabilistic ranking of models via simulation-based training of neural surrogates. However, the reliability of neural surrogates deteriorates when simulation models are misspecified - the very case where model comparison is most needed. Thus, we supplement simulation-based training with a self-consistency (SC) loss on unlabeled real data to improve BMC estimates under empirical distribution shifts. Using a numerical experiment and two case studies with real data, we compare amortized evidence estimates with and without SC against analytic or bridge sampling benchmarks. SC improves calibration under model misspecification when having access to analytic likelihoods. However, it offers limited gains with neural surrogate likelihoods, making it most practical for trustworthy BMC when likelihoods are exact.