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This research advances simulation-based inference by introducing Hierarchical Blockwise Diffusion Sampling to handle misspecified simulators and heterogeneous observations without retraining. The method leverages path-regularized fine-tuning and Girsanov's theorem to correct posterior distributions in complex biological signaling models, demonstrating improved predictive accuracy over standard pretrained approaches.
Scalable Diffusion SBI for Compositional Inference under Simulator Misspecification
arXiv:2609.36950v1 Announce Type: new Abstract: Simulation-based inference is challenging when many heterogeneous observations must be composed, hierarchical latent structure must be preserved, and the simulator is misspecified relative to observed data. We develop sampling and fine-tuning methods for diffusion-based inference in design-conditional settings, where the same simulator is queried across different experimental conditions $\xi$. We extend compositional score-based inference with a continuous-time diffusion coefficient that accounts for the number of observations, avoiding Jacobian and auxiliary-covariance corrections. We introduce Hierarchical Blockwise Diffusion Sampling (HBDS), which infers shared parameters and group-specific latent states using a single pretrained model, with the hierarchy specified only at sampling time. Together, these methods support variable observation sets and groupings without retraining. To address misspecification, we introduce path-regularized fine-tuning that adapts the learned likelihood to observations and transfers corrections to posterior inference. Using Girsanov's theorem, we quantify path divergence between pretrained and fine-tuned models across experimental designs and interpret it alongside predictive errors to distinguish candidate misspecification correction from unnecessary adaptation. We evaluate compositional sampling on exact-score Gaussian and Simple Likelihood, Complex Posterior benchmarks, HBDS with analytic and learned scores on a controlled hierarchical model, and fine-tuning and localization on a separate analytic model with known design-dependent discrepancy. Finally, we apply the framework to 940 measurements across four cell lines in a mechanistic Bone Morphogenetic Protein signaling model, where fine-tuning improves posterior-predictive accuracy relative to the pretrained model and shifts posterior marginals toward the least-squares reference while retaining spread.
Abstract:Simulation-based inference is challenging when many heterogeneous observations must be composed, hierarchical latent structure must be preserved, and the simulator is misspecified relative to observed data. We develop sampling and fine-tuning methods for diffusion-based inference in design-conditional settings, where the same simulator is queried across different experimental conditions $\xi$. We extend compositional score-based inference with a continuous-time diffusion coefficient that accounts for the number of observations, avoiding Jacobian and auxiliary-covariance corrections. We introduce Hierarchical Blockwise Diffusion Sampling (HBDS), which infers shared parameters and group-specific latent states using a single pretrained model, with the hierarchy specified only at sampling time. Together, these methods support variable observation sets and groupings without retraining. To address misspecification, we introduce path-regularized fine-tuning that adapts the learned likelihood to observations and transfers corrections to posterior inference. Using Girsanov's theorem, we quantify path divergence between pretrained and fine-tuned models across experimental designs and interpret it alongside predictive errors to distinguish candidate misspecification correction from unnecessary adaptation. We evaluate compositional sampling on exact-score Gaussian and Simple Likelihood, Complex Posterior benchmarks, HBDS with analytic and learned scores on a controlled hierarchical model, and fine-tuning and localization on a separate analytic model with known design-dependent discrepancy. Finally, we apply the framework to 940 measurements across four cell lines in a mechanistic Bone Morphogenetic Protein signaling model, where fine-tuning improves posterior-predictive accuracy relative to the pretrained model and shifts posterior marginals toward the least-squares reference while retaining spread.
Machine Learning (cs.LG); Quantitative Methods (q-bio.QM); Machine Learning (stat.ML)
arXiv:2609.36950 [cs.LG]
(or arXiv:2609.36950v1 [cs.LG] for this version)
https://doi.org/10.48550/arXiv.2609.36950 Focus to learn more arXiv-issued DOI via DataCite (pending registration)
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