Amortized Spectral Kernel Discovery via Prior-Data Fitted Network

Abstract: Prior-Data Fitted Networks (PFNs) enable efficient amortized inference but lack transparent access to their learned priors and kernels. This opacity hinders their use in downstream tasks, such as surrogate-based optimization, that require explicit covariance models. We introduce an interpretability-driven framework for amortized spectral discovery from pre-trained PFNs with decoupled attention. We perform a mechanistic analysis on a trained PFN that identifies attention latent output as the key intermediary, linking observed function data to spectral structure. Building on this insight, we propose decoder architectures that map PFN latents to explicit spectral density estimates and corresponding stationary kernels via Bochner's theorem. We study this pipeline in both single-realization and multi-realization regimes, contextualizing theoretical limits on spectral identifiability and proving consistency when multiple function samples are available. Empirically, the proposed decoders recover complex multi-peak spectral mixtures and produce explicit kernels that support Gaussian process regression with accuracy comparable to PFNs and optimization-based baselines, while requiring only a single forward pass. This yields orders-of-magnitude reductions in inference time compared to optimization-based baselines.