Fourier Neural Operators (FNOs) offer an efficient paradigm for solving partial differential equations (PDEs). However, FNOs rely on a fixed Fourier basis and hard frequency truncation, which inherently limit their ability to model non-periodic, localized, and fine-scale solution structures. We propose the Stochastic Adaptive Fourier Decomposition Neural Operator (SAFDNO), a spectral neural operator that replaces predefined Fourier modes with an adaptive Takenaka-Malmquist (TM) orthonormal system derived from the theory of Stochastic Adaptive Fourier Decomposition (SAFD). Instead of performing an expensive greedy pole search in classical SAFD, SAFDNO amortizes stochastic pole selection through a neural pole predictor and constructs the adaptive TM system directly from latent features. The resulting operator performs learned filtering on coefficients of analytic branches in the Hardy space with respect to the input-adaptive TM system, preserving the global receptive field of spectral operators while providing a more flexible representation than using fixed spectral bases. Across nine PDE benchmark problems, SAFDNO achieves the best performance on all six regular-grid problems among strong neural operator baselines, with especially notable gains on Darcy, Burgers, and Navier-Stokes, where fixed Fourier modes are often less effective at modeling localized oscillations, sharp transitions, and multiscale structures. SAFDNO also exhibits stronger zero-shot super-resolution performance and shows less performance degradation when deployed on finer discretizations. These results suggest that the input-adaptive TM system provides a promising alternative to fixed spectral representations for neural operator learning.

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