RamanPFN: learning from Raman spectral structure with a tabular foundation model

Raman spectroscopy enables label-free molecular characterization across materials science, analytical chemistry, biomedicine, and industrial process monitoring. However, machine learning for high-dimensional spectroscopy remains constrained by limited labelled data and a mismatch between the physical organization of spectra and feature-agnostic models. Channel coverage alone does not ensure that related bands share a common inference context. Here we present RamanPFN, a general-purpose spectral foundation framework that enables unified in-context inference through physics-guided spectral learning. It captures full-spectrum compositional covariation via Global Compositional Unmixing (GCU), which decomposes distributed, multi-band mixture signatures into shared non-negative latent bases. Simultaneously, it resolves local vibrational structure through Local Vibrational Subspace Encoding (LVSE), which preserves fine-grained peak morphology, intensity fluctuations, and peak shifts within contiguous spectral neighborhoods. Extensive evaluation across 74 diverse public Raman datasets covered 129 regression targets and was further extended to 21 classification tasks. RamanPFN achieved state-of-the-art performance across all reported aggregate metrics against 28 independently reproduced methods spanning chemometrics, spectral neural networks, deep tabular learners and tabular foundation models. RamanPFN establishes a physics-guided paradigm for scientific spectroscopy, enabling data-efficient predictive learning across diverse chemical systems.