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

Machine Learning (ML) has transformed many scientific fields, yet key applications still lack standardized benchmarks. Raman spectroscopy, a widely used technique for non-invasive molecular analysis, is one such field where progress is limited by fragmented datasets, inconsistent evaluation, and models that fail to capture the structure of spectral data. We introduce RamanBench, the first large-scale, fully reproducible benchmark for ML on Raman spectroscopy, consisting of streamlined data access, evaluation protocols and code, as well as a live leaderboard. It unifies 74 datasets (including 16 first released with this benchmark) across four domains, comprising 325,668 spectra and spanning classification and regression tasks under diverse experimental conditions. We benchmark 28 models under a standardized protocol, including classical methods (e.g., PLS), Raman-specific (e.g., RamanNet), Tabular Foundation Model (TFM) (e.g., TabPFN), and time-series approaches (e.g., ROCKET). TFM consistently outperform domain-specific and gradient boosting baselines, while time-series models remain competitive. However, no method generalizes across datasets, revealing a fundamental gap. Therefore, we invite the community to contribute new approaches to our living benchmark, with the potential to accelerate advances in critical applications such as medical diagnostics, biological research, and materials science.

Raman spectra obtained in real world applications are often a noisy combination of several spectra of various substances in a tested sample. Unmixing such spectra into individual components corresponding to each of the substances is of great value and has been a longstanding challenge in Raman spectroscopy. Existing unmixing methods are predominantly designed to invert an overdetermined mixed model and therefore require multiple mixed spectra as input. However, open domain and/or non-cooperative detection applications in Raman spectroscopy such as controlled substance detection, call for single-channel solutions which can identify individual components from thousands of candidates by analyzing only a single noisy mixed spectrum. To our knowledge, sparse regression is the only existing solution which can cope with this scenario, yet it has very low tolerance to noises and can hardly be applicable in practice. To address these limitations, we introduce a novel neural approach for single-channel Raman spectrum unmixing inspired by speech separation. It aims at solving underdetermined systems and can decompose a noisy mixed spectrum from a library of thousands of components (substances). The core of our method is a deep separation neural network (RSSNet) which takes a mixed spectrum as input and outputs spectra of pure components. We created two synthetic datasets of single-channel Raman spectra unmixing and demonstrated feasibility and superiority of RSSNet on these datasets (outperform competing methods by >4dB). Furthermore, we verified that RSSNet, trained solely on synthetic data, can successfully unmix real-world mixed spectra of mixtures of mineral powders, exhibiting strong generalization. Our approach represents a new paradigm for Raman unmixing and enables new possibilities for fast detection of Raman mixtures.

Visible and near-infrared (vis-NIR) and mid-infrared (MIR) spectroscopy enable rapid, cost-effective prediction of soil properties. Yet, translating high-dimensional, highly collinear spectra into accurate soil property predictions remains challenging, particularly when employing machine learning. We systematically investigated regression models and dimensionality reduction approaches for spectroscopic modeling across 85 regression tasks from open benchmark datasets in pedometrics spanning field-scale digital soil mapping and a global soil spectral library. We compared an in-context learning tabular foundation model (TabPFN), a convolutional neural network (CNN), rule-based regression (Cubist), Random Forest, and partial least squares regression (PLSR) using full spectra as well as features derived from principal component analysis (PCA) and partial least squares (PLS) latent variables. TabPFN consistently delivered the best overall performance across scales, including large spectral library tasks with tens of thousands of soil samples. Notably, TabPFN applied directly to full spectra already surpassed all classical baselines, showing that explicit dimensionality reduction is not strictly required for strong performance. Further improvements were achieved through PLS, which proved to be an effective dimensionality reduction strategy for all models. Combining PLS latent variables with TabPFN yielded the best predictions overall. Our findings provide evidence-based guidance for spectroscopic calibration model selection across operational scales, demonstrating that the long-standing advantages of PLSR and modern tabular foundation models complement each other in chemometrics.