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

Raman spectroscopy enables non-destructive, label-free molecular characterization across materials science, biomedicine and process monitoring. Predictive Raman datasets often contain few labelled spectra and thousands of ordered wavenumbers, with informative variation within bands and across distant spectral regions. Latent-variable chemometrics accommodates collinear small-sample data but can obscure fine peak morphology, whereas deep spectral networks resolve this structure only after task-specific training. TabPFN avoids task-specific parameter fitting through pretrained in-context inference, but processes very wide inputs as feature-subsampled views that do not preserve joint visibility of related bands. We present RamanPFN, a spectral representation framework that encodes these dependencies before TabPFN inference. Global Compositional Unmixing constructs non-negative coordinates over the complete spectrum so that distant bands with shared latent variation occupy a common predictive axis. Local Vibrational Subspace Encoding represents contiguous wavenumber regions with multiple orthogonal modes that retain independent changes in peak shape, intensity and position. The representations are evaluated separately and combined at the prediction level. Evaluation covered 150 tasks from 74 public Raman datasets. RamanPFN reduced root-mean-square error by 19.6% on average across 129 regression targets relative to direct TabPFN inference and further reduced the remaining classification error by 9.0% across 21 classification tasks. These results establish explicit spectral representation as an effective interface between high-dimensional Raman measurements and reusable tabular inference.

Using Data-Derived Priors to Guide CNN Architecture Design for NIR Chemometrics

Convolutional neural networks (CNN) for near-infrared (NIR) chemometrics are often designed using generic architectural rules, although spectral datasets differ in sampling, smoothness, redundancy, and sample size. We tested whether these properties can provide empirical priors for CNN design. Across 25 NIR regression tasks, we computed descriptors of dataset size, spectral length and spacing, entropy, intrinsic rank, autocorrelation, and wavelet-scale structure. Two interpretable 1D-CNN scaffolds (a minimal single-convolution model and an extended shallow model with optional branching, dilation, etc) were optimized using five-fold cross-validated Bayesian hyperparameter optimization (HPO). Relationships extracted from near-optimal trials were converted into warm-start heuristics and evaluated directly and through leave-one-dataset-out (LODO) validation. The clearest relationships involved convolutional receptive fields. In the minimal CNN, the preferred kernel fraction decreased with spectral entropy and intrinsic rank, increased with the wavelet energy-support fraction, and the learning rate tended to decrease with training-set size. Direct and LODO heuristics were competitive with HPO, with median test-RMSE ratios of 0.953 and 1.017, respectively. The extended CNN showed similar but less transferable structure across branch usage, dilation, dropout, filter counts, and receptive-field choices. Ten stochastic refits showed seed sensitivity comparable to that of HPO-selected configurations. In a separate experiment, joint preprocessing and CNN HPO outperformed standardized-spectra HPO in 19 of 25 tasks, although gains were dataset-dependent. These results show that spectral descriptors can provide practical CNN design priors, guiding shallow NIR models toward plausible hyperparameter regions before target-specific tuning

Spectral Model eXplainer: a chemically-grounded explainability framework for spectral-based machine learning models

Spectral-based machine learning models have been increasingly deployed in chemometrics and spectroscopy, where predictive accuracy is as important as explainability. Current employed eXplainable Artificial Intelligence (XAI) methods are largely adapted from tabular or generic multivariate domains, assigning relevance to isolated spectral variables rather than to the chemically meaningful spectral zones. Widely adopted tools such as SHapley Additive exPlanations (SHAP), Permutation Feature Importance (PFI), and Variable Importance in Projection scores (VIP) were not designed for the physical continuity and high collinearity of spectral data, and their variable-level outputs require post-hoc aggregation to recover zone-level information. This study introduces the Spectral Model eXplainer (SMX), a post-hoc, global, model-agnostic XAI framework that explains spectral classifiers through expert-informed spectral zones. SMX summarizes each zone via PCA, defines quantile-based logical predicates, estimates predicate relevance with perturbation in stochastic subsamples, and aggregates bag-wise rankings in a directed weighted graph summarized by Local Reaching Centrality. A key component is threshold spectrum reconstruction, which back-projects predicate boundaries to the original spectral domain in natural measurement units, enabling direct visual comparison with measured spectra. The method was evaluated on eight real spectral datasets (six based on X-ray Fluorescence--XRF and two based on Gamma-ray Spectrometry) and one synthetic benchmark with known gr

CNNs for Vis-NIR Chemometrics: From Contradiction to Conditional Design

Near-infrared (NIR; a.k.a.\ NIRS) deep-learning studies in chemometrics increasingly report mutually inconsistent conclusions regarding convolutional neural network (CNN) design, including small versus large kernels, shallow versus deep architectures, raw spectra versus preprocessing, and single-domain training versus transfer learning. As a result, the same architecture can appear superior in one study and inferior in another, creating a practical impasse for chemometric practitioners. In this review, we argue that these contradictions are not evidence of irreconcilable methods but a structurally expected consequence of uncontrolled moderating variables. Specifically, we trace recurring disagreements to (i) the indirect nature of Vis--NIR measurement in water-dominated matrices, (ii) mismatch between effective receptive field (ERF) and the width of informative spectral structure, and (iii) validation design (including split strategy, hyperparameter tuning budget, and exposure to deployment-like shifts) acting as a hidden hyperparameter that can dominate model ranking. Building on evidence from published chemometrics and spectroscopy studies, we propose a conditional design framework that links architecture and preprocessing choices to spectral physics, dataset regime, and intended deployment scenario. Overall, the proposed perspective moves DL Chemometrics from template-driven architecture selection toward reproducible, physics-aware, and deployment-aligned model comparison.