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

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

Near-infrared spectroscopy is increasingly used as a rapid, non-destructive chemical sensing technology for the analysis of food, pharmaceutical, biological, and environmental samples. However, the practical deployment of NIR sensors still depends on calibration models able to handle high-dimensional, collinear spectra, limited sample sizes, preprocessing dependence, spectral outliers, and extrapolation beyond the calibration domain. Here, we evaluate whether tabular foundation models can provide a new calibration strategy for NIR chemical sensing. We benchmark TabPFN on 66 NIR datasets covering 54 regression and 12 classification tasks, and compare direct inference on raw spectra with preprocessing-optimized inference against PLS/PLS-DA, Ridge, Catboost, and one-dimensional convolutional neural networks. The study uses a unified validation framework in which preprocessing and model selection are performed exclusively on calibration data before external test evaluation. In regression, preprocessing-optimized TabPFN achieves the best overall average rank and significantly outperforms PLS, CatBoost, TabPFN on raw spectra, and CNN-1D, while remaining statistically comparable to Ridge. In classification, TabPFN applied directly to raw spectra provides the best average rank, with performance close to the optimized variant. Robustness analyses show that TabPFN provides strong average predictive performance but that its advantage decreases on spectral outliers and extrapolated samples, where classical chemometric models remain competitive. These results suggest that tabular foundation models can complement established chemometric workflows for NIR chemical sensing, especially in small- to medium-sized calibration settings, while highlighting the need for spectroscopy-specific priors and uncertainty-aware deployment strategies.

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.