Rejections Based on Predictive Uncertainty Enable Reliable Routine Soil Spectroscopy

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.

Near-Infrared (NIR) spectroscopy has emerged as a promising alternative to traditional soil analysis methods, offering advantages such as speed, low cost, and non-destructive testing. This work proposes a machine learning (ML) approach to calibrate predictive models for carbon (C) and nitrogen (N) content in Oxisols and Inceptisols, utilizing NIR spectral data acquired with a portable MyNIR device. Various preprocessing methods were evaluated, with the most effective being the Savitzky-Golay (SG) filter and a robust outlier removal method based on the Nonlinear Iterative Partial Least Squares (NIPALS) algorithm coupled with a Huber loss function. Multiple validation strategies were compared, including 10-fold cross-validation, leave-one-out, and holdout via the Kennard-Stone method, followed by standardization. Stacking ensemble learning models were employed, using Partial Least Squares (PLS), Support Vector Regression (SVR), and Ridge as base models, with linear regression as the meta-model. The models were evaluated using R2, Root Mean Squared Error (RMSE), Mean Absolute Error (MAE), and Ratio of Performance Deviation (RPD) metrics. The performance gap between soil types suggests the influence of pedological characteristics. Furthermore, the models achieved an RPD > 2.0 with low overfitting, validating the potential of this approach for rapid C and N quantification. This study contributes to the optimization of sustainable agricultural practices, aligning with the demand for efficient and environmentally friendly analytical methods. The developed technique enables faster decision-making for producers and consultants based on organic matter content, fertility indicators, and nutrient availability.

Top-soil organic carbon (SOC) prediction is fundamental to agricultural sustainability, land use policy and fertilization planning. Existing approaches face two limitations: they pair hand-crafted covariates with classical ML or single-modal deep models that miss rich spectral and temporal information, and grid-based architectures ignore the irregular spatial structure of field measurements. We introduce SpTGNN, a multi-modal spatio-temporal graph neural network addressing both. SpTGNN represents soil measurements as nodes in a heterogeneous graph with three edge types (spatial proximity, spectral similarity, elevation), and applies relational graph attention to learn separate patterns per relation. A fine-tuned TerraMind encoder extracts node features from Sentinel-2, Sentinel-1 and DEM signals, combined with per-sample environmental covariates and learned positional and temporal embeddings. A sparse Mixture-of-Experts module fuses the four streams via top-$k$ routing. Uncertainty is captured by pairing heteroscedastic regression (aleatoric) with deep ensembles (epistemic), and a Moran's $I$ penalty regularizes spatial autocorrelation. We evaluate on a global SOC corpus split into three regional instances ($\sim$49k samples globally, Africa $\sim$26k, Europe $\sim$14k). Our 5-member deep ensemble reports $R^2=0.762$, RMSE $=3.51\pm0.48$ g/kg and MAPE $=22.9\%$ on the Africa test split, improving over a tabular XGBoost baseline; the best single checkpoint reaches validation $R^2=0.864$. Ablations confirm the heterogeneous graph, MoE fusion and fine-tuned backbone each contribute substantively, and the ensemble UQ stack achieves post-calibration ECE of $0.031$ (hybrid) and $0.026$ ($β$-NLL). To our knowledge, this is the first framework to unify foundation-model feature extraction, heterogeneous graph attention and decomposed uncertainty quantification for SOC estimation.