Explainable TabPFN-Based Machine Learning for Single-Plant Yield Estimation and Trait Prioritization in Faba Bean (Vicia faba L.)

Faba bean yield reflects complex relationships among genotype, environment, and agronomic traits. This study evaluated an explainable Tabular Prior-data Fitted Network (TabPFN) framework for estimating plot-mean single-plant yield and prioritizing traits using 398 plot-level observations, 13 measured agronomic predictors, and six derived features. On the reference 80/20 split, TabPFN achieved the best values for all four test metrics (R² = 0.8746, RMSE = 1.9132 g plant⁻¹, MAE = 1.0819 g plant⁻¹, and MAPE = 8.16%). The Friedman test detected differences among the six models (χ²(5) = 16.75, p = 0.005); Nemenyi comparisons distinguished TabPFN from HistGradientBoosting and SVR, whereas the Holm-corrected Wilcoxon analysis confirmed only the TabPFN–SVR difference. Across 10 repeated 80/20 splits, TabPFN obtained the highest mean test R² (0.8614 ± 0.0691), ranked first in eight splits, and produced a higher R² than every tuned baseline in at least eight splits. SHAP, permutation importance, and LOCO analyses emphasized pod-, seed-, and biomass-related predictors. Repeated-split ablation showed that derived features improved TabPFN consistently, whereas removing selected target-proximal yield variables reduced performance for every model. The framework is therefore a harvest-time trait-estimation and trait-prioritization tool rather than an early-season forecasting system. Notably, TabPFN achieved this performance without the 100-trial Optuna search used for each baseline; only n_estimators was screened over four prespecified values.