Abstract
Background In precision agriculture, especially in hydroponic systems where environmental management affects both production and resource efficiency, interpretable modeling of crop phenological stages is crucial. Typical visualization-based approaches are generally expensive and ecologically dependent. To classify and visualize lettuce growth stages (Seedling, Vegetative Growth, Heading, Bolting and Senescence) using temperature, humidity, total dissolved solids (TDS) and pH, this study proposed XGB-StageVision, a sensor-powered machine learning setup combining supervised and unsupervised learning techniques. Using XG Boost, LightGBM, CatBoost, ExtraTrees, Random Forest and LSTM under an 80/20 train-test split, a dataset of 3,169 unique observations from 70 hydroponically grown lettuce plants was evaluated. Methods and Results XGB-StageVision achieved 99.86% test accuracy, a ROC AUC of 1.00, an MCC of 0.9982 and perfect precision, recall, F1 scores and specificity across all classes, performing competitively with the best baseline models, including LightGBM, which achieved statistically comparable cross validation performance. The unsupervised t-SNE visualization showed clearly distinct structural clusters across growth stages, while SHAP revealed temperature as the strongest predictor (≈75% contribution), followed by TDS. Novel Contributions SHAP, LIME and t-SNE provided global, local and structural interpretability and transparent perspectives on environmental influences regarding plant development. Statistical analysis and 10-fold cross-validation were used to further test the model’s robustness, reliability and generalizability. Conclusion XGB-StageVision provides an IoT-ready, interpretable and imaging-free system for monitoring lettuce growth stages in real time. The framework combines supervised predictive modeling with unsupervised structural visualization to ensure transparency, sustainability and high performance, supporting resource-efficient, data-driven strategic planning in contemporary hydroponic agriculture to lower monitoring costs, optimize inputs and improve yield consistency.