A generalizable and interpretable model for early warning of pest-induced crop diseases using environmental data

Abstract

Pest infestations and resulting crop diseases threaten global food security. Traditional pest and disease monitoring methods are time-consuming and prone to delays, thus necessitating the development of effective prediction strategies that facilitate early and timely detection. In response to this challenge, this research proposes a generalizable and interpretable machine learning model to predict two major rice pests—Green Leafhopper and Yellow Stem Borer—and a No Pest class using environmental data collected from various regions in India. The dataset, comprising factors such as temperature, humidity, and rainfall, underwent rigorous preprocessing. Key features like temperature difference, humidity difference, and vapor pressure deficit were engineered to enhance the model’s performance. Twelve baseline models were trained and their performance was evaluated using F1 scores and AUC values due to the imbalanced nature of the dataset. Through statistical analysis of baseline models, Random Forest, Balanced Random Forest, XGBoost, and CatBoost models, were selected for hyperparameter tuning via Optuna. The tuned CatBoost model demonstrated superior performance, achieving AUC values of 0.99 for Green Leafhoppers, 0.98 for Yellow Stem Borers, 1.00 for No Pest class and an overall F1 score of 0.9414 with a mean AUC value of 0.9912 across all classes. Additionally, Explainable Artificial Intelligence techniques, particularly SHAP, were employed to interpret the model’s predictions, identifying the relative importance of environmental factors in pest occurrence. This interpretability aligns the model’s predictions with established agronomic knowledge, enhancing its practical utility for early pest and disease detection. The generalizability of the proposed model suggests it can be adapted to other crops and regions, offering a valuable tool for early warning systems in agriculture, promoting sustainable practices, and reducing crop losses due to pests and diseases.