Identification of Tobacco Leaf Diseases Using Hyperspectral Imaging and Machine Learning with SHAP Interpretability Analysis

Peng Luo¹Yang Yang²Zhang Huilai¹Man Yi²Xianguo Zhou²Yide Yang²Chen Huabao¹Min Yan^2*Chunxian Jiang^1*

• ¹College of Agronomy, Sichuan Agricultural University, Chengdu, China
• ²Yibin Municipal Company of Sichuan Provincial Tobacco Corporation, Yibin, China

Tobacco leaf diseases significantly affect yield and quality, underscoring the need for rapid and nondestructive diagnostic tools. Although hyperspectral imaging (HSI) has been applied in tobacco pathology, most existing studies focus on single diseases and lack generalized, interpretable frameworks for multi-class identification. In this study, hyperspectral images of healthy leaves and four major diseases-brown spot, wildfire, Tobacco Mosaic Virus (TMV), and Potato virus Y (PVY)- were collected to construct a balanced, leaf-independent dataset. Pixels were grouped by leaf ID, and the entire dataset was strictly partitioned at the leaf level to prevent pixel-level data leakage and ensure generalization to unseen leaves. Multiple preprocessing techniques, wavelength-selection methods, and machine-learning classifiers were systematically compared. A compact ANN model integrating Savitzky-Golay preprocessing and SPA-based wavelength selection achieved the best overall performance while requiring only a small number of informative wavelengths. A Transformer model provided slightly stronger predictive capacity but depended on full-spectrum inputs and substantially higher computational cost. Pixel-level predictions enabled lesion-area-based severity estimation for the two leaf-spot diseases. SHAP analysis highlighted physiologically meaningful spectral regions associated with pigment absorption and structural variation. Overall, this study presents an efficient and interpretable HSI framework for multi-disease tobacco diagnosis, supporting the development of practical hyperspectral or multispectral systems.