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A PCA-based deep feature optimization framework for explainable orange fruit disease classification
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DOI：10.1186/s12870-026-09984-8.png)
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Abstract
En 中文
Accurate classification of orange fruit diseases is important for precision agriculture and yield protection. This study develops and rigorously benchmarks a hybrid deep-feature framework for classifying Black Spot, Canker, Fresh, and Greening oranges (1,090 images), combining deep feature extraction, PCA-based dimensionality reduction, and classical machine-learning classification. Eight backbones (seven CNNs and a Vision Transformer, ViT) and four classifiers (32 configurations in total) were evaluated under 5 × 5 repeated stratified cross-validation, with PCA fitted exclusively on training-fold features in every iteration to eliminate data leakage. The proposed ViT + PCA+SVM configuration achieved the highest mean accuracy, 99.12%±0.71%, significantly outperforming every CNN-based backbone, including DenseNet201 + PCA + SVM (98.48%±0.81%, p < 0.001). A dedicated variance-retention sensitivity analysis justifies the 98% threshold used throughout, and ablation experiments confirm that PCA substantially reduces feature dimensionality (by ~ 55.7% for ViT and ~ 76.6% for DenseNet201) without a significant loss of accuracy for either backbone. Explainability analysis — occlusion sensitivity and SHAP for the proposed ViT model, and Grad-CAM and SHAP for the DenseNet201 comparison model — shows that both configurations base predictions on biologically relevant, disease-affected regions of the fruit rather than spurious cues. These results identify ViT + PCA+SVM as the most accurate configuration evaluated, with DenseNet201 + PCA + SVM as a closely competitive, more compact convolutional alternative for intelligent orchard disease-monitoring systems.
Keywords:
Orange disease detection
CNN-based classification
Deep feature extraction
Interpretable machine learning
SHAP-based explanation
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