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It is significant to identify the moldy status of stored maize by fungi infection in the early stage. Hyperspectral imaging (HSI) combined with the sparse auto-encoders (SAE) and convolutional neural network (CNN) algorithms was used to classify the moldy grades of maize kernels. The HSI data were obtained in the range of 400–1000 nm, and four grades from health to heavy mildew were distinguished using the measured fungal spores of maize. The depth spectral features were represented using SAE and the image features were extracted by CNN. K nearest neighbors, support vector machine (SVM), and partial least squares discriminant analysis classifiers were combined with the spectral and image features to establish classification models to identify the different moldy grades of maize kernels. The comparison results indicated that the fusion of SAE and CNN combined with the SVM classifier to construct the SAE-CNN-SVM model had the most satisfactory identification result with high correct recognition rates of 99.47% and 98.94% for the training and testing sets, respectively, and the values of sensitivity and specificity were 0.95–1. The moldy grades were presented intuitively on the maize image based on pixels or kernel-wise. Therefore, the HSI with the SAE-CNN-SVM model had good recognition ability for the early detection of moldy maize kernels, which could potentially provide technical support for the development of online detection of moldy maize kernels during storage. [ABSTRACT FROM AUTHOR]