Rapid and accurate identification of bakanae pathogens carried by rice seeds based on hyperspectral imaging and deep transfer learning.

ABSTRACT

Bakanae disease is a common seed-borne disease of rice. Rapid and accurate detection of bakanae pathogens carried by rice seeds is essential for the health of rice germplasm resources and the safety of rice production. This study aims to propose a general framework for species identification of major bakanae pathogens carried by rice seeds based on hyperspectral imaging and deep transfer learning. Seven varieties of rice seeds and four kinds of bakanae pathogens were analyzed. One-dimensional deep convolution neural networks (DCNNs) were first constructed using complete datasets. They achieved accuracies larger than 96.5% on the testing sets of most datasets, exceeding the conventional SVM and PLS-DA models. Then the developed DCNNs were transferred to detect other complete training sets. Most of the deep transferred models achieved comparable or even better performance than the original DCNNs. Two smaller target training sets were further constructed by randomly selecting spectra from the complete training sets. As the size of the target training sets reduced, the accuracies of all models on the corresponding testing sets also decreased gradually. Visualization analysis were conducted using the t-distribution stochastic neighbor embedding (t-SNE) algorithm and a proposed gradient-weighted activation wavelength (Grad-AW) method. They all showed that deep transfer learning could utilize the representation patterns in the source datasets to improve the target tasks. The overall results indicated that the bakanae pathogens were all identified accurately under our proposed framework. Hyperspectral imaging combined with deep transfer learning provided a new idea for the quality detection of large-scale seeds in modern seed industry.