Deep learning for plant bioinformatics: an explainable gradient-based approach for disease detection

Abstract

Emerging in the realm of bioinformatics, plant bioinformatics integrates computational and statistical methods to study plant genomes, transcriptomes, and proteomes. With the introduction of high-throughput sequencing technologies and other omics data, the demand for automated methods to analyze and interpret these data has increased. We propose a novel explainable gradient-based approach EG-CNN model for both omics data and hyperspectral images to predict the type of attack on plants in this study. We gathered gene expression, metabolite, and hyperspectral image data from plants afflicted with four prevalent diseases: powdery mildew, rust, leaf spot, and blight. Our proposed EG-CNN model employs a combination of these omics data to learn crucial plant disease detection characteristics. We trained our model with multiple hyperparameters, such as the learning rate, number of hidden layers, and dropout rate, and attained a test set accuracy of 95.5%. We also conducted a sensitivity analysis to determine the model’s resistance to hyperparameter variations. Our analysis revealed that our model exhibited a notable degree of resilience in the face of these variations, resulting in only marginal changes in performance. Furthermore, we conducted a comparative examination of the time efficiency of our EG-CNN model in relation to baseline models, including SVM, Random Forest, and Logistic Regression. Although our model necessitates additional time for training and validation due to its intricate architecture, it demonstrates a faster testing time per sample, offering potential advantages in real-world scenarios where speed is paramount. To gain insights into the internal representations of our EG-CNN model, we employed saliency maps for a qualitative analysis. This visualization approach allowed us to ascertain that our model effectively captures crucial aspects of plant disease, encompassing alterations in gene expression, metabolite levels, and spectral discrepancies within plant tissues. Leveraging omics data and hyperspectral images, this study underscores the potential of deep learning methods in the realm of plant disease detection. The proposed EG-CNN model exhibited impressive accuracy and displayed a remarkable degree of insensitivity to hyperparameter variations, which holds promise for future plant bioinformatics applications.