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Plant disease identification using explainable 3D deep learning on hyperspectral images

Plant methods, 2019-08, Vol.15 (1), p.98-98, Article 98 [Peer Reviewed Journal]

COPYRIGHT 2019 BioMed Central Ltd. ;2019. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. ;The Author(s) 2019 ;ISSN: 1746-4811 ;EISSN: 1746-4811 ;DOI: 10.1186/s13007-019-0479-8 ;PMID: 31452674

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Title:
Plant disease identification using explainable 3D deep learning on hyperspectral images
Author: Nagasubramanian, Koushik ; Jones, Sarah ; Singh, Asheesh K ; Sarkar, Soumik ; Singh, Arti ; Ganapathysubramanian, Baskar
Subjects: Agricultural production ; Agricultural research ; Artificial intelligence ; Artificial neural networks ; Barley ; Charcoal rot ; Charcoal rot disease ; Classification ; Computer engineering ; Crop yield ; Cubes ; Deep convolutional neural network ; Deep learning ; Diagnosis ; Economic models ; Fungal diseases ; Hyperspectral ; Hyperspectral imaging ; Identification ; Image classification ; Image processing ; Infections ; Land use ; Leaves ; Machine learning ; Medical imaging ; Model accuracy ; Neural networks ; Novels ; Phenotyping ; Plant diseases ; Precision farming ; Ratings & rankings ; Saliency map ; Signs and symptoms ; Soybean ; Soybeans ; Visualization ; Wavelengths
Is Part Of: Plant methods, 2019-08, Vol.15 (1), p.98-98, Article 98
Description: Hyperspectral imaging is emerging as a promising approach for plant disease identification. The large and possibly redundant information contained in hyperspectral data cubes makes deep learning based identification of plant diseases a natural fit. Here, we deploy a novel 3D deep convolutional neural network (DCNN) that directly assimilates the hyperspectral data. Furthermore, we interrogate the learnt model to produce physiologically meaningful explanations. We focus on an economically important disease, charcoal rot, which is a soil borne fungal disease that affects the yield of soybean crops worldwide. Based on hyperspectral imaging of inoculated and mock-inoculated stem images, our 3D DCNN has a classification accuracy of 95.73% and an infected class F1 score of 0.87. Using the concept of a saliency map, we visualize the most sensitive pixel locations, and show that the spatial regions with visible disease symptoms are overwhelmingly chosen by the model for classification. We also find that the most sensitive wavelengths used by the model for classification are in the near infrared region (NIR), which is also the commonly used spectral range for determining the vegetative health of a plant. The use of an explainable deep learning model not only provides high accuracy, but also provides physiological insight into model predictions, thus generating confidence in model predictions. These explained predictions lend themselves for eventual use in precision agriculture and research application using automated phenotyping platforms.
Publisher: England: BioMed Central Ltd
Language: English
Identifier: ISSN: 1746-4811
EISSN: 1746-4811
DOI: 10.1186/s13007-019-0479-8
PMID: 31452674
Source: PubMed Central
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Plant disease identification using explainable 3D deep learning on hyperspectral images

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