An explainable deep machine vision framework for plant stress phenotyping

By Sambuddha Ghosal, David Blystone, Asheesh K. Singh, Baskar Ganapathysubramanian, Arti Singh, Soumik Sarkar. Proceedings of the National Academy of Sciences of the United States of America, 2018

472 citations recorded by the source corpus.

Significance Plant stress identification based on visual symptoms has predominately remained a manual exercise performed by trained pathologists, primarily due to the occurrence of confounding symptoms. However, the manual rating process is tedious, is time-consuming, and suffers from inter- and intrarater variabilities. Our work resolves such issues via the concept of explainable deep machine learning to automate the process of plant stress identification, classification, and quantification. We construct a very accurate model that can not only deliver trained pathologist-level performance but can also explain which visual symptoms are used to make predictions. We demonstrate that our method is applicable to a large variety of biotic and abiotic stresses and is transferable to other imaging conditions and plants. Current approaches for accurate identification, classification, and quantification of biotic and abiotic stresses in crop research and production are predominantly visual and require specialized training. However, such techniques are hindered by subjectivity resulting from inter- and intrarater cognitive variability. This translates to erroneous decisions and a significant waste of resources. Here, we demonstrate a machine learning framework’s ability to identify and classify a diverse set of foliar stresses in soybean [Glycine max (L.) Merr.] with remarkable accuracy. We also present an explanation mechanism, using the top-K high-resolution feature maps that isolate the visual symptoms used to make predictions. This unsupervised identification of visual symptoms provides a quantitative measure of stress severity, allowing for identification (type of foliar stress), classification (low, medium, or high stress), and quantification (stress severity) in a single framework without detailed symptom annotation by experts. We reliably identified and classified several biotic (bacterial and fungal diseases) and abiotic (chemical injury and nutrient deficiency) stresses by learning from over 25,000 images. The learned model is robust to input image perturbations, demonstrating viability for high-throughput deployment. We also noticed that the learned model appears to be agnostic to species, seemingly demonstrating an ability of transfer learning. The availability of an explainable model that can consistently, rapidly, and accurately identify and quantify foliar stresses would have significant implications in scientific research, plant breeding, and crop production. The trained model could be deployed in mobile platforms (e.g., unmanned air vehicles and automated ground scouts) for rapid, large-scale scouting or as a mobile application for real-time detection of stress by farmers and researchers.

Subfields: Ecology, Plant Science

View Paper: https://www.semanticscholar.org/paper/3bcdf9cc129d6e39d9ede590672b3f1ad41acd49

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Citations in the corpus

Toward Interpretable Machine Learning: Transparent Deep Neural Networks and Beyond (2020, methodology): “Interpretable and non-linear models have been successfully applied to many other tasks, including the detection of lesions in diabetic retinopathy data [115], the validation of predictions in dermatology [157], plant stress classiﬁcation [41], or the analysis of galaxy morphologies [164].”
A Survey of Deep Convolutional Neural Networks Applied for Prediction of Plant Leaf Diseases (2021, background): “These augmentation techniques increase a training data set by artificially generating modified forms of images [41].”
Plant Disease Detection and Classification by Deep Learning (2019, methodology): “…plain backgrounds which are not realistic scenarios for identification and classification of the diseases [25,27,32,56–58 ,60, 61, 65, 72, 77 , 78 ], except for a few of them that Plants 2019 , 8 , 468 9 of 22 Then, the probabilities were placed into the form of a matrix in order to…”
Explainable Machine Learning for Scientific Insights and Discoveries (2019, methodology): “Reference [66] uses interpretation tools for image-based plant stress phenotyping.”
Convolutional Neural Networks for Image-Based High-Throughput Plant Phenotyping: A Review (2020, methodology): “(a) and (b) were reproduced using figures from [55, 56], respectively.”
Deep Learning for Classification and Severity Estimation of Coffee Leaf Biotic Stress (2019, methodology): “Ghosal et al. (2018) developed a framework based on CNN able to identify and classify a set of 8 stresses (biotic and abiotic) aﬀecting soybean leaves.”
Explaining Deep Neural Networks and Beyond: A Review of Methods and Applications (2021, background): “[50] also rely on training and explaining DNN image classifiers to get novel insights, this time in the area of plant stress classification.”
Plant Disease Detection and Classification by Deep Learning—A Review (2021, background): “[43], developed a deep CNN framework to identify and classify 8 kinds of soybean stress.”