Automatic Detection of Flavescence Dorée Symptoms Across White Grapevine Varieties Using Deep Learning

Justine Boulent; Pierre-Luc St-Charles; Samuel Foucher; Jérome Théau

doi:10.3389/frai.2020.564878

Automatic Detection of Flavescence Dorée Symptoms Across White Grapevine Varieties Using Deep Learning

Front Artif Intell. 2020 Nov 30:3:564878. doi: 10.3389/frai.2020.564878. eCollection 2020.

Authors

Justine Boulent^{1

2

3}, Pierre-Luc St-Charles⁴, Samuel Foucher², Jérome Théau^{1

3}

Affiliations

¹ Department of Applied Geomatics, Université de Sherbrooke, Sherbrooke, QC, Canada.
² Computer Research Institute of Montréal, Montréal, QC, Canada.
³ Quebec Centre for Biodiversity Science (QCBS), Montréal, QC, Canada.
⁴ Applied Machine Learning Research Team, Mila, Montréal, QC, Canada.

Abstract

Flavescence dorée (FD) is a grapevine disease caused by phytoplasmas and transmitted by leafhoppers that has been spreading in European vineyards despite significant efforts to control it. In this study, we aim to develop a model for the automatic detection of FD-like symptoms (which encompass other grapevine yellows symptoms). The concept is to detect likely FD-affected grapevines so that samples can be removed for FD laboratory identification, followed by uprooting if they test positive, all to be conducted quickly and without omission, thus avoiding further contamination in the fields. Developing FD-like symptoms detection models is not simple, as it requires dealing with the complexity of field conditions and FD symptoms' expression. To address these challenges, we use deep learning, which has already been proven effective in similar contexts. More specifically, we train a Convolutional Neural Network on image patches, and convert it into a Fully Convolutional Network to perform inference. As a result, we obtain a coarse segmentation of the likely FD-affected areas while having only trained a classifier, which is less demanding in terms of annotations. We evaluate the performance of our model trained on a white grape variety, Chardonnay, across five other grape varieties with varying FD symptoms expressions. Of the two largest test datasets, the true positive rate for Chardonnay reaches 98.48% whereas for Ugni-Blanc it drops to 8.3%, underlining the need for a multi-varietal training dataset to capture the diversity of FD symptoms. To obtain more transparent results and to better understand the model's sensitivity, we investigate its behavior using two visualization techniques, Guided Gradient-weighted Class Activation Mapping and the Uniform Manifold Approximation and Projection. Such techniques lead to a more comprehensive analysis with greater reliability, which is essential for in-field applications, and more broadly, for all applications impacting humans and the environment.

Keywords: Flavescence dorée; convolutional neural networks; explainable artificial intelligence; fully convolutional networks; grapevine yellows; plant diseases detection; precision viticulture; smart farming.