Plant phenotyping with limited annotation: Doing more with less

Abstract

Abstract Deep learning (DL) methods have transformed the way we extract plant traits—both under laboratory as well as field conditions. Evidence suggests that “well‐trained” DL models can significantly simplify and accelerate trait extraction as well as expand the suite of extractable traits. Training a DL model typically requires the availability of copious amounts of annotated data; however, creating large‐scale annotated dataset requires nontrivial efforts, time, and resources. This limitation has become a major bottleneck in deploying DL tools in practice. Self‐supervised learning (SSL) methods give exciting solution to this problem, as these methods use unlabeled data to produce pretrained models for subsequent fine‐tuning on labeled data and have demonstrated superior transfer learning performance on down‐stream classification tasks. We investigated the application of SSL methods for plant stress classification using few labels. We select a plant stress classification problem to test the effectiveness of SSL, as it is a fundamentally challenging problem due to (a) disease classification which depends on the abnormalities in a small number of pixels, (b) high data imbalance across different classes, and (c) fewer annotated and available plant stress images than in other domains. We compared seven SSL approaches spanning four broad classes of SSL methods on soybean [ Glycine max L. (Merr.)] plant stress dataset and report that pretraining on unlabeled plant stress images significantly outperforms transfer learning methods using random initialization for plant stress classification. In summary, SSL‐based model initialization and data curation improves annotation efficiency for plant stress classification tasks and will circumvent data annotation challenges associated with DL methods.

Plant phenotyping relevance

植物ストレス画像から形質・状態を抽出する深層学習手法を比較検証し、自己教師あり学習によるアノテーション効率向上を評価しており、表現型抽出法が研究の中心である。

Code and data availability

The paper's data availability statement explicitly points to a public GitHub repository containing the authors' data and code for the soybean stress SSL phenotyping analysis.