Journal Article

Plant phenotyping with limited annotation: Doing more with less

Nagasubramanian, Koushik, Ganapathysubramanian, Baskar, Singh, Arti, Singh, Asheesh, Sarkar, Soumik

2022

Overview

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. Core Ideas Self‐supervised learning (SSL)‐based pretraining provides excellent model initializations. Self‐supervised representations are annotation efficient and transferable for soybean stress classification. Barlow Twins was the best SSL method for annotation efficiency.

• Publisher: John Wiley & Sons, Inc,Wiley
• Subject: Active learning / Annotations / Classification / data collection / Datasets / Deep learning / Efficiency / Glycine max / Machine learning / Neural networks / phenotype / Phenotyping / Plant extracts / plant stress / Soybeans / Transfer learning