Machine Learning Undercounts Reproductive Organs on Herbarium Specimens but Accurately Derives Their Quantitative Phenological Status: A Case Study of Streptanthus tortuosus

• Published in: Plants (Basel) 2021-11, Vol.10 (11), p.2471
• Main Authors: Love, Natalie L. R., Bonnet, Pierre, Goëau, Hervé, Joly, Alexis, Mazer, Susan J.
• Format: Article
• Language: English
• Subjects: Accuracy; Archives & records; Artificial Intelligence; Automation; Biodiversity and Ecology; Climate change; Climate models; Computer Science; Computer Vision and Pattern Recognition; deep learning; Environment and Society; Environmental Sciences; Estimates; Evaluation; Flowering; Flowers & plants; Fruits; Learning algorithms; Machine Learning; Modeling and Simulation; Multimedia; natural history collections; object detection; Object recognition; Observers; Organs; Ovaries; Phenology; Precipitation; regional convolutional neural network; Reproductive organs; Streptanthus tortuosus; visual data classification
• ISSN: 2223-7747; 2223-7747
• DOI: 10.3390/plants10112471

Machine learning (ML) can accelerate the extraction of phenological data from herbarium specimens; however, no studies have assessed whether ML-derived phenological data can be used reliably to evaluate ecological patterns. In this study, 709 herbarium specimens representing a widespread annual herb, Streptanthus tortuosus, were scored both manually by human observers and by a mask R-CNN object detection model to (1) evaluate the concordance between ML and manually-derived phenological data and (2) determine whether ML-derived data can be used to reliably assess phenological patterns. The ML model generally underestimated the number of reproductive structures present on each specimen; however, when these counts were used to provide a quantitative estimate of the phenological stage of plants on a given sheet (i.e., the phenological index or PI), the ML and manually-derived PI’s were highly concordant. Moreover, herbarium specimen age had no effect on the estimated PI of a given sheet. Finally, including ML-derived PIs as predictor variables in phenological models produced estimates of the phenological sensitivity of this species to climate, temporal shifts in flowering time, and the rate of phenological progression that are indistinguishable from those produced by models based on data provided by human observers. This study demonstrates that phenological data extracted using machine learning can be used reliably to estimate the phenological stage of herbarium specimens and to detect phenological patterns.