Image-Based Automated Species Identification: Can Virtual Data Augmentation Overcome Problems of Insufficient Sampling?. (18th June 2021)

• Record Type: Journal Article
• Authors: Klasen, Morris; Ahrens, Dirk; Eberle, Jonas; Steinhage, Volker
• Editors: Bond, Jason
• Is Part Of: Systematic biology. Volume 71:Number 2(2022)
• Page Start: 320
• Page End: 333
• Publication Date: 2021-06-18
• Subjects: Biology -- Classification -- Periodicals; Biology -- Periodicals; Biologie -- Classification -- Périodiques; Biologie -- Périodiques; 578.012
• DOI: 10.1093/sysbio/syab048
• Languages: English
• ISSNs: 1063-5157

Abstract

Abstract: Automated species identification and delimitation is challenging, particularly in rare and thus often scarcely sampled species, which do not allow sufficient discrimination of infraspecific versus interspecific variation. Typical problems arising from either low or exaggerated interspecific morphological differentiation are best met by automated methods of machine learning that learn efficient and effective species identification from training samples. However, limited infraspecific sampling remains a key challenge also in machine learning. In this study, we assessed whether a data augmentation approach may help to overcome the problem of scarce training data in automated visual species identification. The stepwise augmentation of data comprised image rotation as well as visual and virtual augmentation. The visual data augmentation applies classic approaches of data augmentation and generation of artificial images using a generative adversarial networks approach. Descriptive feature vectors are derived from bottleneck features of a VGG-16 convolutional neural network that are then stepwise reduced in dimensionality using Global Average Pooling and principal component analysis to prevent overfitting. Finally, data augmentation employs synthetic additional sampling in feature space by an oversampling algorithm in vector space. Applied on four different image data sets, which include scarab beetle genitalia ( Pleophylla, Schizonycha ) as well as wing patterns of bees ( Osmia ) and cattleheart butterflies ( Parides ), our augmentation approach outperformed a deep learning baseline approach by means of resulting identification accuracy with nonaugmented data as well as a traditional 2D morphometric approach (Procrustes analysis of scarab beetle genitalia). [Deep learning; image-based species identification; generative adversarial networks; limited infraspecific sampling; synthetic oversampling.]