Deep learning image analysis for filamentous fungi taxonomic classification: Dealing with small data sets with class imbalance and hierarchical grouping

Deep learning applications in taxonomic classification for animals and plants from images have become popular, while those for microorganisms are still lagging behind. Our study investigated the potential of deep learning for the taxonomic classification of hundreds of filamentous fungi from colony images, which is typically a task that requires specialized knowledge. We isolated soil fungi, annotated their taxonomy using standard molecular barcode techniques, and took images of the fungal colonies grown in petri dishes (n = 606). We applied a convolutional neural network with multiple training approaches and model architectures to deal with some common issues in ecological datasets: small amounts of data, class imbalance, and hierarchically structured grouping. Model performance was overall low due mainly to the relatively small data set, class imbalance, and the high morphological plasticity exhibited by fungal colonies. However, our approach indicates that morphological features such as color, patchiness, and colony extension rate, could be used for the recognition of fungal colonies at higher taxonomic ranks (i.e., phylum, class, and order). Model explanation implies that image recognition characters appear at different positions within the colony (e.g., outer or inner hyphae), depending on the taxonomic resolution. Our study suggests the potential of deep learning applications for better understanding the taxonomy and ecology of filamentous fungi amenable to axenic culturing. Meanwhile, our study also highlights some technical challenges in deep learning image analysis in ecology, highlighting that the domain of applicability of these methods needs to be carefully considered.