bioRxivEvolutionary Biology
Hierarchy-guided Neural Networks for Species Classification
M. Elhamod, K. M. Diamond, A. M. Maga, Y. Bakis, H. L. Bart, P. Mabee, W. Dahdul, J. Leipzig, J. Greenberg, B. Avants, A. Karpatne
Abstract
O_LISpecies classification is an important task that is the foundation of industrial, commercial, ecological, and scientific applications involving the study of species distributions, dynamics, and evolution. C_LIO_LIWhile conventional approaches for this task use off-the-shelf machine learning (ML) methods such as existing Convolutional Neural Network (ConvNet) architectures, there is an opportunity to inform the ConvNet architecture using our knowledge of biological hierarchies among taxonomic classes. C_LIO_LIIn this work, we propose a new approach for species classification termed Hierarchy-Guided Neural Network (HGNN), which infuses hierarchical taxonomic information into the neural networks training to guide the structure and relationships among the extracted features. We perform extensive experiments on an illustrative use-case of classifying fish species to demonstrate that HGNN outperforms conventional ConvNet models in terms of classification accuracy, especially under scarce training data conditions. C_LIO_LIWe also observe that HGNN shows better resilience to adversarial occlusions, when some of the most informative patch regions of the image are intentionally blocked and their effect on classification accuracy is studied. C_LI
- assay: imaging
- research focus: cell type annotation
- research focus: clustering
- research focus: benchmarking
- approach: deep learning
- approach: transformer / foundation model
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