Machine Learning Applications of Convolutional Neural Networks and Unet Architecture to Predict and Classify Demosponge Behavior

• Main Authors: Dominica Harrison, Fabio Cabrera De Leo, Warren J. Gallin, Farin Mir, Simone Marini, Sally P. Leys
• Format: Article
• Language: English
• Published: MDPI AG 2021-09-01
• Series: Water
• Subjects: convolutional neural networks (CNN); unet; machine learning; semantic segmentation; demosponge behavior; classification
• Online Access: https://www.mdpi.com/2073-4441/13/18/2512

Biological data sets are increasingly becoming information-dense, making it effective to use a computer science-based analysis. We used convolution neural networks (CNN) and the specific CNN architecture Unet to study sponge behavior over time. We analyzed a large time series of hourly high-resolution still images of a marine sponge, <i>Suberites concinnus</i> (Demospongiae, Suberitidae) captured between 2012 and 2015 using the NEPTUNE seafloor cabled observatory, off the west coast of Vancouver Island, Canada. We applied semantic segmentation with the Unet architecture with some modifications, including adapting parts of the architecture to be more applicable to three-channel images (RGB). Some alterations that made this model successful were the use of a dice-loss coefficient, Adam optimizer and a dropout function after each convolutional layer which provided losses, accuracies and dice scores of up to 0.03, 0.98 and 0.97, respectively. The model was tested with five-fold cross-validation. This study is a first step towards analyzing trends in the behavior of a demosponge in an environment that experiences severe seasonal and inter-annual changes in climate. The end objective is to correlate changes in sponge size (activity) over seasons and years with environmental variables collected from the same observatory platform. Our work provides a roadmap for others who seek to cross the interdisciplinary boundaries between biology and computer science.