Journal Article

Deep learning of material transport in complex neurite networks

Barati Farimani, Amir, Zhang, Yongjie Jessica, Li, Angran

2021

Overview

Neurons exhibit complex geometry in their branched networks of neurites which is essential to the function of individual neuron but also brings challenges to transport a wide variety of essential materials throughout their neurite networks for their survival and function. While numerical methods like isogeometric analysis (IGA) have been used for modeling the material transport process via solving partial differential equations (PDEs), they require long computation time and huge computation resources to ensure accurate geometry representation and solution, thus limit their biomedical application. Here we present a graph neural network (GNN)-based deep learning model to learn the IGA-based material transport simulation and provide fast material concentration prediction within neurite networks of any topology. Given input boundary conditions and geometry configurations, the well-trained model can predict the dynamical concentration change during the transport process with an average error less than 10% and 120 ∼ 330 times faster compared to IGA simulations. The effectiveness of the proposed model is demonstrated within several complex neurite networks.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 639/166/985 / 639/705/1042 / Algorithms / Axons / Boundary conditions / Computational Biology - methods / Computer Simulation / Deep Learning / Differential equations / Geometry / Humanities and Social Sciences / Humans / Immunoglobulin A / Mathematical models / Models, Theoretical / multidisciplinary / Nerve Net - metabolism / Nerve Net - physiology / Neural networks / Neural Networks, Computer / Neurites - physiology / Neurons - physiology / Partial differential equations / Science / Science (multidisciplinary) / Topology / Transport processes