A GPU-based computational framework that bridges neuron simulation and artificial intelligence

• Published in: Nature communications Vol. 14; no. 1; pp. 5798 - 18
• Main Authors: Zhang, Yichen, He, Gan, Ma, Lei, Liu, Xiaofei, Hjorth, J. J. Johannes, Kozlov, Alexander, He, Yutao, Zhang, Shenjian, Kotaleski, Jeanette Hellgren, Tian, Yonghong, Grillner, Sten, Du, Kai, Huang, Tiejun
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 18.09.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 631/378/116/2392; 631/378/116/2396; 639/705/1042; Algorithms; Artificial Intelligence; Brain; Computational efficiency; Computational neuroscience; Computing costs; Excitability; Humanities and Social Sciences; Humans; Image classification; Linear equations; multidisciplinary; Nervous system; Neurons; Neurosciences; Pyramidal Cells; Science; Science (multidisciplinary); Simulation; Software; Spine
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-41553-7

Biophysically detailed multi-compartment models are powerful tools to explore computational principles of the brain and also serve as a theoretical framework to generate algorithms for artificial intelligence (AI) systems. However, the expensive computational cost severely limits the applications in both the neuroscience and AI fields. The major bottleneck during simulating detailed compartment models is the ability of a simulator to solve large systems of linear equations. Here, we present a novel D endritic H ierarchical S cheduling (DHS) method to markedly accelerate such a process. We theoretically prove that the DHS implementation is computationally optimal and accurate. This GPU-based method performs with 2-3 orders of magnitude higher speed than that of the classic serial Hines method in the conventional CPU platform. We build a DeepDendrite framework, which integrates the DHS method and the GPU computing engine of the NEURON simulator and demonstrate applications of DeepDendrite in neuroscience tasks. We investigate how spatial patterns of spine inputs affect neuronal excitability in a detailed human pyramidal neuron model with 25,000 spines. Furthermore, we provide a brief discussion on the potential of DeepDendrite for AI, specifically highlighting its ability to enable the efficient training of biophysically detailed models in typical image classification tasks. High computational cost severely limit the applications of biophysically detailed multi-compartment models. Here, the authors present DeepDendrite, a GPU-optimized tool that drastically accelerates detailed neuron simulations for neuroscience and AI, enabling exploration of intricate neuronal processes and dendritic learning mechanisms in these fields.