Large-Scale Simulation of Neural Networks with Biophysically Accurate Models on Graphics Processors
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Efficient simulation of large-scale mammalian brain models provides a crucial computational means for understanding complex brain functions and neuronal dynamics. However, such tasks are hindered by significant computational complexities. In this work, we attempt to address the significant computational challenge in simulating large-scale neural networks based on the most biophysically accurate Hodgkin-Huxley (HH) neuron models. Unlike simpler phenomenological spiking models, the use of HH models allows one to directly associate the observed network dynamics with the underlying biological and physiological causes, but at a significantly higher computational cost. We exploit recent commodity massively parallel graphics processors (GPUs) to alleviate the significant computational cost in HH model based neural network simulation. We develop look-up table based HH model evaluation and efficient parallel implementation strategies geared towards higher arithmetic intensity and minimum thread divergence. Furthermore, we adopt and develop advanced multi-level numerical integration techniques well suited for intricate dynamical and stability characteristics of HH models. On a commodity CPU card with 240 streaming processors, for a neural network with one million neurons and 200 million synaptic connections, the presented GPU neural network simulator is about 600X faster than a basic serial CPU based simulator, 28X faster than the CPU implementation of the proposed techniques, and only two to three times slower than the GPU based simulation using simpler spiking models.
Wang, Mingchao (2012). Large-Scale Simulation of Neural Networks with Biophysically Accurate Models on Graphics Processors. Master's thesis, Texas A&M University. Available electronically from