FPGA-based biophysically-meaningful modeling of olivocerebellar neurons

Georgios Smaragdos, Sebastian Isaza, Martijn Van Eijk, Ioannis Sourdis, Christos Strydis

Research output: Contribution to journalConference articleAcademicpeer-review

39 Citations (Scopus)

Abstract

The Inferior-Olivary nucleus (ION) is a well-charted region of the brain, heavily associated with sensorimotor control of the body. It comprises ION cells with unique properties which facilitate sensory processing and motor-learning skills. Various simulation models of ION-cell networks have been written in an attempt to unravel their mysteries. However, simulations become rapidly intractable when biophysically plausible models and meaningful network sizes (100 cells) are modeled. To overcome this problem, in this work we port a highly detailed ION cell network model, originally coded in Matlab, onto an FPGA chip. It was first converted to ANSI C code and extensively profiled. It was, then, translated to HLS C code for the Xilinx Vivado toolflow and various algorithmic and arithmetic optimizations were applied. The design was implemented in a Virtex 7 (XC7VX485T) device and can simulate a 96-cell network at real-time speed, yielding a speedup of 700 compared to the original Matlab code and 12.5 compared to the reference C implementation running on a Intel Xeon 2.66GHz machine with 20GB RAM. For a 1,056-cell network (non-real-time), an FPGA speedup of 45 against the C code can be achieved, demonstrating the design's usefulness in accelerating neuroscience research. Limited by the available on-chip memory, the FPGA can maximally support a 14,400-cell network (non-real-time) with online parameter configurability for cell state and network size. The maximum throughput of the FPGA IONnetwork accelerator can reach 2.13 GFLOPS.

Original languageEnglish
Pages (from-to)89-98
Number of pages10
JournalACM/SIGDA International Symposium on Field Programmable Gate Arrays - FPGA
DOIs
Publication statusPublished - 2014
Event2014 ACM/SIGDA International Symposium on Field Programmable Gate Arrays, FPGA 2014 - Monterey, CA, United States
Duration: 26 Feb 201428 Feb 2014

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