Techniques for FPGA neural modeling

Abstract

Neural simulations and general dynamical system modeling consistently push the limits of available computational horsepower. This is occurring for a number of reasons: 1) models are progressing in complexity as our biological understanding increases, 2) high-level analysis tools including parameter searches and sensitivity analyses are becoming more prevalent, and 3) computational models are increasingly utilized alongside with biological preparations in a dynamic clamp configuration. General-purpose computers, as the primary target for modeling problems, are the simplest platform to implement models due to the rich variety of available tools. However, computers, limited by their generality, perform sub-optimally relative to custom hardware solutions. The goal of this thesis is to develop a new cost-effective and easy-to-use platform delivering orders of magnitude improvement in throughput over personal computers.

We suggest that FPGAs, or field programmable gate arrays, provide an outlet for dramatically enhanced performance. FPGAs are high-speed, reconfigurable devices that can implement any digital logic operation using an array of parallel computing elements. Already common in fields such as signal processing, radar, medical imaging, and consumer electronics, FPGAs have yet to gain traction in neural modeling due to their steep learning curve and lack of sufficient tools despite their high-performance capability. The overall objective of this work has been to overcome the shortfalls of FPGAs to enable adoption of FPGAs within the neural modeling community.

We embarked on an incremental process to develop an FPGA-based modeling environment. We first developed a prototype multi-compartment motoneuron model using a standard digital-design methodology. FPGAs at this point were shown to exceed software simulations by 10x to 100x. Next, we developed canonical modeling methodologies for manual generation of typical neural model topologies. We then developed a series of tools and techniques for analog interfacing, digital protocol processing, and real-time model tuning. This thesis culminates with the development of Dynamo, a fully-automated model compiler for the direct conversion of a model description into an FPGA implementation.