Simulation Update

Last month I wrote about recreating a brain simulation model in an article I read about (Hamker, 2005).  As I discussed there, the Hamker article describes a computational firing-rate model of several brain areas thought to play a role in spatial and non-spatial attention.  As I’m very interested in building computational brain models myself and am just getting started, I am attempting to recreate their simulation using Matlab.

This is still a work in progress, but I now have an initial version that models input and two of the brain areas, V4 and IT.  The simulation also displays graphs of the resulting firing rates over time for each simulated neuron.  The Matlab files are available here.

The biggest issue I’ve come across so far has been optimizing performance.  In my initial version of the simulation, solving the equation system took a prohibitive amount of time – simulating 5 neurons for 3 milliseconds of model time took several minutes, and the system ultimately needs to model around 250 neurons for 3000 milliseconds.  Ultimately the problem turned out to be the differential equation solver algorithm.  I initially used Matlab’s default “ode45″ solver, since the model appeared to be simple and I didn’t expect the system to be “stiff”, but switching to the “ode15s” solver (a “stiff” solver) drastically reduced the execution time.

Reference

Hamker, F. H. (2005). The reentry hypothesis: The putative interaction of the frontal eye field, ventrolateral prefrontal cortex, and areas V4, IT for attention and eye movement. Cerebral Cortex, 15, 431-447.