Parameter optimization using CMA-ES (Jedrzejewski-Szmek et al 2018)


"Computational models in neuroscience can be used to predict causal relationships between biological mechanisms in neurons and networks, such as the effect of blocking an ion channel or synaptic connection on neuron activity. Since developing a biophysically realistic, single neuron model is exceedingly difficult, software has been developed for automatically adjusting parameters of computational neuronal models. The ideal optimization software should work with commonly used neural simulation software; thus, we present software which works with models specified in declarative format for the MOOSE simulator. Experimental data can be specified using one of two different file formats. The fitness function is customizable as a weighted combination of feature differences. The optimization itself uses the covariance matrix adaptation-evolutionary strategy, because it is robust in the face of local fluctuations of the fitness function, and deals well with a high-dimensional and discontinuous fitness landscape. We demonstrate the versatility of the software by creating several model examples of each of four types of neurons (two subtypes of spiny projection neurons and two subtypes of globus pallidus neurons) by tuning to current clamp data. ..."

Model Type: Neuron or other electrically excitable cell

Cell Type(s): Neostriatum medium spiny direct pathway GABA cell; Neostriatum medium spiny indirect pathway GABA cell; Globus pallidus neuron; Neostriatum spiny neuron

Currents: I Na,t; I K

Model Concept(s): Methods; Parameter Fitting

Simulation Environment: MOOSE/PyMOOSE

Implementer(s): Jedrzejewski-Szmek, Zbigniew ; Jedrzejewska-Szmek, Joanna ; Blackwell, Avrama [avrama at gmu.edu]

References:

J╚ędrzejewski-Szmek Z, Abrahao KP, J╚ędrzejewska-Szmek J, Lovinger DM, Blackwell KT. (2018). Parameter Optimization Using Covariance Matrix Adaptation-Evolutionary Strategy (CMA-ES), an Approach to Investigate Differences in Channel Properties Between Neuron Subtypes. Frontiers in neuroinformatics 12 [PubMed]