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Description:
cubnm 0.0.3
cuBNM toolbox is designed for efficient biophysical network modeling of
the brain on GPUs and CPUs.
Overview
cuBNM toolbox simulates neuronal activity of network nodes (neural mass models)
which are connected through the structural connectome using GPUs/CPUs.
Currently three models (rWW, rWWEx and Kuramoto) are implemented, but the
modular design of the code makes it possible to include additional models in
future. The simulated activity of model neurons is fed into the Balloon-Windkessel
model to calculate simulated BOLD signal. Functional connectivity (FC) and
functional connectivity dynamics (FCD) from the simulated BOLD signal are
calculated efficiently on GPUs/CPUs and compared to FC and FCD matrices
derived from empirical BOLD signals to assess similarity (goodness-of-fit)
of the simulated to empirical BOLD signal.
The toolbox supports parameter optimization algorithms including grid search and
evolutionary optimizers (via pymoo), such as the covariance matrix adaptation-evolution
strategy (CMA-ES). Parallelization within the grid or the iterations of
evolutionary optimization is done at the level of simulations (across the GPU
‘blocks’), and nodes (across each block’s ‘threads’). The models can incorporate
global or regional free parameters that are fit to empirical data using the
provided optimization algorithms. Regional parameters can be homogeneous or vary
across nodes based on a parameterized combination of fixed maps or independent
free parameters for each node or group of nodes.
GPU usage is the primary focus of the toolbox but it also supports running the
simulations on single or multiple cores of CPU. CPUs will be used if no GPUs are
detected or if requested by the user.
At its core the toolbox runs highly parallelized simulations using C++/CUDA, while the
user interface is written in Python and allows for user control over simulation
configurations:
Documentation
Please find the documentations on installation, usage examples and API at
https://cubnm.readthedocs.io.
License
For personal and professional use. You cannot resell or redistribute these repositories in their original state.
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