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Reproducibility #57
Reproducibility #57
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All of it looks good to me. I just think the new initial mean membrane potential and the newly introduced structure_reversed require a little bit of documentation describing the reasoning behind these. |
I could have found the problem that |
Why did K_stable = None produce non-existing connectivity? Shouldn't this simply use the connectivity matrix as determined from the anatomical data? |
What I meant is that: in the current version of MAM, |
OK, thanks for clarifying. |
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All of it looks good to me. I just think the new initial mean membrane potential and the newly introduced structure_reversed require a little bit of documentation describing the reasoning behind these.
I would add a comment to the code along the lines of "The initial membrane potential distribution is chosen to be centered on a hyperpolarized state to limit synchronous initial firing, which could bring the model into a high-activity state when the parameters are set according to the metastable condition." |
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Thanks for finding these issues and improving the code. In addition to @albada suggestions, I only pointed out one more thing regarding the parameter cc_weights_I_factor
, please check and confirm if what I wrote is correct.
This PR aims to improve reproducibility by setting the default parameters to those used to produce the dynamics of the metastable state in Schmidt et al. (2018). It also removes redundancies such as the stabilization matrix K_stable.npy and unused parameters in default_parameters.py.
In the README and code one now finds a small description on how to run the model in the ground and metastable state. This might need refining.
In addition, it adds a missing object "structure_revered" to the model class that is needed for analysis.