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josura / c2c-sepia

Multi agent model for perturbations in networks of networks. Used for Cell-to-cell communication with enriched pathways, using scRNA-seq or spatial data
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Saturation implementation is ambigous #53

Closed josura closed 2 months ago

josura commented 4 months ago

The saturation function should be customizable and the implementation for the current version of MASFENON is ambiguous, since it applies the saturation only if the value is greater than (max_value), but the saturation function is non-linear, meaining that there will be a step on the values generated (ambiguous results, since greater values will end up lower than lesser values).

josura commented 4 months ago

Related to the issue, the hyperbolic tangent function is unstable and will give NaN values even for values higher than 2000, so it needs to be changed

josura commented 2 months ago

Custom saturation was added in main in commit d5bcb7e , while the default saturation is a linear function (y=x) as long as it is between the boundaries of the saturation. closing the issue.