GINsim / GINsim-python

Python bindings for GINsim and bioLQM
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biolqm: Invalid fixpoint returned #2

Closed pauleve closed 6 years ago

pauleve commented 6 years ago

When computing fixpoint on model http://ginsim.org/sites/default/files/Traynard_MultiLevel_MamCC_Apr2016.zginml biolqm returns a strange fixpoint with a value -1 for CycA, as illustrated in the following notebook: https://gist.github.com/pauleve/e31dddff15e82b770a4f32de99b24bc4

aurelien-naldi commented 6 years ago

It is not an error but I can see why it is confusing! As the computation of fixpoints is using decision diagrams, the extracted results are paths in the diagram: -1 means that this variable is not used in the path, the state is stable no matter its value. The example represents two fixpoints, matching the result obtained with pint. It is easy to extract all fully-defined fixpoints, I can update the code to do this by default, proposing to get this compressed result as an option instead.

aurelien-naldi commented 6 years ago

With the last commit, bioLQM unfolds such patterns by default, a command-line switch allows to keep them