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Block (scc) expansion #119
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@@ -1180,6 +1189,18 @@ def expand_scc(self, find_motif_avoidant_attractors: bool = True) -> bool: | |||
""" | |||
return expand_source_SCCs(self, check_maa=find_motif_avoidant_attractors) | |||
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def expand_block(self, find_motif_avoidant_attractors: bool = True) -> bool: |
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just a reminder that we should (eventually) either add proper docstrings to the expansion methods or else mark them as private
def source_nodes( | ||
network: BooleanNetwork, ctx: SymbolicContext | None = None | ||
) -> list[str]: | ||
""" |
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Could you add the parameters and returns to this docstring?
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Or I suppose I could do it; I think it's straightforward here, and it looks like it's the only one that needs it.
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(I just did this)
@@ -1,4 +1,4 @@ | |||
biodivine_aeon==1.0.0a6 | |||
biodivine_aeon==1.0.0a8 |
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also need to update in requirements-dev.txt
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(I just did this)
As discussed, I'll merge this and close #118. |
For completeness, here is also the performance comparison: The geomean on non-trivial benchmarks (>1s) is 26%, 20%, 5%, 17% better on BBM, NCF, NK2, NK3. |
This PR builds on #118 and introduces a new "scc-like" expansion algorithm that is more efficient and (hopefully) easier to follow and prove.
Main advantages of the new approach:
Performance TL;DR:
How does it work:
Other minor notes: