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jcrozum / pystablemotifs

Python library for attractor identification and control in Boolean networks
MIT License
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Better handling of source nodes #10

Closed jcrozum closed 4 years ago

jcrozum commented 4 years ago

Source node stable motifs should all be merged to help avoid clutter and combinatorial explosion.

With N source nodes, we have 2N stable motifs and 2^N combinations that result in (2^N) (N!)^2 nodes in the succession diagram. Better to merge these into the 2^N unique combinations from the start to save a factor of (N!)^2 in the diagram size.

jcrozum commented 4 years ago

Now, by default, stable motifs corresponding to source nodes are merged and used for reduction before any other motifs. Primary stable motifs (i.e., not conditionally stable motifs) that exist for all input configurations are stored and printed in the motif reduction summary.

rekaalbert commented 4 years ago

I really like the new implementation!

On Tue, Mar 10, 2020 at 3:05 PM Jordan Rozum notifications@github.com wrote:

Now, by default, stable motifs corresponding to source nodes are merged and used for reduction before any other motifs. Primary stable motifs (i.e., not conditionally stable motifs) that exist for all input configurations are stored and printed in the motif reduction summary.

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jgtz commented 4 years ago

When I saw this, I was trying to think what was the best thing to do with treating signal-independent stable motifs. Some stable motifs might be signal-independent, while some might be independent on only a subset of the signals. I think what you are implementing (doing only completely signal-independent ones, and then reducing all source nodes) is the best trade-off.