search

jcrozum / pystablemotifs

Python library for attractor identification and control in Boolean networks
MIT License
28 stars 7 forks source link

Attractor counting and access #31

Closed jcrozum closed 4 years ago

jcrozum commented 4 years ago

Right now, the number of attractors that we are reporting in the RBN tests is not correct. This is a bug. The attractor summary does output the correct information, however. We should be storing these counts in the SuccessionDiagram objects.

Also, we should make the attractor information more readily accessible from the SuccessionDiagram object. It is a little bit unwieldy right now. Dávid had some thoughts along these lines, but I bring it up here because it's related to the bug I mentioned.

jcrozum commented 4 years ago

If we find a motif-avoidant attractor in the reduced system, I do not think it guarantees the existence of one in the original system. This is because an attractor of the reduced system can lift up to a non-terminal SCC of the unreduced STG.

Naldi et al. (2011) has some details on when this can happen, but it is a tough read: https://core.ac.uk/download/pdf/81989194.pdf

The code gets this wrong right now; if it finds N>1 such attractors, it says there are between 1 and N "missed" attractors, but it is really between 0 and N, I think.

rekaalbert commented 4 years ago

I agree; 0 is a possibility.

On Tue, Apr 28, 2020 at 4:18 PM Jordan Rozum notifications@github.com wrote:

If we find a motif-avoidant attractor in the reduced system, I do not think it guarantees the existence of one in the original system. This is because an attractor of the reduced system can lift up to a non-terminal SCC of the unreduced STG.

Naldi et al. (2011) has some details on when this can happen, but it is a tough read: https://core.ac.uk/download/pdf/81989194.pdf

The code gets this wrong right now; if it finds N>1 such attractors, it says there are between 1 and N "missed" attractors, but it is really between 0 and N, I think.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/jcrozum/StableMotifs/issues/31#issuecomment-620832267, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADLEUXPRYPVIYXJDUDOM7VTRO423BANCNFSM4MQLJ4JQ .

-- Reka Albert Distinguished Professor of Physics and Biology Pennsylvania State University 104 Davey Laboratory, PMB 261 University Park, PA 16802 Phone: (814) 865-1141 Web: https://www.ralbert.me https://www.ralbert.me

jcrozum commented 4 years ago

The miscounting bug is fixed in the master branch. I will close this issue and open a new one for improving the internal storage.