F_vs_K Plot on 'vsn-normalization.xls' -- Adding prior

Recovered Network (PDF) Threshold = 1.6

Recovered Network (PDF) Threshold = 3

Data: vsn-normalization.xls. ONLY Control network
Steps:
1. Adding 1 known connection as prior each time. Total is 10 tests, coming from 10 connections.
2. Retrain vbssm model and find optimal K value (10 retrainings all show k = 6 is the optimum)
3. Compare the recovered network with the known connections

Notes:
1." tdcF" and "tdcG" have *No* Entries in vsn-normalization.xls. Therefore, the following 4 intersections,

tdcA pp tdcF
tdcA pp tdcG
tdcR pp tdcF
tdcR pp tdcG

are excluded in the prior-test. There are 10 known connetions as prior candidates.
2. In CBDioZ, threshold = 1.6 / 3, consistent with that in the previous no-prior test.


------- Original Email --------------
Juan
I looked at your results. I see a few of the known connections in
top50®.sif in any of the reconstructed Control network. For instance,

tdcA pd tdcB
tdcA pd tdcC
tdcA pd tdcD
tdcA pd tdcE

are ok but the following are missing

tdcA pp tdcA
tdcA pp tdcF
tdcA pp tdcG


tdcR pp tdcA
tdcR pp tdcB
tdcR pp tdcC
tdcR pp tdcE
tdcR pp tdcF
tdcR pp tdcG
tdcR pp tdcD

You need to cross-check the .sif files carefully to see what is correct.

What I suggest is that we concentrate on the Control network for now, and start to add the known connections in top50&reg.sif as priors. You might want to do these 1 regulator at a time, and retrain the vbssm models. I guess you will need to repeat the F vs K plots first. What we ought to see is that known connections persist in the models.

By the way ihfAihfB pp tdcA should be

ihfA pp tdcA
ihfB pp tdcA

etc.

Please let me know if you have any questions about this.


Thanks

David