Control Kernel Identification

[dglmoore]

Description

It would be useful to have a function that returns a list of the control kernel nodes of a given synchronous network.

Kim, Junil, Sang-Min Park, and Kwang-Hyun Cho. "Discovery of a kernel for controlling biomolecular regulatory networks."Scientific reports 3 (2013): 2223.

Proposed API

"""
:param net: the network for which to find the control kernel
:param n: the number of nodes in `net` (None if it is `net` sized)
:returns: the indices of the control kernel nodes
"""
def control_kernel(net, n=None)

Example Usage

>>> s_pombe = TWNetwork.read("fission-yeast-nodes.txt", "fission-yeast-edges.txt")
>>> ck_nodes = control_kernel(s_pombe)
>>> ck_nodes
[ 2, 3, 6, 7 ]
>>> s_pombe.names[ck_nodes]
[ "Ste9", "Rum1", "Wee1", "Cdc25" ]

[dglmoore]

@thyamu Can you please add a reference to the original CK paper to my above description?

[thyamu]

Scientific reports 2013 Kim-1.pdf

[bcdaniels]

I/we think that there are two main distinct types of control: "pinning" and "intervention".

[hbsmith]

We talked about different definitions of control kernels that we could implement, and the need to formalize these definitions in some kind of outline/document.

[siyuzhou]

@bcdaniels I prefer the name "override" to "intervention". :)

[bcdaniels]

The concept of a control kernel may be related to Stu's ideas of "frozen cores".

[bcdaniels]

Note that the computing of control kernels is now implemented in our fork of Neet, here: https://github.com/Collective-Logic-Lab/Neet There is still work to be done in integrating this more elegantly into the Neet framework: see Collective-Logic-Lab#3