ResponseNet

ResponseNet is a pathway reconstruction algorithm which finds subnetworks using linear programming, considering an interactome as a way to send ‘flow’ from sources to targets. See the original paper and the corresponding reimplementation of it: https://github.com/Reed-CompBio/ResponseNet.

ResponseNet takes one optional parameter:

• gamma: (int) controls the size of the output graph: more gamma means more ‘flow’ gets passed along starting from the sources.

Dataset Usage

ResponseNet uses sources, targets, and edge weights. ResponseNet uses edge direction information, but returns an undirected subnetwork.

Implementation Details

Internally, ResponseNet only takes in directed graphs. SPRAS will automatically convert edges to directed edges as necessary. For more information, see the section on algorithm directionality.