All Pairs

All Pairs Shortest Paths is an algorithm which, given a weighted interactome, will return the induced edge subnetwork of the interactome consisting of all of the shortest paths from every single source to every single target with respect to a cartesian product.

All Pairs does not take any arguments. Its source code is at https://github.com/Reed-CompBio/all-pairs-shortest-paths licensed under MIT.

Dataset Usage

All Pairs Shortest Paths uses sources, targets, and edge weights. All Pairs Shortest Paths uses edge direction information. However, All Pairs Shortest Paths always returns an undirected subnetwork.

Implementation Details

Internally, All Pairs Shortest Paths only accepts fully undirected or directed graphs. SPRAS will automatically convert edges to directed edges as necessary. For more information, see the section on algorithm directionality.