Number of cliques of sizes 3 in a given network

[srikanth bezawada]

Hello Cytoscape,

I would like to find the number of cliques of sizes 3 in a given network, where the cliques need not be maximal cliques. Have you come across a Java library which does this ? I need to integrate this in my Cytoscape app.

Thanks,
Srikanth.

[Scooter Morris]

Hi Srikanth,

JUNG has some clique finding algorithms you could look at.

-- scooter

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[srikanth bezawada]

Hi Scooter,
 
Looks like Jung doesn't support clique finding methods. jgrapht supports only biggest maximal cliques. 

In my case, I needed all cliques of size=3 and need not be maximal. For now, I'm using below snippet.

public double findThreeCliques(CyNetwork network) { // finds no.of three cliques
    List < CyNode > nList = network.getNodeList();
    List < CyEdge > eList = network.getEdgeList();
    int cliques = 0;
    for (CyEdge e: eList) {
        for (CyNode n: nList) {
            if (network.containsEdge(n, e.getSource()) && network.containsEdge(n, e.getTarget())) {
                cliques++;
            }
        }
    }

    return cliques;
}

Thanks,

Srikanth.B.

[alex.pico]

Duplicate. Answered on cytoscape-discuss: https://groups.google.com/forum/?hl=en_US/#!topic/cytoscape-discuss/sxoW9NGpzjo

[srikanth bezawada]

The above pseudo code is not entirely correct since it doesn't exclude duplicates.

Thanks,

Srikanth.B.