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Table 9 Pseudo codes of CFA

From: Protein complex prediction based on k-connected subgraphs in protein interaction network

Step1:// Find maximal k-connected subgraphs

Procedure REFINE

Input: Graph G = (V, E) and a parameter k.

Output: All vertices in G of degree less than k are removed.

The reduced graph is returned.

Procedure COMPONENT

Input: Connected graph H = (V, E) and a parameter k.

Output: Fragment the graph H into k-connected subgraphs.

If H does not have more than k vertices,

Then stop.

Find some u1,..., u h (h < k) in H such that H - {u 1,...,u h } is not a connected subgraph.

If such a set u1,..., u h is found,

Then for all connected component c in H - {u1,...,u h },

call COMPONENT(c,k)

Else return H as a result.

Procedure k-CONNECTED

Input: Graph G = (V,E)

Output: COMPONENT(REFINE(G,k),k).

Step2:// Filtering

Procedure CFA

Input: Graph G = (V, E)

Output: Maximal k-connected subgraphs in G of size at least 4.

Set k to 1

While Ck is not empty

   Set Ck to the result of k-CONNECTED(G).

   Increment k.

Set G 1 to 1-connected subgraphs from C 1 with the diameter < 4.

Set Gk to k-connected subgraphs from Ck with the diameter < k (for k ≥ 2)

Set U to the union of Gk's (k ≥ 1)

Remove all subgraphs of size less than 4 in the set U.