HKC: An Algorithm to Predict Protein Complexes in Protein-Protein Interaction Networks

Pseudocode 2

Procedure Cluster Finding.

Input:

 PPI network (an indirect simple graph): 𝐺=(𝑉,𝐸)

 Node score threshold: T₁ and T₂

 Cohesion threshold: T₃

Output:

 The predicted protein clusters: Clusters

Call Scoring

Call ClusterFinding

Call Filtering

// step2: Cluster finding

Procedure ClusterFinding

 S = Sort(𝑉) // sort all nodes descendingly according to node score, for nodes

      // with the same score put the one with higher degree ahead

 n = the first node in S

 Clusters = a empty list of cluster

 while 𝑛 is not the last node in S do

  if 𝑛 is not seen then

   C = hkc(neighborhood(n))

   for all node q in C do

    if 𝑞 is seen or score(q) < score(n)*T₁ then

     remove q in C

    end if

   end for

   mark all nodes in C seen

   for all node m in C do

    if m is expanded then continue

    for all i in neighbors of m do

     co = the cohesion between i and C

     if score(i) >= score(m)*T₁  and

      score(i) <= score(m)*T₂  and

      co >= T₃  then

       add i to C

     end if

    end for

    mark m expanded

   end for

   add C to Clusters

  end if

  n = the next node of n in S

 end while

end procedure