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

Pseudocode 3

Procedure Filtering.

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

// step3: Filtering

Procedure Filtering

 for all cluster c in Clusters do

  if the size of c is less than 3 then

   remove c in Clusters

  end if

 end for

 for all cluster c in Clusters do

  den(c) = the density of c

  s = size of c

  score(c) = den(c)* s  // compute the score of cluster

 end for

 for all cluster 𝑐₁, 𝑐₂ in Clusters do

  o = the overlap ratio of 𝑐₁ and 𝑐₂

  if 𝑜 > 0.95 then

   if score(𝑐₁) > score(𝑐₂) then delete 𝑐₂ in Clusters

   else delete 𝑐₁ in Clusters

   end if

  end if

 end for

  Clusters = sort Clusters descendingly according to cluster scores

end procedure