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Table 2 The cluster overlap refinement algorithm

From: Accuracy improvement in protein complex prediction from protein interaction networks by refining cluster overlaps

OverlapOptimization (S, minCov, minCons, minCss)

1  for each g S

2    if Cov(g) <minCov or Cons(g) <minCons

3       Add g into S'

4    end if

5    else

6       Assign all nodes a value of 0

7       Increment the value of each node in g

8       count ← 1

9       Find overlapping clusters with g

10       for each overlapping cluster c

11          gg c

12          Increment the value of each node in c

13          countcount +1

14       end for

15       Remove from g any node with a value less than (n × minCss)

16       if g is not redundant

17          Add g into S'

18       end if

19    end else

20    end for

21    return S '

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  1. This algorithm takes as input a set of preliminary clusters, S, generated by any density-based clustering methods. It returns the refined set of clusters, S', as output.