Table 3 Optimal parameters
From: Evaluation of clustering algorithms for protein-protein interaction networks
Algorithm | Parameter | Optimized for accuracy | Optimized for separation |
|---|---|---|---|
MCL | Inflation | 1.8 | 1.8 |
MCODE | Depth | 100 | 5 |
| Â | Node score percentage | 0 | 0 |
| Â | Haircut | TRUE | TRUE |
| Â | Fluff | FALSE | FALSE |
| Â | Percentage for complex fluffing | 0.2 | 0.9 |
RNSC | Diversification frequency | 50 | 50 |
| Â | Shuffling diversification length | 9 | 3 |
| Â | Tabu length | 50 | 50 |
| Â | Tabu list tolerance | 1 | 1 |
| Â | Number of experiments | 3 | 3 |
| Â | Naive stopping tolerance | 1 | 15 |
| Â | Scaled stopping tolerance | 15 | 15 |
SPC | Number of nearest neighbours | 15 | 10 |
| Â | Temperature | 0.132 | 0.116 |