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 |
 | Node score percentage | 0 | 0 |
 | Haircut | TRUE | TRUE |
 | Fluff | FALSE | FALSE |
 | Percentage for complex fluffing | 0.2 | 0.9 |
RNSC | Diversification frequency | 50 | 50 |
 | Shuffling diversification length | 9 | 3 |
 | Tabu length | 50 | 50 |
 | Tabu list tolerance | 1 | 1 |
 | Number of experiments | 3 | 3 |
 | Naive stopping tolerance | 1 | 15 |
 | Scaled stopping tolerance | 15 | 15 |
SPC | Number of nearest neighbours | 15 | 10 |
 | Temperature | 0.132 | 0.116 |