From: Improved method for protein complex detection using bottleneck proteins
PPI network dataset | Reference dataset | Algorithm | Optimal parameters | Number of protein complexes | Recall | Precision | F1 score |
---|---|---|---|---|---|---|---|
DIP | MIPS | Proposed | CC = 0.9, BC = 1% | 269 | 0.5556 | 0.3086 | 0.3968 |
 |  | [16] | CC = 0.51, BC = 20% | 76 | 0.3210 | 0.4605 | 0.3783 |
 |  | Link Cluster | Partition_density = 0.30 | 1,177 | 0.7037 | 0.1427 | 0.2373 |
 |  | MCL | Granularity = 2.00 | 614 | 0.5679 | 0.0739 | 0.1298 |
 |  | MCODE | Node_score = 0.10 | 83 | 0.2930 | 0.2530 | 0.2729 |
 | CYC | Proposed | CC = 0.6, BC = 1% | 646 | 0.4877 | 0.4860 | 0.4869 |
 |  | [16] | CC = 0.38, BC = 20% | 333 | 0.3898 | 0.4114 | 0.4003 |
 |  | Link Cluster | Partition_density = 0.29 | 1,179 | 0.5932 | 0.2858 | 0.3857 |
 |  | MCL | Granularity = 2.40 | 639 | 0.4746 | 0.1690 | 0.2493 |
 |  | MCODE | Node_score = 0.10 | 83 | 0.2119 | 0.5542 | 0.3065 |
Bio-GRID | MIPS | Proposed. | CC = 1.0, BC = 1% | 127 | 0.3457 | 0.4724 | 0.3709 |
 |  | [16] | CC = 0.54, BC = 20% | 69 | 0.2346 | 0.3623 | 0.2848 |
 |  | Link Cluster | Partition_density = 0.30 | 10,463 | 0.5926 | 0.0893 | 0.1552 |
 |  | MCL | Granularity = 3.60 | 216 | 0.2099 | 0.0556 | 0.0879 |
 |  | MCODE | Node_score = 0.10 | 120 | 0.086 | 0.0500 | 0.0633 |
 | CYC | Proposed | CC = 1.0, BC = 15% | 506 | 0.3260 | 0.3814 | 0.3515 |
 |  | [16] | CC = 0.43, BC = 30% | 324 | 0.2500 | 0.2160 | 0.2318 |
 |  | Link Cluster | Partition_density = 0.28 | 10,915 | 0.5297 | 0.2802 | 0.3697 |
 |  | MCL | Granularity = 3.00 | 225 | 0.1144 | 0.1111 | 0.1127 |
 |  | MCODE | Node_score = 0.10 | 120 | 0.0593 | 0.1167 | 0.0787 |
I2D | CORUM | Proposed | CC = 0.8, BC = 5% | 2,508 | 0.4100 | 0.3545 | 0.3802 |
 |  | [16] | CC = 0.41, BC = 20% | 1,132 | 0.2961 | 0.2491 | 0.2706 |
 |  | Link Cluster | Partition_density = 0.21 | 8,033 | 0.4576 | 0.1595 | 0.2378 |
 |  | MCL | Granularity = 1.60 | 750 | 0.0623 | 0.0587 | 0.0604 |
 |  | MCODE | Node_score = 0.10 | 251 | 0.0469 | 0.1076 | 0.0652 |