Table 1.
Benchmark results using solely the unweighted PPI network with respect to the CYC2008 gold standard
| Algorithm | Coverage | # Complexes | FRAC | MMR | ACC | PR | |
|---|---|---|---|---|---|---|---|
| |
GMFTP |
1168 |
179 |
0.868 |
0.591 |
0.765 |
0.593 |
| |
AP |
1363 |
207 |
0.697 |
0.785 |
0.497 |
0.444 |
| |
CFinder |
1161 |
114 |
0.653 |
0.439 |
0.693 |
0.440 |
| |
ClusterONE |
1293 |
203 |
0.847 |
0.571 |
0.775 |
0.564 |
| |
Linkcomm |
1126 |
407 |
0.903 |
0.646 |
0.744 |
0.456 |
| Collins |
MCL |
1178 |
187 |
0.840 |
0.537 |
0.779 |
0.529 |
| |
MCODE |
853 |
115 |
0.743 |
0.496 |
0.730 |
0.593 |
| |
MINE |
1101 |
138 |
0.771 |
0.499 |
0.756 |
0.547 |
| |
SPICi |
958 |
124 |
0.708 |
0.448 |
0.728 |
0.570 |
| |
SR-MCL |
1304 |
337 |
0.875 |
0.625 |
0.755 |
0.481 |
| |
GMFTP |
1464 |
271 |
0.841 |
0.489 |
0.742 |
0.457 |
| |
AP |
1815 |
274 |
0.667 |
0.659 |
0.346 |
0.310 |
| |
CFinder |
1158 |
137 |
0.638 |
0.378 |
0.701 |
0.424 |
| |
ClusterONE |
1624 |
294 |
0.783 |
0.449 |
0.725 |
0.391 |
| |
Linkcomm |
1381 |
604 |
0.870 |
0.548 |
0.703 |
0.372 |
| Gavin |
MCL |
1301 |
240 |
0.696 |
0.421 |
0.713 |
0.422 |
| |
MCODE |
899 |
155 |
0.710 |
0.438 |
0.685 |
0.492 |
| |
MINE |
1242 |
212 |
0.804 |
0.454 |
0.710 |
0.436 |
| |
SPICi |
1008 |
184 |
0.746 |
0.434 |
0.697 |
0.478 |
| |
SR-MCL |
1750 |
735 |
0.819 |
0.539 |
0.701 |
0.327 |
| |
GMFTP |
1244 |
270 |
0.756 |
0.474 |
0.722 |
0.491 |
| |
AP |
2506 |
391 |
0.575 |
0.433 |
0.242 |
0.182 |
| |
CFinder |
1143 |
115 |
0.433 |
0.281 |
0.555 |
0.268 |
| |
ClusterONE |
2044 |
539 |
0.720 |
0.431 |
0.708 |
0.326 |
| |
Linkcomm |
962 |
425 |
0.701 |
0.460 |
0.675 |
0.428 |
| Krogan core |
MCL |
1933 |
388 |
0.671 |
0.377 |
0.691 |
0.299 |
| |
MCODE |
640 |
95 |
0.463 |
0.268 |
0.583 |
0.406 |
| |
MINE |
937 |
157 |
0.616 |
0.359 |
0.664 |
0.450 |
| |
SPICi |
1249 |
224 |
0.628 |
0.356 |
0.689 |
0.409 |
| |
SR-MCL |
2585 |
1833 |
0.884 |
0.575 |
0.686 |
0.197 |
| |
GMFTP |
1197 |
265 |
0.652 |
0.398 |
0.692 |
0.469 |
| |
AP |
3522 |
461 |
0.461 |
0.232 |
0.117 |
0.096 |
| |
CFinder |
914 |
88 |
0.287 |
0.172 |
0.543 |
0.277 |
| |
ClusterONE |
1114 |
239 |
0.481 |
0.296 |
0.633 |
0.407 |
| |
Linkcomm |
1925 |
998 |
0.652 |
0.424 |
0.687 |
0.317 |
| Krogan extended |
MCL |
2973 |
531 |
0.503 |
0.254 |
0.636 |
0.190 |
| |
MCODE |
619 |
84 |
0.343 |
0.188 |
0.506 |
0.345 |
| |
MINE |
902 |
162 |
0.564 |
0.316 |
0.650 |
0.451 |
| |
SPICi |
1584 |
295 |
0.525 |
0.258 |
0.645 |
0.311 |
| |
SR-MCL |
3637 |
2644 |
0.702 |
0.431 |
0.617 |
0.154 |
| |
GMFTP |
1705 |
376 |
0.580 |
0.296 |
0.639 |
0.329 |
| |
AP |
4662 |
517 |
0.441 |
0.219 |
0.091 |
0.086 |
| |
CFinder |
635 |
75 |
0.263 |
0.119 |
0.453 |
0.297 |
| |
ClusterONE |
1402 |
346 |
0.429 |
0.227 |
0.554 |
0.280 |
| |
Linkcomm |
3396 |
1829 |
0.630 |
0.386 |
0.629 |
0.203 |
| DIP |
MCL |
4007 |
609 |
0.451 |
0.234 |
0.628 |
0.173 |
| |
MCODE |
540 |
95 |
0.210 |
0.108 |
0.402 |
0.211 |
| |
MINE |
1135 |
260 |
0.536 |
0.268 |
0.585 |
0.333 |
| |
SPICi |
2103 |
403 |
0.455 |
0.228 |
0.583 |
0.245 |
| |
SR-MCL |
4825 |
3222 |
0.674 |
0.376 |
0.583 |
0.141 |
| |
GMFTP |
2456 |
434 |
0.687 |
0.377 |
0.723 |
0.378 |
| |
AP |
5632 |
206 |
0.316 |
0.064 |
0.027 |
0.044 |
| |
CFinder |
1729 |
110 |
0.220 |
0.127 |
0.512 |
0.186 |
| |
ClusterONE |
2580 |
473 |
0.610 |
0.318 |
0.683 |
0.325 |
| |
Linkcomm |
4119 |
4446 |
0.678 |
0.459 |
0.701 |
0.243 |
| BioGRID |
MCL |
3652 |
335 |
0.314 |
0.158 |
0.520 |
0.126 |
| |
MCODE |
1087 |
136 |
0.297 |
0.154 |
0.514 |
0.294 |
| |
MINE |
2414 |
409 |
0.576 |
0.308 |
0.663 |
0.304 |
| |
SPICi |
2756 |
501 |
0.483 |
0.261 |
0.652 |
0.281 |
| SR-MCL | 5593 | 1097 | 0.496 | 0.273 | 0.594 | 0.143 |