Table 2. Overall link prediction performance comparison on six human PPI networks (Precision@k).
| Method Name | HI-II-14 | HI-III | Lit-BM-13 | BioGRID | Bioplex | Hein et al | Mean |
|---|---|---|---|---|---|---|---|
| CH2-L3 | 19.0±0.5 | 20.1±0.3 | 14.6±0.3 | 9.3±0.2 | 14.1±0.4 | 26.8±0.5 | 17.3 |
| L3 | 19.2±0.3 | 19.9±0.2 | 15.0±0.6 | 9.5±0.2 | 13.5±0.2 | 26.6±0.3 | 17.3 |
| HO-VGAE+CH2-L3 | 17.7±0.2 | 18.8±0.3 | 10.8±0.1 | 10.6±0.3 | 12.6±0.2 | 13.0±0.2 | 13.9 |
| HO-VGAE+L3 | 17.7±0.1 | 18.5±0.3 | 10.9±0.1 | 10.4±0.2 | 12.6±0.3 | 13.1±0.5 | 13.8 |
| HO-VGAE | 17.6±0.1 | 18.5±0.4 | 10.6±0.5 | 10.4±0.3 | 12.4±0.3 | 12.8±0.3 | 13.7 |
| VGAE+L3 | 15.5±0.2 | 17.0±0.3 | 9.1±0.2 | 9.2±0.4 | 10.8±0.4 | 11.7±0.3 | 12.2 |
| VGAE | 15.2±0.4 | 16.5±0.3 | 8.9±0.2 | 9.0±0.2 | 10.1±0.3 | 11.2±0.4 | 11.8 |
| GraRep | 12.6±0.3 | 14.8±0.2 | 8.0±0.4 | 9.8±0.3 | 9.2±0.4 | 10.8±0.3 | 10.6 |
| HOPE | 12.7±0.6 | 11.4±0.3 | 7.8±0.1 | 7.9±0.3 | 7.0±0.3 | 8.1±0.1 | 9.2 |
| LINE | 11.4±0.2 | 11.0±0.1 | 6.1±0.3 | 8.5±0.3 | 8.6±0.3 | 9.1±0.3 | 9.2 |
| SDNE | 8.5±0.3 | 10.2±0.2 | 4.1±0.2 | 7.1±0.1 | 7.4±0.1 | 7.6±0.2 | 7.5 |
| GF | 7.7±0.2 | 6.9±0.1 | 7.7±0.5 | 5.1±0.3 | 4.4±0.1 | 7.3±0.1 | 6.5 |
| DeepWalk | 6.7±0.3 | 8.9±0.4 | 3.3±0.0 | 5.0±0.1 | 6.0±0.1 | 5.8±0.2 | 5.9 |
| AA | 4.6±0.3 | 5.3±0.1 | 4.8±0.2 | 2.0±0.0 | 5.2±0.1 | 13.1±0.7 | 5.8 |
| node2vec | 4.8±0.1 | 8.5±0.1 | 1.5±0.0 | 3.1±0.2 | 5.3±0.2 | 4.3±0.3 | 4.6 |
| CN | 0.0±0.0 | 5.7±0.1 | 6.5±0.3 | 2.1±0.1 | 4.9±0.0 | 0.3±0.0 | 3.2 |
| PA | 3.9±0.2 | 4.5±0.3 | 2.3±0.0 | 1.8±0.0 | 0.7±0.0 | 3.1±0.1 | 2.7 |