Table 3.
The reported performance and efficiency of PPI deep learning methods.a
| Method | Acc. (%) | Prec. (%) | Sen. (%) | Spec. (%) | F1 (%) | MCC (%) | AUC | AUPRC | Training time | Training environment | Benchmark |
|---|---|---|---|---|---|---|---|---|---|---|---|
| DeepPPI [35] | 94.43 | 96.65 | 92.06 | NA | NA | 88.97 | NA | NA | 369 s | Intel Xeon E2520 CPU with 16G memory | S. cerevisiae Core Subset from DIP |
| DPPI [33] | 94.55 | 96.68 | 92.24 | NA | NA | NA | NA | NA | NA | 32 AMD 6272 CPUs | S. cerevisiae core subset from DIP |
| DeepFE-PPI [36] | 94.78 | 96.45 | 92.99 | NA | NA | 89.62 | NA | NA | 1008 s | Intel Core i5-7400 with 16G memory | S. cerevisiae core subset from DIP |
| PIPR [34] | 97.09 | 97.00 | 97.17 | 97.00 | 97.09 | 94.17 | NA | NA | 150 s | NVIDIA GeForce GTX 1080 Ti GPU | S. cerevisiae core subset from DIP |
| S-VGAE [51] | 99.15 | 98.90 | 99.41 | 98.89 | 99.15 | NA | NA | NA | NA | NVIDIA GeForce GTX 1080 GPU with 7 GB memory | H. sapiens PPIs from HPRD |
| Liu’s work [77] | 95.33 | 97.02 | 93.55 | NA | NA | NA | NA | NA | NA | NA | S. cerevisiae core subset from DIP |
| DeepViral [66] | NA | NA | NA | NA | NA | NA | 0.800 | NA | NA | Nvidia Tesla V100 GPU | Host and pathogen PPIs from HPIDB |
| FSNN-LGBM [52] | 98.70 | 99.11 | 98.28 | 99.12 | NA | 97.41 | 0.997 | NA | NA | NA | S. cerevisiae core subset from DIP |
| DeepTrio [40] | 97.55 | 98.95 | 96.12 | 98.98 | 97.52 | 95.15 | NA | NA | NA | NVIDIA Tesla P100 GPU with 16 GB memory | S. cerevisiae PPIs from BioGRID |
| FSFDW [78] | NA | NA | NA | NA | NA | NA | 0.794 | NA | NA | NA | E. coli PPI dataset |
| NXTfusion [68] | NA | NA | NA | NA | NA | NA | 0.988 | 0.778 | NA | NA | H. sapiens PPIs used in FPClass [93] |
| MTT [57] | NA | 93.53 | 94.05 | NA | 93.79 | NA | 0.980 | 0.980 | NA | NVIDIA GTX 1080-Ti GPU with 11 GB memory | VirusMINT database |
| CAMP [79] | NA | NA | NA | NA | NA | NA | 0.872 | 0.641 | 2 h | 48 CPU cores and one NVIDIA GeForce GTX 1080Ti GPU | Protein-peptides interactions from the RCSB PDB and DrugBank |
| D-SCRIPT [60] | NA | 72.8 | 27.8 | NA | NA | NA | 0.833 | 0.516 | 3 days | A single 32 GB GPU | H. sapiens PPIs from STRING |
| TAGPPI [63] | 97.81 | 98.10 | 98.26 | 98.10 | 97.80 | 95.63 | 0.977 | NA | NA | NVIDIA TITAN RTX with 24 GB memory | S. cerevisiae PPIs from DIP |
a
NA, not available from the original paper.