Table 2 Hyperparameters of BiNE for different datasets
Parameter names | Nuclear receptors | Ion channels | GPCR | Enzymes | DrugBank |
|---|---|---|---|---|---|
Maximum iterations | 100 | 100 | 100 | 1000 | 100 |
Learning rate | 0.1 | 0.1 | 0.1 | 0.1 | 0.01 |
Number of negative samples \(\mathrm{ns}\) | 4 | 4 | 4 | 4 | 2 |
Size of window \(\mathrm{ws}\) | 5 | 7 | 5 | 5 | 5 |
Trade-off parameter α | 0.01 | 0.01 | 0.01 | 0.01 | 0.01 |
Trade-off parameter β | 0.1 | 0.1 | 0.1 | 0.1 | 0.01 |
Trade-off parameter γ | 0.1 | 1 | 0.1 | 0.1 | 0.1 |
Embedding size of BiNE | 64 | 128 | 32 | 128 | 128 |
Embedding size of drug-target pairs | 128 | 256 | 64 | 256 | 256 |
Walk stopping probability | 0.15 | 0.15 | 0.15 | 0.15 | 0.15 |
Walk restart probability | 0.7 | 0.7 | 0 | 0.7 | 0.7 |