Table 2.
Benchmark datasets collected from existing literatures for binary classification prediction task
| Dataset name | Drugs | DDIs | Drug-related information | Data resource |
|---|---|---|---|---|
| Db_152 | – | 1,178,210 | SMILES | DRKG |
| Db_253 | 548 | 48,584 | Substructure: 881 Target: 780 Enzyme: 129 Transporter: 78 Pathway: 253 Indication: 4,897 Side effect: 4,897 Off side effect: 9,496 |
TWOSIDES, SIDER, OFFSIDES, PubChem, DrugBank, KEGG |
| Db_354 | 1,537 | 34,282 | SMILES | DrugBank |
| Db_455 | 2,578 | 612,388 | – | DrugBank |
| Db_556 | – | 48,548 | SMILES | DrugBank,53 |
| Db_657 | 1,752 | 504,468 | Morgan fingerprint | DrugBank |
| Db_758 | 1,562 | 180,576 | Chemical structures, ATC, DBP (899 drug targets and 222 non-target proteins) | DrugBank,59,60 |
| Db_858 | 1,934 | 230,887 | ||
| Db_961 | 2,367 | 209,494 | Target: 2,411 Enzyme: 285 Pathway: 314 Substructure: 699 |
DrugBank, KEGG, PubChem |
| Db_1055 | 1,925 | 56,983 | – | KEGG |
| Db_1162 | 613 | 80,702 | Enzyme: 454 Pathway: 533 Side effect: 4,859 Substructure: 811 Target: 2,670 Node2vec: 613 PRL: 978 |
DrugBank, CTD,63 KEGG, SIDER, LINCS64,65,66,67 |
| Db_1268 | 841 | 82,620 | Target: 1,333 Enzyme: 214 Pathway: 307 Substructure: 619 |
DrugBank, KEGG, PubChem |
| Db_1369 | 1,850 | 443,046 | SMILES | Drugbank |
| Db_1469 | 1,322 | 83,040 | BIOSNAP70 | |
| Db_1571 | – | 2,898,937 | – | DrugBank, KEGG, TWOSIDES, MEDLINE,72 OFFSIDES, PharmGKB53,73,74,75,76 |
| Db_1677 | 10,533 | 1,195,972 | SMILES | DrugBank, OGB-biokg78 |
| Db_1777 | 1,925 | 56,983 | DrugBank, KEGG |
Note: ‘Drugs’ represents the number of drugs in the dataset, ‘DDIs’ represents the numbers of drug-drug interactions, ‘Drug-related information’ represents other drug-related features in the dataset, ‘Data resource’ represents the source of the data, ‘-’ represents no clear explanation in the original literature.