Bio-network classification on KEGG (10-fold stratified K-Fold cross-validation)
78.6Precision (Human Diseases)PATHMAMBA
Evaluation Results
| Method | Links | |||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| PATHMAMBAEncoder=ESM-2 650M2025.02 | 78.6 | 80 | 91.5 | 97.2 | 67 | 70.3 | 66.7 | 49.7 | 74.4 | |
| PATHMAMBA w/ 150MEncoder=ESM-2 150M2025.02 | 76.4 | 76.4 | 90.6 | 97.5 | 63.9 | 68.8 | 65.3 | 51 | 72.8 | |
| PATHMAMBA w/ 3BEncoder=ESM-2 3B2025.02 | 75.2 | 72.6 | 91.7 | 97.3 | 66.1 | 66.3 | 65.6 | 55 | 74.2 | |
| PATHMAMBA w/ 35MEncoder=ESM-2 35M2025.02 | 74.8 | 75.1 | 91.4 | 96.9 | 63.4 | 66.3 | 63.3 | 51 | 72.2 | |
| GPSEncoder=ESM-2 650M2025.02 | 74.4 | 72.9 | 89.3 | 95.5 | 63.4 | 65.8 | 62.9 | 50.7 | 72.6 | |
| Graph-MambaEncoder=ESM-2 650M2025.02 | 70.7 | 71.2 | 89.7 | 96.7 | 62.6 | 66.3 | 70 | 46.3 | 72.3 | |
| GINEncoder=ESM-2 650M2025.02 | 68.8 | 69.7 | 91.2 | 94.4 | 62.9 | 63.8 | 60.6 | 49.7 | 71.7 | |
| GCNEncoder=ESM-2 650M2025.02 | 63.2 | 66.9 | 89.5 | 95.8 | 64.4 | 63 | 57 | 35.7 | 68.3 | |
| GATEncoder=ESM-2 650M2025.02 | 63 | 64.3 | 93.2 | 97 | 65.9 | 70.3 | 56 | 37 | 69 | |
| GraphSAGEEncoder=ESM-2 650M2025.02 | 58.3 | 63.3 | 89 | 95.9 | 55.3 | 57.5 | 52.6 | 33.7 | 63.2 | |
| PATHMAMBA w/o ESM-2Encoder=None2025.02 | 38 | 58.5 | 66.9 | 58.5 | 24.1 | 6.3 | 37.8 | 37.7 | 44 |