Table 1 Summary of all datasets and tasks
Task | Reference | Train size | Validation size | Test size | Task | Projector used | Evaluation metric |
|---|---|---|---|---|---|---|---|
General PPI prediction | |||||||
Gold-standard PPI | 163019 | 59260 | 52048 | Binary classification | MLP | AUPRC | |
Human-PPI | 26319 | 234 | 180 | Binary classification | MLP | Accuracy | |
Yeast-PPI | 4945 | 95 | 394 | Binary classification | MLP | Accuracy | |
PDB-Bind | 4945 | 95 | 394 | Regression | MLP | Pearson correlation | |
SKEMPI | 4777 | – | 1929 | Regression | MLP | Pearson correlation | |
MutaionalPPI | 3406 | – | – | Binary classification | MLP | AUPRC | |
Antibody tasks | |||||||
FLAB (Binding 422) | 422 | – | – | Regression | Ridge regression | R2 | |
FLAB (Binding 2048) | 2048 | – | – | Regression | Ridge regression | R2 | |
FLAB (Binding 4275) | 4275 | – | – | Regression | Ridge regression | R2 | |
FLAB (Expression 4275) | 4275 | – | – | Regression | Ridge regression | R2 | |
SARS-CoV2 binding | 86929 | – | – | Regression | Ridge regression | Spearman rank | |
TCR-Epitope-MHC tasks | |||||||
TDC-Tchard | 522239 | – | 71666 | Binary classification | MLP | AUROC | |
TCR-Epitope-HLA | 28144 | 71036 | 2806 | Binary classification | MLP | AUROC | |
TCR-epitope interface prediction | 122 | – | – | Interface prediction | CNN | AUPRC | |
