Peptide-protein interaction prediction on Propedia PPI (Random split)
94.66ROC-AUCESM-2 (35M)
Evaluation results
| Method | Links | ||||
|---|---|---|---|---|---|
| ESM-2 (35M)Params=34M, Classifier Head=MLP2025.12 | 94.66 | 84.74 | 0.6886 | 87.87 | |
| ESM-2 (150M)Params=148M, Classifier Head=MLP2025.12 | 94.34 | 84.18 | 0.6822 | 87.4 | |
| HELM-BERTParams=54.2M, Classifier Head=MLP2025.12 | 94.2 | 82.79 | 0.6705 | 87.03 | |
| ESM-2 (650M)Params=651M, Classifier Head=MLP2025.12 | 94.16 | 83.24 | 0.6704 | 87.03 | |
| Peptide DescriptorsClassifier Head=MLP2025.12 | 93.2 | 82.33 | 0.6589 | 86.19 | |
| MoLFormer–XLParams=44.4M, Classifier Head=MLP2025.12 | 92.18 | 78.66 | 0.6178 | 84.27 | |
| PeptideCLMParams=43.0M, Classifier Head=MLP2025.12 | 91.9 | 78.07 | 0.6036 | 84.05 | |
| ESM-2 (650M)Params=651M, Classifier Head=Linear2025.12 | 62.05 | 27.06 | 0.1315 | 58.09 | |
| HELM-BERTParams=54.2M, Classifier Head=Linear2025.12 | 61.22 | 27.04 | 0.1254 | 57.74 | |
| ESM-2 (150M)Params=148M, Classifier Head=Linear2025.12 | 61.09 | 26.26 | 0.1235 | 57.57 | |
| ESM-2 (35M)Params=34M, Classifier Head=Linear2025.12 | 60.47 | 25.57 | 0.1176 | 57.19 | |
| PeptideCLMParams=43.0M, Classifier Head=Linear2025.12 | 59.56 | 26.25 | 0.1066 | 56.58 | |
| MoLFormer–XLParams=44.4M, Classifier Head=Linear2025.12 | 59.49 | 26.15 | 0.0991 | 56.09 | |
| Peptide DescriptorsClassifier Head=Linear2025.12 | 55.84 | 23.11 | 0.0665 | 54.12 |