Variant Effect Prediction on Variant Effect
0.856Spearman CorrelationESM2-150M All-pos MLM+JEPA
Evaluation Results
| Method | Links | |
|---|---|---|
| ESM2-150M All-pos MLM+JEPABackbone=ESM2-150M, Objective=All-pos MLM+JEPA2026.05 | 0.856 | |
| AMPLIFY-120M Masked-posBackbone=AMPLIFY-120M, Objective=Masked-pos2026.05 | 0.851 | |
| AMPLIFY-120M All-pos MLM+JEPABackbone=AMPLIFY-120M, Objective=All-pos MLM+JEPA2026.05 | 0.848 | |
| ESM2-150M Masked-pos (run 1)Backbone=ESM2-150M, Objective=Masked-pos (run 1)2026.05 | 0.847 | |
| ESM2-35M Masked-pos (AdamW)Backbone=ESM2-35M, Objective=Masked-pos (AdamW)2026.05 | 0.846 | |
| ESM2-150M Masked-pos (run 2)Backbone=ESM2-150M, Objective=Masked-pos (run 2)2026.05 | 0.843 | |
| Rand-Init-35M Masked-posBackbone=Rand-Init-35M, Objective=Masked-pos2026.05 | 0.838 | |
| MLM+JEPA @90kBackbone=-, Objective=MLM+JEPA @90k2026.05 | 0.836 | |
| ProteinBERT2-35M Masked-posBackbone=ProteinBERT2-35M, Objective=Masked-pos2026.05 | 0.833 | |
| ESM2-35M Masked-pos (SGDm)Backbone=ESM2-35M, Objective=Masked-pos (SGDm)2026.05 | 0.832 | |
| ProteinBERT2-150M masked-posBackbone=-, Objective=ProteinBERT2-150M masked-pos2026.05 | 0.832 | |
| ESM2-35M All-pos MLM+JEPABackbone=ESM2-35M, Objective=All-pos MLM+JEPA2026.05 | 0.829 | |
| ESM2-150M MLM-onlyBackbone=ESM2-150M, Objective=MLM-only2026.05 | 0.825 | |
| Rand-Init-35M MLM-onlyBackbone=Rand-Init-35M, Objective=MLM-only2026.05 | 0.814 | |
| AMPLIFY-120M MLM-onlyBackbone=AMPLIFY-120M, Objective=MLM-only2026.05 | 0.805 | |
| ProteinBERT2-35M All-pos MLM+JEPABackbone=ProteinBERT2-35M, Objective=All-pos MLM+JEPA2026.05 | 0.802 | |
| ESM2-35M MLM-onlyBackbone=ESM2-35M, Objective=MLM-only2026.05 | 0.8 | |
| ESM2-150M EMA (4h) EMABackbone=ESM2-150M EMA (4h), Objective=EMA2026.05 | 0.798 | |
| ESM2-150M BaselineBackbone=ESM2-150M, Objective=Baseline2026.05 | 0.796 | |
| Rand-Init-35M All-pos MLM+JEPABackbone=Rand-Init-35M, Objective=All-pos MLM+JEPA2026.05 | 0.791 | |
| JEPA-only @90kBackbone=-, Objective=JEPA-only @90k2026.05 | 0.791 | |
| ESM2-35M BaselineBackbone=ESM2-35M, Objective=Baseline2026.05 | 0.79 | |
| AMPLIFY-120M BaselineBackbone=AMPLIFY-120M, Objective=Baseline2026.05 | 0.79 | |
| ESM2-150M rand-init MLM-onlyBackbone=-, Objective=ESM2-150M rand-init MLM-only2026.05 | 0.781 | |
| AMPLIFY-120M JEPA-onlyBackbone=AMPLIFY-120M, Objective=JEPA-only2026.05 | 0.753 | |
| ProteinBERT2-35M BaselineBackbone=ProteinBERT2-35M, Objective=Baseline2026.05 | 0.75 | |
| ProteinBERT2-35M MLM-onlyBackbone=ProteinBERT2-35M, Objective=MLM-only2026.05 | 0.74 | |
| Rand-Init-35M JEPA-onlyBackbone=Rand-Init-35M, Objective=JEPA-only2026.05 | 0.739 | |
| ESM2-150M JEPA-onlyBackbone=ESM2-150M, Objective=JEPA-only2026.05 | 0.708 | |
| ESM2-35M JEPA-onlyBackbone=ESM2-35M, Objective=JEPA-only2026.05 | 0.67 | |
| ProteinBERT2-35M JEPA-onlyBackbone=ProteinBERT2-35M, Objective=JEPA-only2026.05 | 0.652 | |
| Rand-Init-35M BaselineBackbone=Rand-Init-35M, Objective=Baseline2026.05 | 0.557 |