Catalytic Activity Prediction on Enzyme
0.58Spearman CorrelationAMPLIFY-120M Baseline
Evaluation Results
| Method | Links | |
|---|---|---|
| AMPLIFY-120M BaselineBackbone=AMPLIFY-120M, Objective=Baseline2026.05 | 0.58 | |
| AMPLIFY-120M All-pos MLM+JEPABackbone=AMPLIFY-120M, Objective=All-pos MLM+JEPA2026.05 | 0.571 | |
| AMPLIFY-120M MLM-onlyBackbone=AMPLIFY-120M, Objective=MLM-only2026.05 | 0.567 | |
| AMPLIFY-120M Masked-posBackbone=AMPLIFY-120M, Objective=Masked-pos2026.05 | 0.557 | |
| ESM2-150M MLM-onlyBackbone=ESM2-150M, Objective=MLM-only2026.05 | 0.55 | |
| ESM2-35M Masked-pos (SGDm)Backbone=ESM2-35M, Objective=Masked-pos (SGDm)2026.05 | 0.549 | |
| ESM2-150M All-pos MLM+JEPABackbone=ESM2-150M, Objective=All-pos MLM+JEPA2026.05 | 0.548 | |
| ESM2-150M BaselineBackbone=ESM2-150M, Objective=Baseline2026.05 | 0.547 | |
| ESM2-150M Masked-pos (run 1)Backbone=ESM2-150M, Objective=Masked-pos (run 1)2026.05 | 0.547 | |
| ESM2-35M BaselineBackbone=ESM2-35M, Objective=Baseline2026.05 | 0.544 | |
| ESM2-150M Masked-pos (run 2)Backbone=ESM2-150M, Objective=Masked-pos (run 2)2026.05 | 0.543 | |
| ESM2-150M EMA (4h) EMABackbone=ESM2-150M EMA (4h), Objective=EMA2026.05 | 0.538 | |
| ESM2-35M Masked-pos (AdamW)Backbone=ESM2-35M, Objective=Masked-pos (AdamW)2026.05 | 0.533 | |
| MLM+JEPA @90kBackbone=-, Objective=MLM+JEPA @90k2026.05 | 0.526 | |
| ESM2-35M MLM-onlyBackbone=ESM2-35M, Objective=MLM-only2026.05 | 0.515 | |
| Rand-Init-35M MLM-onlyBackbone=Rand-Init-35M, Objective=MLM-only2026.05 | 0.508 | |
| ProteinBERT2-150M masked-posBackbone=-, Objective=ProteinBERT2-150M masked-pos2026.05 | 0.506 | |
| ProteinBERT2-35M Masked-posBackbone=ProteinBERT2-35M, Objective=Masked-pos2026.05 | 0.494 | |
| ProteinBERT2-35M MLM-onlyBackbone=ProteinBERT2-35M, Objective=MLM-only2026.05 | 0.478 | |
| ESM2-35M All-pos MLM+JEPABackbone=ESM2-35M, Objective=All-pos MLM+JEPA2026.05 | 0.473 | |
| Rand-Init-35M Masked-posBackbone=Rand-Init-35M, Objective=Masked-pos2026.05 | 0.468 | |
| ProteinBERT2-35M All-pos MLM+JEPABackbone=ProteinBERT2-35M, Objective=All-pos MLM+JEPA2026.05 | 0.465 | |
| Rand-Init-35M All-pos MLM+JEPABackbone=Rand-Init-35M, Objective=All-pos MLM+JEPA2026.05 | 0.462 | |
| ESM2-150M rand-init MLM-onlyBackbone=-, Objective=ESM2-150M rand-init MLM-only2026.05 | 0.461 | |
| Rand-Init-35M JEPA-onlyBackbone=Rand-Init-35M, Objective=JEPA-only2026.05 | 0.46 | |
| ProteinBERT2-35M BaselineBackbone=ProteinBERT2-35M, Objective=Baseline2026.05 | 0.442 | |
| JEPA-only @90kBackbone=-, Objective=JEPA-only @90k2026.05 | 0.442 | |
| AMPLIFY-120M JEPA-onlyBackbone=AMPLIFY-120M, Objective=JEPA-only2026.05 | 0.437 | |
| Rand-Init-35M BaselineBackbone=Rand-Init-35M, Objective=Baseline2026.05 | 0.432 | |
| ESM2-150M JEPA-onlyBackbone=ESM2-150M, Objective=JEPA-only2026.05 | 0.415 | |
| ESM2-35M JEPA-onlyBackbone=ESM2-35M, Objective=JEPA-only2026.05 | 0.391 | |
| ProteinBERT2-35M JEPA-onlyBackbone=ProteinBERT2-35M, Objective=JEPA-only2026.05 | 0.37 |