Remote Homology detection on Remote Homology
52F1-macroBaseline
Evaluation Results
| Method | Links | |
|---|---|---|
| BaselineBackbone=ESM2-150M2026.05 | 52 | |
| Masked-pos (run 1)Backbone=ESM2-150M, Seeds=42/123/4562026.05 | 51.3 | |
| Masked-pos (run 2)Backbone=ESM2-150M, Seeds=422026.05 | 51.1 | |
| All-pos MLM+JEPABackbone=ESM2-150M2026.05 | 50.6 | |
| BaselineBackbone=ESM2-35M2026.05 | 44.2 | |
| MLM-onlyBackbone=ESM2-150M2026.05 | 44 | |
| MLM+JEPA @90kTraining step=90k2026.05 | 43.2 | |
| Masked-pos (AdamW)Backbone=ESM2-35M2026.05 | 42.8 | |
| Masked-pos (SGDm)Backbone=ESM2-35M2026.05 | 41.7 | |
| MLM-onlyBackbone=AMPLIFY-120M2026.05 | 41 | |
| MLM-onlyBackbone=ESM2-35M2026.05 | 40.5 | |
| Masked-posBackbone=AMPLIFY-120M2026.05 | 39.8 | |
| All-pos MLM+JEPABackbone=AMPLIFY-120M2026.05 | 39.7 | |
| BaselineBackbone=AMPLIFY-120M2026.05 | 39.1 | |
| MLM-onlyBackbone=Rand-Init-35M2026.05 | 25.3 | |
| ProteinBERT2-150M masked-pos2026.05 | 22.4 | |
| Masked-posBackbone=Rand-Init-35M2026.05 | 21.1 | |
| All-pos MLM+JEPABackbone=ESM2-35M2026.05 | 19.3 | |
| BaselineBackbone=ProteinBERT2-35M2026.05 | 10.8 | |
| MLM-onlyBackbone=ProteinBERT2-35M2026.05 | 10.7 | |
| All-pos MLM+JEPABackbone=Rand-Init-35M2026.05 | 9.6 | |
| ESM2-150M rand-init MLM-only2026.05 | 8.9 | |
| BaselineBackbone=Rand-Init-35M2026.05 | 8.7 | |
| All-pos MLM+JEPABackbone=ProteinBERT2-35M2026.05 | 8.5 | |
| JEPA-onlyBackbone=Rand-Init-35M2026.05 | 7.1 | |
| JEPA-onlyBackbone=ESM2-150M2026.05 | 6 | |
| JEPA-onlyBackbone=AMPLIFY-120M2026.05 | 4.6 | |
| JEPA-onlyBackbone=ESM2-35M2026.05 | 3.4 | |
| JEPA-onlyBackbone=ProteinBERT2-35M2026.05 | 1.5 |