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ResearchFormerly WizWand

Variant Effect Prediction on Variant Effect

0.856Spearman CorrelationESM2-150M All-pos MLM+JEPA
0.545040.625770.70650.78723May 8, 2026
Updated 5mo ago

Evaluation results

MethodLinks
ESM2-150M All-pos MLM+JEPABackbone=ESM2-150M, Objective=All-pos MLM+JEPA2026.050.856
AMPLIFY-120M Masked-posBackbone=AMPLIFY-120M, Objective=Masked-pos2026.050.851
AMPLIFY-120M All-pos MLM+JEPABackbone=AMPLIFY-120M, Objective=All-pos MLM+JEPA2026.050.848
ESM2-150M Masked-pos (run 1)Backbone=ESM2-150M, Objective=Masked-pos (run 1)2026.050.847
ESM2-35M Masked-pos (AdamW)Backbone=ESM2-35M, Objective=Masked-pos (AdamW)2026.050.846
ESM2-150M Masked-pos (run 2)Backbone=ESM2-150M, Objective=Masked-pos (run 2)2026.050.843
Rand-Init-35M Masked-posBackbone=Rand-Init-35M, Objective=Masked-pos2026.050.838
MLM+JEPA @90kBackbone=-, Objective=MLM+JEPA @90k2026.050.836
ProteinBERT2-35M Masked-posBackbone=ProteinBERT2-35M, Objective=Masked-pos2026.050.833
ESM2-35M Masked-pos (SGDm)Backbone=ESM2-35M, Objective=Masked-pos (SGDm)2026.050.832
ProteinBERT2-150M masked-posBackbone=-, Objective=ProteinBERT2-150M masked-pos2026.050.832
ESM2-35M All-pos MLM+JEPABackbone=ESM2-35M, Objective=All-pos MLM+JEPA2026.050.829
ESM2-150M MLM-onlyBackbone=ESM2-150M, Objective=MLM-only2026.050.825
Rand-Init-35M MLM-onlyBackbone=Rand-Init-35M, Objective=MLM-only2026.050.814
AMPLIFY-120M MLM-onlyBackbone=AMPLIFY-120M, Objective=MLM-only2026.050.805
ProteinBERT2-35M All-pos MLM+JEPABackbone=ProteinBERT2-35M, Objective=All-pos MLM+JEPA2026.050.802
ESM2-35M MLM-onlyBackbone=ESM2-35M, Objective=MLM-only2026.050.8
ESM2-150M EMA (4h) EMABackbone=ESM2-150M EMA (4h), Objective=EMA2026.050.798
ESM2-150M BaselineBackbone=ESM2-150M, Objective=Baseline2026.050.796
Rand-Init-35M All-pos MLM+JEPABackbone=Rand-Init-35M, Objective=All-pos MLM+JEPA2026.050.791
JEPA-only @90kBackbone=-, Objective=JEPA-only @90k2026.050.791
ESM2-35M BaselineBackbone=ESM2-35M, Objective=Baseline2026.050.79
AMPLIFY-120M BaselineBackbone=AMPLIFY-120M, Objective=Baseline2026.050.79
ESM2-150M rand-init MLM-onlyBackbone=-, Objective=ESM2-150M rand-init MLM-only2026.050.781
AMPLIFY-120M JEPA-onlyBackbone=AMPLIFY-120M, Objective=JEPA-only2026.050.753
ProteinBERT2-35M BaselineBackbone=ProteinBERT2-35M, Objective=Baseline2026.050.75
ProteinBERT2-35M MLM-onlyBackbone=ProteinBERT2-35M, Objective=MLM-only2026.050.74
Rand-Init-35M JEPA-onlyBackbone=Rand-Init-35M, Objective=JEPA-only2026.050.739
ESM2-150M JEPA-onlyBackbone=ESM2-150M, Objective=JEPA-only2026.050.708
ESM2-35M JEPA-onlyBackbone=ESM2-35M, Objective=JEPA-only2026.050.67
ProteinBERT2-35M JEPA-onlyBackbone=ProteinBERT2-35M, Objective=JEPA-only2026.050.652
Rand-Init-35M BaselineBackbone=Rand-Init-35M, Objective=Baseline2026.050.557