Protein property prediction on 15-task protein benchmark suite (test)
74.21Macro Mean ScoreMasked-pos ESM2-150M (Run 2)
Evaluation results
| Method | Links | |||
|---|---|---|---|---|
| Masked-pos ESM2-150M (Run 2)Family=ESM2-150M, Training Duration=8h, Seed=42, Evaluation Protocol=Linear probing2026.05 | 74.21 | 0.0066 | 0.0121 | |
| Masked-pos ESM2-150M (Run 1)Family=ESM2-150M, Training Duration=8h, Benchmark Seeds=42/123/456, Evaluation Protocol=Linear probing2026.05 | 73.85 | 0.003 | 0.0084 | |
| Masked-pos AMPLIFY-120MFamily=AMPLIFY-120M, Training Duration=8h, Seed=42, Evaluation Protocol=Linear probing2026.05 | 72.2 | -0.0019 | 0.0194 | |
| Masked-pos ESM2-35M (AdamW)Family=ESM2-35M, Training Duration=8h, Optimizer=AdamW, Optimization Steps=100k, Benchmark Seeds=42/123/456, Evaluation Protocol=Linear probing2026.05 | 71.26 | 0.0113 | 0.0591 | |
| Masked-pos ESM2-35M (SGDm)Family=ESM2-35M, Training Duration=8h, Optimizer=SGDm, Optimization Steps=100k, Benchmark Seeds=42/123/456, Evaluation Protocol=Linear probing2026.05 | 70.45 | 0.0032 | 0.051 | |
| Masked-pos ProteinBERT2-35MFamily=ProteinBERT2-35M, Training Duration=8h, Initialization=scratch, Evaluation Protocol=Linear probing2026.05 | 69.05 | 0.1267 | 0.0828 | |
| Masked-pos ProteinBERT2-150MFamily=ProteinBERT2-150M, Training Duration=8h, Initialization=scratch, Evaluation Protocol=Linear probing2026.05 | 68.7 | 0.1 | — | |
| Masked-pos ESM2-35M (Rand-init)Family=Rand-Init-35M, Training Duration=8h, Initialization=rand-init, Evaluation Protocol=Linear probing2026.05 | 67.62 | 0.1466 | 0.1003 | |
| Rand-init ESM2-150M (MLM-only)Family=ESM2-150M Rand-Init, Pre-training Objective=MLM-only, Training Duration=8h, Seed=42, Evaluation Protocol=Linear probing2026.05 | 59.03 | — | — |