Zero-Shot Mutation Effect Prediction
Key Distinctions
- Masked vs autoregressive: ESM-1v uses MLM — mask position i, compare log-probs. Autoregressive models (ProtGPT2) compare full sequence log-likelihoods.
- Single-site vs epistatic: ESM-1v computes single-site marginals independently. For epistatic questions use ESM-IF1 or DMS-fine-tuned models.
- ΔΔG vs ΔlogP: ESM scores track evolutionary fitness, not thermodynamic stability — correlated but not identical.
- **Benchmark f
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