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Предложение single mutations

Ранжирование одиночных замен относительно parent.

Generative task

Биологическая и инженерная цель

Предложить небольшой набор substitutions для эксперимента.

Стратегия	Что генерирует	Представление	Примеры	Ограничение	Sampling	Novel topology	Integrated scoring	Complexity
Zero-shot PLM likelihood	Ranked mutations	Sequence tokens	Efficient evolution with ESM-1v	Evolutionary plausibility ≠ affinity prediction	Likelihood-guided ranking	Нет	Ensemble likelihood	Число positions × 19 substitutions
Complex inverse-folding scores	Ranked mutations	Backbone-conditioned sequence	Structural evolution (ESM-IF1 complex)	Нужен credible complex	Enumeration + likelihood	Нет	Conditional likelihood	Complex size

Архитектурное решение	Практическое следствие
Zero-shot scoring	Не требует labels, но не моделирует epistasis.

Инструмент	Generated object	Публикация	Evidence
Efficient evolution with ESM-1v	Ranked single-amino-acid substitutions	Peer-reviewed	4 prospective functional validation
ESM-IF1	Sequence and sequence likelihood conditioned on backbone	ICML 2022 main track (A*)	2 retrospective in primary paper; 4 when embedded in later structural-evolution workflow
Structural evolution (ESM-IF1 complex)	Ranked sequence mutations preserving complex structure	Peer-reviewed	4 prospective functional validation

ESM-1v antibody evolution и structural evolution имеют prospective functional evidence.