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masked language modeling

technology5 mentionslast seen Oct 6, 2026

A standard objective for training protein language models implemented by randomly masking individual residues at a fixed rate.

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masked language modeling

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masked language modelingapplies toprotein fitness prediction

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preprintarXivSep 14, 2026Structure-Aware Masking for Protein Representation Learning
Masked language modeling (MLM) is the standard objective for training protein language models, typically implemented by randomly masking individual residues at a fixed rate (e.g., 15%). This practice implicitly assumes that all sequence positions contribute equally to representation learning. In downstream fitness prediction tasks, however, protein sequences are governed by three-dimensional structural dependencies