Published on Mar 10, 2025 by Arcadia Science Paired residue prediction dependencies in ESM2
Contributors (A-Z)
Paired residue prediction dependencies in ESM2
Purpose
This notebook details a quick analysis we performed on the ESM2 (Evolutionary Scale Modeling) models [1] for masked token prediction. We stumbled upon a counterintuitive result related to the effect that masking one residue has on the distribution of another.
Before jumping into our results, let’s first establish what masked token prediction is, how it works, and our consequent motivation for this analysis.
View the notebook
The full notebook pub is available here.
The source code to generate it is available in this GitHub repo (DOI: 10.5281/zenodo.15002836).
In the future, we hope to host notebook pubs directly on our publishing platform. Until that’s possible, we’ll create stubs like this with key metadata like the DOI, author roles, citation information, and an external link to the pub itself.
