Extended Data Fig. 1: ESM masked versus wildtype marginals.
From: Efficient evolution of human antibodies from general protein language models
(a) Representative scatter plots showing all possible single-site substitutions to an antibody sequence plotted according to their log-likelihood ratios to wildtype, where likelihoods are computed based on either masked marginals (y-axis) or wildtype marginals (x-axis). A red dashed line is plotted where masked and wildtype marginal values are equal. The wildtype marginal log-likelihoods are consistently lower overall, effectively serving to make the α parameter more stringent, while (b) the rank-based correlation between masked marginals and wildtype marginals is close to 1 in all cases.
