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. 2024 Jul 2;15:5566. doi: 10.1038/s41467-024-49798-6

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — a Extrapolating to single-site mutants whose mutated positions do not occur in the training set, evaluated by Spearman correlation. Error bars are centered at average performance and indicate the standard deviation caused by five random splits. SaProt (FSFP) is significantly better than all baselines with the largest P value among all training sizes being 0.016 (two-sided Mann–Whitney U test). Analogous results measured by NDCG are shown in Supplementary Fig. 4a. b Summary of how often the best extrapolative Spearman correlation for single-site mutants on a certain dataset is achieved by a PLM, where the colors represent different strategies applied to the best PLMs. c Extrapolating to multi-site mutants whose individual mutations have no overlap with the mutations in the training data, evaluated by Spearman correlation. Error bars are centered at average performance and indicate the standard deviation caused by five random splits. SaProt (FSFP) is significantly better than all baselines with the largest P value among all training sizes being 0.0079 (two-sided Mann–Whitney U test). Analogous results measured by NDCG are shown in Supplementary Fig. 4b. d Similar to (b) but counted for the best extrapolative performance on multi-site mutants. Source data are provided as a Source Data file.