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. 2022 May 30;19(7):865–870. doi: 10.1038/s41592-022-01486-3

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© The Author(s) 2022

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 2 — a, Rank of correct structure in results for MSNovelist (blue), and naïve generation (orange), with ranking by modified Platt score (solid line) or by RNN score (dashed line), and comparison to database search (CSI:FingerID on PubChem; green) for the GNPS dataset (n = 3,863). b, Rank of correct structure in results for MSNovelist and naïve generation, with ranking by modified Platt score or ordered by model probability, and comparison to database search for GNPS-OK dataset (n = 1,507). c, Tanimoto similarity of best incorrect candidate to correct structure for MSNovelist, naïve generation, database search, best candidate from training set and random candidate from training set. d, Modified Platt score of top candidates, for MSNovelist, naïve generation, database search, best candidate from training set (light blue) and random candidate from training set (red) e, Three randomly chosen examples of incorrect predictions (top candidate) from GNPS dataset. Structures 1a, 2a and 3a represent de novo prediction; structures 1b, 2b and 3b represent a correct result. Red marks sites predicted incorrectly by the model (or the entire molecule if the prediction was completely wrong), and blue marks the corresponding correct alternative.