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Title: Improving the performance of models for one-step retrosynthesis through re-ranking
Authors: Lin, Min Htoo
Tu, Zhengkai
Coley, Connor W.
Keywords: Science::Chemistry
Issue Date: 2022
Source: Lin, M. H., Tu, Z. & Coley, C. W. (2022). Improving the performance of models for one-step retrosynthesis through re-ranking. Journal of Cheminformatics, 14(1), 15-.
Journal: Journal of Cheminformatics 
Abstract: Retrosynthesis is at the core of organic chemistry. Recently, the rapid growth of artificial intelligence (AI) has spurred a variety of novel machine learning approaches for data-driven synthesis planning. These methods learn complex patterns from reaction databases in order to predict, for a given product, sets of reactants that can be used to synthesise that product. However, their performance as measured by the top-N accuracy in matching published reaction precedents still leaves room for improvement. This work aims to enhance these models by learning to re-rank their reactant predictions. Specifically, we design and train an energy-based model to re-rank, for each product, the published reaction as the top suggestion and the remaining reactant predictions as lower-ranked. We show that re-ranking can improve one-step models significantly using the standard USPTO-50k benchmark dataset, such as RetroSim, a similarity-based method, from 35.7 to 51.8% top-1 accuracy and NeuralSym, a deep learning method, from 45.7 to 51.3%, and also that re-ranking the union of two models' suggestions can lead to better performance than either alone. However, the state-of-the-art top-1 accuracy is not improved by this method.
ISSN: 1758-2946
DOI: 10.1186/s13321-022-00594-8
Schools: School of Physical and Mathematical Sciences 
Rights: © 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 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 The Creative Commons Public Domain Dedication waiver (http://creativeco applies to the data made available in this article, unless otherwise stated in a credit line to the data.
Fulltext Permission: open
Fulltext Availability: With Fulltext
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