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Mapping the space of chemical reactions using attention-based neural networks

Matters Arising to this article was published on 05 July 2021

A preprint version of the article is available at arXiv.


Organic reactions are usually assigned to classes containing reactions with similar reagents and mechanisms. Reaction classes facilitate the communication of complex concepts and efficient navigation through chemical reaction space. However, the classification process is a tedious task. It requires identification of the corresponding reaction class template via annotation of the number of molecules in the reactions, the reaction centre and the distinction between reactants and reagents. Here, we show that transformer-based models can infer reaction classes from non-annotated, simple text-based representations of chemical reactions. Our best model reaches a classification accuracy of 98.2%. We also show that the learned representations can be used as reaction fingerprints that capture fine-grained differences between reaction classes better than traditional reaction fingerprints. The insights into chemical reaction space enabled by our learned fingerprints are illustrated by an interactive reaction atlas providing visual clustering and similarity searching.

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Fig. 1: Data representation and task.
Fig. 2: BERT reaction classification model.
Fig. 3: Attention weights interpretation.
Fig. 4: Reaction atlases.
Fig. 5: Nearest-neighbour queries.

Data availability

The Schneider 50k dataset is publicly available25. We provide a new reaction dataset (USPTO 1k TPL), derived from the work of Lowe50, containing the 1,000 most common reaction templates as classes. It can be accessed through The commercial Pistachio (version 191118) dataset can be obtained from NextMove Software38. Pistachio relies on Leadmine58 to text-mine patent data. The dataset comes with reaction classes assigned using NameRxn (

Code availability

The rxnfp code and the experiments on the public datasets, as well as an interactive TMAP, are provided at


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D.P. and J.-L.R. acknowledge financial support by the Swiss National Science Foundation (NCCR TransCure). We thank L. Rudin for the careful proofreading of our manuscript.

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Authors and Affiliations



P.S. and A.C.V. conceived the initial idea for the project. P.S., D.P., A.C.V. and V.H.N. trained models, performed the classification experiments and analysed the results. P.S. investigated the reaction fingerprints and wrote the code base. P.S., D.P. and D.K. worked on the reaction atlases. The project was supervised by T.L. and J.-L.R. All authors took part in discussions and contributed to the writing of the manuscript.

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Correspondence to Philippe Schwaller.

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The authors declare no competing interests.

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Peer review information Nature Machine Intelligence thanks the anonymous reviewers for their contribution to the peer review of this work.

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Supplementary information

Supplementary Information

Supplementary Notes 1–3, Figs. 1–3 and Tables 1–5.

Supplementary Data

Interactive reaction atlas.

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Schwaller, P., Probst, D., Vaucher, A.C. et al. Mapping the space of chemical reactions using attention-based neural networks. Nat Mach Intell 3, 144–152 (2021).

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