Data-Driven Chemical Reaction Classification, Fingerprinting and Clustering using Attention-Based Neural Networks. Philippe Schwaller, Daniel Probst, Alain C. Vaucher, Vishnu H Nair, Teodoro Laino, & Jean-Louis Reymond ChemRxiv, December, 2019. ![Data-Driven Chemical Reaction Classification, Fingerprinting and Clustering using Attention-Based Neural Networks [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex Organic reactions are usually assigned to classes grouping reactions with similar reagents and mechanisms. The classification process is a tedious task, requiring first an accurate mapping of the reaction (atom mapping) followed by the identification of the corresponding reaction class template. In this work, we present two transformer-based models that infer reaction classes from the SMILES representation of chemical reactions. Our best model reaches a classification accuracy of 98.2%. We study the incorrect predictions of the models and show that they reveal different biases and mistakes in the underlying data set. Using the embeddings of our classification model, we introduce reaction fingerprints that do not require knowing the reaction center or distinguishing between reactants and reagents. This conversion from chemical reactions to feature vectors enables efficient clustering and similarity search in the reaction space. We compare the reaction clustering for combinations of self-supervised, supervised, and molecular shingle-based reaction representations.
@article{philippe_schwaller_data-driven_2019,
title = {Data-{Driven} {Chemical} {Reaction} {Classification}, {Fingerprinting} and {Clustering} using {Attention}-{Based} {Neural} {Networks}},
url = {https://chemrxiv.org/articles/Data-Driven_Chemical_Reaction_Classification_with_Attention-Based_Neural_Networks/9897365},
doi = {10.26434/chemrxiv.9897365.v2},
abstract = {Organic reactions are usually assigned to classes grouping reactions with similar reagents and mechanisms. The classification process is a tedious task, requiring first an accurate mapping of the reaction (atom mapping) followed by the identification of the corresponding reaction class template. In this work, we present two transformer-based models that infer reaction classes from the SMILES representation of chemical reactions. Our best model reaches a classification accuracy of 98.2\%. We study the incorrect predictions of the models and show that they reveal different biases and mistakes in the underlying data set. Using the embeddings of our classification model, we introduce reaction fingerprints that do not require knowing the reaction center or distinguishing between reactants and reagents. This conversion from chemical reactions to feature vectors enables efficient clustering and similarity search in the reaction space. We compare the reaction clustering for combinations of self-supervised, supervised, and molecular shingle-based reaction representations.},
journal = {ChemRxiv},
author = {{Philippe Schwaller} and {Daniel Probst} and {Alain C. Vaucher} and {Vishnu H Nair} and {Teodoro Laino} and {Jean-Louis Reymond}},
month = dec,
year = {2019},
keywords = {BERT, Chemical Reactions, Clustering analysis, Fingerprints, SMILES, SMILES string representation, SMILES-Encoded Molecular Structures, classification, deep learning, machine learning, organic chemistry, organic synthesis, transformer},
}
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