An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification
Abstract Assigning or proposing a catalysing enzyme given a chemical or biochemical reaction is of great interest to life sciences and chemistry alike. The exploration and design of metabolic pathways and the challenge of finding more sustainable enzyme-catalysed alternatives to traditional organic...
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| Format: | Article |
| Language: | English |
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BMC
2023-11-01
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| Series: | Journal of Cheminformatics |
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| Online Access: | https://doi.org/10.1186/s13321-023-00784-y |
| _version_ | 1827633367385899008 |
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| author | Daniel Probst |
| author_facet | Daniel Probst |
| author_sort | Daniel Probst |
| collection | DOAJ |
| description | Abstract Assigning or proposing a catalysing enzyme given a chemical or biochemical reaction is of great interest to life sciences and chemistry alike. The exploration and design of metabolic pathways and the challenge of finding more sustainable enzyme-catalysed alternatives to traditional organic reactions are just two examples of tasks that require an association between reaction and enzyme. However, given the lack of large and balanced annotated data sets of enzyme-catalysed reactions, assigning an enzyme to a reaction still relies on expert-curated rules and databases. Here, we present a data-driven explainable human-in-the-loop machine learning approach to support and ultimately automate the association of a catalysing enzyme with a given biochemical reaction. In addition, the proposed method is capable of predicting enzymes as candidate catalysts for organic reactions amendable to biocatalysis. Finally, the introduced explainability and visualisation methods can easily be generalised to support other machine-learning approaches involving chemical and biochemical reactions. |
| first_indexed | 2024-03-09T14:58:33Z |
| format | Article |
| id | doaj.art-e4d5fb2e60cd4041af525717570cb3e5 |
| institution | Directory Open Access Journal |
| issn | 1758-2946 |
| language | English |
| last_indexed | 2024-03-09T14:58:33Z |
| publishDate | 2023-11-01 |
| publisher | BMC |
| record_format | Article |
| series | Journal of Cheminformatics |
| spelling | doaj.art-e4d5fb2e60cd4041af525717570cb3e52023-11-26T14:04:06ZengBMCJournal of Cheminformatics1758-29462023-11-0115111310.1186/s13321-023-00784-yAn explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classificationDaniel Probst0Signal Processing Laboratory 2, Institute of Electrical and Micro Engineering, School of Engineering, EPFLAbstract Assigning or proposing a catalysing enzyme given a chemical or biochemical reaction is of great interest to life sciences and chemistry alike. The exploration and design of metabolic pathways and the challenge of finding more sustainable enzyme-catalysed alternatives to traditional organic reactions are just two examples of tasks that require an association between reaction and enzyme. However, given the lack of large and balanced annotated data sets of enzyme-catalysed reactions, assigning an enzyme to a reaction still relies on expert-curated rules and databases. Here, we present a data-driven explainable human-in-the-loop machine learning approach to support and ultimately automate the association of a catalysing enzyme with a given biochemical reaction. In addition, the proposed method is capable of predicting enzymes as candidate catalysts for organic reactions amendable to biocatalysis. Finally, the introduced explainability and visualisation methods can easily be generalised to support other machine-learning approaches involving chemical and biochemical reactions.https://doi.org/10.1186/s13321-023-00784-yMachine learningEnzymatic reactionsExplainable machine learningCheminformatics |
| spellingShingle | Daniel Probst An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification Journal of Cheminformatics Machine learning Enzymatic reactions Explainable machine learning Cheminformatics |
| title | An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification |
| title_full | An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification |
| title_fullStr | An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification |
| title_full_unstemmed | An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification |
| title_short | An explainability framework for deep learning on chemical reactions exemplified by enzyme-catalysed reaction classification |
| title_sort | explainability framework for deep learning on chemical reactions exemplified by enzyme catalysed reaction classification |
| topic | Machine learning Enzymatic reactions Explainable machine learning Cheminformatics |
| url | https://doi.org/10.1186/s13321-023-00784-y |
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