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Improving the quality of chemical language model outcomes with atom-in-SMILES tokenization
Cited 6 time in
Web of Science
Cited 7 time in Scopus
- Authors
- Issue Date
- 2023-05
- Publisher
- Chemistry Central
- Citation
- Journal of Cheminformatics, Vol.15 No.1, p. 55
- Abstract
- Tokenization is an important preprocessing step in natural language processing that may have a significant influence on prediction quality. This research showed that the traditional SMILES tokenization has a certain limitation that results in tokens failing to reflect the true nature of molecules. To address this issue, we developed the atom-in-SMILES tokenization scheme that eliminates ambiguities in the generic nature of SMILES tokens. Our results in multiple chemical translation and molecular property prediction tasks demonstrate that proper tokenization has a significant impact on prediction quality. In terms of prediction accuracy and token degeneration, atom-in-SMILES is more effective method in generating higher-quality SMILES sequences from AI-based chemical models compared to other tokenization and representation schemes. We investigated the degrees of token degeneration of various schemes and analyzed their adverse effects on prediction quality. Additionally, token-level repetitions were quantified, and generated examples were incorporated for qualitative examination. We believe that the atom-in-SMILES tokenization has a great potential to be adopted by broad related scientific communities, as it provides chemically accurate, tailor-made tokens for molecular property prediction, chemical translation, and molecular generative models.
- ISSN
- 1758-2946
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Related Researcher
- Graduate School of Convergence Science & Technology
- Dept. of Molecular and Biopharmaceutical Sciences
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