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Automated Extraction of Chemical Synthesis Actions from Experimental Procedures

preprint
submitted on 24.12.2019 and posted on 26.12.2019 by Alain C. Vaucher, Federico Zipoli, Joppe Geluykens, Vishnu H Nair, Philippe Schwaller, Teodoro Laino
Experimental procedures for chemical synthesis are commonly reported in prose in patents or in the scientific literature. The automatic extraction of the details necessary to reproduce and validate a synthesis in a chemical laboratory is quite often a tedious task, requiring extensive human intervention. Here, we present a method to convert unstructured experimental procedures written in English to structured synthetic steps (action sequences) reflecting all the steps needed to successfully conduct the corresponding chemical reactions. To achieve this, we design a set of synthesis actions with predefined properties and a deep-learning transformer-based model to convert experimental procedures to a textual representation of action sequences. The model is first pretrained on vast amounts of data generated automatically with a custom rule-based natural language processing approach, and then refined on a smaller set of manually annotated samples. Predictions on our test set resulted in a perfect match of the full action sequence for 64.5% of sentences.

History

Email Address of Submitting Author

ava@zurich.ibm.com

Institution

IBM Research - Zurich

Country

Switzerland

ORCID For Submitting Author

0000-0001-7554-0288

Declaration of Conflict of Interest

No conflict of interest.

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