Automated extraction of chemical synthesis actions from experimental procedures.

Nature Communications
Alain C VaucherTeodoro Laino

Abstract

Experimental procedures for chemical synthesis are commonly reported in prose in patents or in the scientific literature. The extraction of the details necessary to reproduce and validate a synthesis in a chemical laboratory is often a tedious task requiring extensive human intervention. We present a method to convert unstructured experimental procedures written in English to structured synthetic steps (action sequences) reflecting all the operations 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 sequence to sequence model based on the transformer architecture to convert experimental procedures to action sequences. The model is pretrained on vast amounts of data generated automatically with a custom rule-based natural language processing approach and refined on manually annotated samples. Predictions on our test set result in a perfect (100%) match of the action sequence for 60.8% of sentences, a 90% match for 71.3% of sentences, and a 75% match for 82.4% of sentences.

References

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Citations

Sep 29, 2020·Nature Communications
Mar 6, 2021·IScience·Olga KononovaGerbrand Ceder
Apr 27, 2021·Analytica Chimica Acta·Lucas B AyresCarlos D Garcia
May 8, 2021·Nature Communications·Alain C VaucherTeodoro Laino
Jun 4, 2021·Drug Discovery Today·Joshua MeyersNathan Brown
Jun 9, 2021·ChemMedChem·Fabian H KnaupFelix Hausch
Jun 12, 2021·Journal of Chemical Information and Modeling·Jiang GuoRegina Barzilay
Jun 15, 2021·Chemical Science·Tuo JiangJeffrey W Bode
Jul 24, 2021·Journal of Chemical Information and Modeling·Jiang GuoRegina Barzilay
Dec 29, 2020·Accounts of Chemical Research·Liam WilbrahamLeroy Cronin
Sep 28, 2021·Briefings in Bioinformatics·Jingxin DongXiangxiang Zeng

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Methods Mentioned

BETA
column chromatography
nuclear magnetic resonance

Software Mentioned

SciFinder
LeadMine
Reaxys
ChemicalTagger
doccano
ChemDataExtractor
MakeSolution
py
textdistance
SentencePiece

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