Theoretical and Computational Chemistry

Automated Extraction of Chemical Synthesis Actions from Experimental Procedures

Abstract

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.

Content

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Supplementary material

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SI
Thumbnail image of supplementary_data_1_actions_for_test_set.txt
supplementary data 1 actions for test set
Thumbnail image of supplementary_data_2_top_5_sequences.txt
supplementary data 2 top 5 sequences