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A machine learning approach to molecular structure recognition in chemical literature

Author(s)
Tabchouri, Sophia.
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Other Contributors
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science.
Advisor
Regina Barzilay.
Terms of use
MIT theses are protected by copyright. They may be viewed, downloaded, or printed from this source but further reproduction or distribution in any format is prohibited without written permission. http://dspace.mit.edu/handle/1721.1/7582
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Abstract
Reaction diagrams in chemistry papers contain essential reaction information that is not available in the text. In order to extract comprehensive reaction information from chemistry literature, it is vital to convert these diagrams into a format compatible with searchable cheminformatic databases. Existing methods rely on rule-based procedures that have difficulty generalizing to noisy or different styled images. In this thesis, I implement a deep learning pipeline for identifying molecules in chemical diagrams and 'translating' the images into their corresponding SMILES strings. Diagram segmentation is performed using Mask R-CNN trained on an automatically generated set of diagrams. Translation to SMILES strings is performed using a neural machine translation model augmented with domain adaptation. Experimental results suggest that this model outperforms both rule-based and machine learning based models on diagrams extracted from real chemical literature.
Description
This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
 
Thesis: M. Eng. in Computer Science and Engineering, Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2019
 
Cataloged from student-submitted PDF version of thesis.
 
Includes bibliographical references (pages 53-55).
 
Date issued
2019
URI
https://hdl.handle.net/1721.1/123132
Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Publisher
Massachusetts Institute of Technology
Keywords
Electrical Engineering and Computer Science.

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  • Electrical Engineering and Computer Sciences - Master's degree
  • Electrical Engineering and Computer Sciences - Master's degree

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