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Chemical Structure Recognition (CSR) System: Automatic Analysis of 2D Chemical Structures in Document Images

Syed Saqib Bukhari; Zaryab Iftikhar; Andreas Dengel
In: Proceedings ICDAR'19. International Conference on Document Analysis and Recognition (ICDAR-2019), September 20-25, Pages 1262-1267, ISBN 978-1-7281-3015-6, IEEE, 9/2019.


In this era of advanced technology and automation, information extraction has become a very common practice for the analysis of data. A technique known as Optical Character Recognition (OCR) is used for recognition of text. The purpose is to extract textual data for automatic information analysis or natural language processing of document images. However, in the field of cheminformatics where it is required to recognize 2D molecular structures as they are published in research journals or patent documents, OCR is not adequate for processing, as chemical compounds can be represented both in textual as well as in graphical format. The digital representation of an image based chemical structure allows not only patent analysis teams to provide customize insights but also cheminformatic research groups to enhance their molecular structure databases, which further can be used for querying structure as well as sub-structural patterns. Some tools have been made for extraction and processing of image-based molecular structures. Optical Structure Recognition Application (OSRA) being one of the tools that partially fulfill the task of recognizing chemical structural in document images into chemical formats (SMILES, SDF, or MOL). However, it has few problems such as poor character recognition, false structure extraction, and slow processing. In this paper, we have developed a prototype Chemical Structure Recognition (CSR) system using modern and advanced image processing open-source libraries, which allows us to extract structural information of a chemical structure embedded in the form of a digital raster image. The CSR system is capable of processing chemical information contained in chemical structure image and generates the SMILES or MOL representation. For performance evaluation, we have used two different data sets to measure the potential of the CSR system. It yields better results than OSRA that depict accurate recognition, fast extraction, and correctness of great sign...

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