Published in

SpringerOpen, Journal of Cheminformatics, 1(12), 2020

DOI: 10.1186/s13321-020-00469-w

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DECIMER: towards deep learning for chemical image recognition

Journal article published in 2020 by Kohulan Rajan, Achim Zielesny, Christoph Steinbeck ORCID
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

AbstractThe automatic recognition of chemical structure diagrams from the literature is an indispensable component of workflows to re-discover information about chemicals and to make it available in open-access databases. Here we report preliminary findings in our development of Deep lEarning for Chemical ImagE Recognition (DECIMER), a deep learning method based on existing show-and-tell deep neural networks, which makes very few assumptions about the structure of the underlying problem. It translates a bitmap image of a molecule, as found in publications, into a SMILES. The training state reported here does not yet rival the performance of existing traditional approaches, but we present evidence that our method will reach a comparable detection power with sufficient training time. Training success of DECIMER depends on the input data representation: DeepSMILES are superior over SMILES and we have a preliminary indication that the recently reported SELFIES outperform DeepSMILES. An extrapolation of our results towards larger training data sizes suggests that we might be able to achieve near-accurate prediction with 50 to 100 million training structures. This work is entirely based on open-source software and open data and is available to the general public for any purpose.