ChemGrapher: Optical Graph Recognition of Chemical Compounds by Deep Learning

In drug discovery, knowledge of the graph structure of chemical compounds is essential. Many thousands of scientific articles and patents in chemistry and pharmaceutical sciences have investigated chemical compounds, but in many cases the details of the structure of these chemical compounds is published only as an image. A tool to analyze these images automatically and convert them into a chemical graph structure would be useful for many applications, such as drug discovery. A few such tools are available and they are mostly derived from optical character recognition. However, our evaluation of the performance of these tools reveals that they make often mistakes in recognizing the correct bond multiplicity and stereochemical information. In addition, errors sometimes even lead to missing atoms in the resulting graph. In our work, we address these issues by developing a compound recognition method based on machine learning. More specifically, we develop a deep neural network model for optical compound recognition. The deep learning solution presented here consists of a segmentation model, followed by three classification models that predict atom locations, bonds and charges. Furthermore, this model not only predicts the graph structure of the molecule but also produces all information necessary to relate each component of the resulting graph to the source image. This solution is scalable and can rapidly process thousands of images. Finally, we compare empirically the proposed method to a well-established tool and observe significant error reduction.