Molecule Property Prediction Based on Spatial Graph Embedding

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Abstract

Accurate prediction of molecular properties is important for new compound design, which is a crucial step in drug discovery. In this paper, molecular graph data is utilized for property prediction based on graph convolution neural networks. In addition, a convolution spatial graph embedding layer (C-SGEL) is introduced to retain the spatial connection information on molecules. And, multiple C-SGELs are stacked to construct a convolution spatial graph embedding network (C-SGEN) for end-to-end representation learning. In order to enhance the robustness of the network, molecular fingerprints are also combined with C-SGEN to build a composite model for predicting molecular properties. Our comparative experiments have shown that our method is accurate and achieves the best results on some open benchmark datasets.

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