Abstract—Materials Genomics initiative has the goal of rapidly synthesizing materials with a given set of desired properties using data science techniques. An important step in this direction is the ability to predict the outcomes of complex chemical reactions. Some graphbased feature learning algorithms have been proposed recently. However, the comprehensive relationship between atoms or structures is not learned properly and not explainable, and multiple graphs cannot be handled. In this paper, chemical reaction processes are formulated as translation processes. Both atoms and edges are mapped to vectors represent ing the structural information. We employ the graph convolution layers to learn meaningful information of atom graphs, and further employ its variations, message passing networks (MPNN) and edge attention graph convolution network (EAGCN) to learn edge representations. Particularly, multiview EAGCN groups and maps edges to a set of representations for the properties of the chemical bond between atoms from multiple views. Each bond is viewed from its atom type, bond type, distance and neighbor environment. The final node and edge representations are mapped to a sequence defined by the SMILES of the molecule and then fed to a decoder model with attention. To make full usage of multiview information, we propose multiview attention model to handle self correlation inside each atom or edge, and mutual correlation between edges and atoms, both of which are important in chemical reaction processes. We have evaluated our method on the standard benchmark datasets (that have been used by all the prior works), and the results show that edge embedding with multiview attention achieves superior accuracy compared to existing techniques.
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Multiview spectral graph convolution with consistent edge attention for molecular modeling
Although graph convolutional networks (GCNs) that extend the convolution operation from images to graphs have led to competitive performance, the existing GCNs are still difficult to handle a variety of applications, especially cheminformatics problems. Recently multiple GCNs are applied to chemical compound structures which are represented by the hydrogendepleted molecular graphs of different size. GCNs built for a binary adjacency matrix that reflects the connectivity among nodes in a graph do not account for the edge consistency in multiple molecular graphs, that is, chemical bonds (edges) in different molecular graphs can be similar due to the similar enthalpy and interatomic distance. In this paper, we propose a variant of GCN where a molecular graph is first decomposed into multiple views of the graph, each comprising a specific type of edges. In each view, an edge consistency constraint is enforced so that similar edges in different graphs can receive similar attention weights when passing information. Similarly to prior work, we prove that in each layer, our method corresponds to a spectral filter derived by the first order Chebyshev approximation of graph Laplacian. Extensive experiments demonstrate the substantial advantages of the proposed technique in quantitative structureactivity relationship prediction.
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 Award ID(s):
 1718738
 NSFPAR ID:
 10253605
 Date Published:
 Journal Name:
 Neurocomputing
 Volume:
 445
 ISSN:
 09252312
 Page Range / eLocation ID:
 1225
 Format(s):
 Medium: X
 Sponsoring Org:
 National Science Foundation
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