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 hydrogen-depleted 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 interatomicmore »
Predicting Outcomes of Chemical Reactions: A Seq2Seq Approach with Multi-view Attention and Edge Embedding
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 graph-based 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, multi-view 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 multi-view information, we propose multi-view more »
- Award ID(s):
- 1718738
- Publication Date:
- NSF-PAR ID:
- 10179119
- Journal Name:
- Proceedings of International Joint Conference on Neural Networks
- ISSN:
- 2161-4407
- Sponsoring Org:
- National Science Foundation
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