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We present a systematic investigation using graph neural networks (GNNs) to model organic chemical reactions. To do so, we prepared a dataset collection of four ubiquitous reactions from the organic chemistry literature. We evaluate seven different GNN architectures for classification tasks pertaining to the identification of experimental reagents and conditions. We find that models are able to identify specific graph features that affect reaction conditions and lead to accurate predictions. The results herein show great promise in advancing molecular machine learning.
Origin-destination (OD) matrices are often used in urban planning, where a city is partitioned into regions and an element (i, j) in an OD matrix records the cost (e.g., travel time, fuel consumption, or travel speed) from region i to region j. In th
Genetic mutations can cause disease by disrupting normal gene function. Identifying the disease-causing mutations from millions of genetic variants within an individual patient is a challenging problem. Computational methods which can prioritize dise
The graph Laplacian regularization term is usually used in semi-supervised representation learning to provide graph structure information for a model $f(X)$. However, with the recent popularity of graph neural networks (GNNs), directly encoding graph
Graph neural networks (GNNs) have achieved great success in recent years. Three most common applications include node classification, link prediction, and graph classification. While there is rich literature on node classification and graph classific
Data augmentation has been widely used to improve generalizability of machine learning models. However, comparatively little work studies data augmentation for graphs. This is largely due to the complex, non-Euclidean structure of graphs, which limit