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Register a new userGraph Neural Networks for the Prediction of Substrate-Specific Organic Reaction Conditions
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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.
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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 this paper, we partition a day into multiple intervals, e.g., 96 15-min intervals and each interval is associated with an OD matrix which represents the costs in the interval; and we consider sparse and stochastic OD matrices, where the elements represent stochastic but not deterministic costs and some elements are missing due to lack of data between two regions. We solve the sparse, stochastic OD matrix forecasting problem. Given a sequence of historical OD matrices that are sparse, we aim at predicting future OD matrices with no empty elements. We propose a generic learning framework to solve the problem by dealing with sparse matrices via matrix factorization and two graph convolutional neural networks and capturing temporal dynamics via recurrent neural network. Empirical studies using two taxi datasets from different countries verify the effectiveness of the proposed framework.
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 disease-causing mutations have, therefore, enormous applications. It is well-known that genes function through a complex regulatory network. However, existing variant effect prediction models only consider a variant in isolation. In contrast, we propose VEGN, which models variant effect prediction using a graph neural network (GNN) that operates on a heterogeneous graph with genes and variants. The graph is created by assigning variants to genes and connecting genes with an gene-gene interaction network. In this context, we explore an approach where a gene-gene graph is given and another where VEGN learns the gene-gene graph and therefore operates both on given and learnt edges. The graph neural network is trained to aggregate information between genes, and between genes and variants. Variants can exchange information via the genes they connect to. This approach improves the performance of existing state-of-the-art models.
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 structure $A$ into a model, i.e., $f(A, X)$, has become the more common approach. While we show that graph Laplacian regularization brings little-to-no benefit to existing GNNs, and propose a simple but non-trivial variant of graph Laplacian regularization, called Propagation-regularization (P-reg), to boost the performance of existing GNN models. We provide formal analyses to show that P-reg not only infuses extra information (that is not captured by the traditional graph Laplacian regularization) into GNNs, but also has the capacity equivalent to an infinite-depth graph convolutional network. We demonstrate that P-reg can effectively boost the performance of existing GNN models on both node-level and graph-level tasks across many different datasets.
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 classification, GNN for link prediction is relatively less studied and less understood. One common practice in previous works is to first compute node representations through a GNN, and then directly aggregate two node representations as a link representation. In this paper, we show the limitations of such an approach, and propose a labeling trick to make GNNs learn better link representations. Labeling trick assigns labels to nodes as their additional features according to nodes relationships with the target link. We show theoretically that GNNs applied to such labeled graphs can learn most expressive link representations. We also show that one state-of-the-art link prediction model, SEAL, exactly uses a labeling trick. Labeling trick brings up to 195% performance gains over plain GNNs, achieving 3 first places on the OGB link prediction leaderboard.
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 limits possible manipulation operations. Augmentation operations commonly used in vision and language have no analogs for graphs. Our work studies graph data augmentation for graph neural networks (GNNs) in the context of improving semi-supervised node-classification. We discuss practical and theoretical motivations, considerations and strategies for graph data augmentation. Our work shows that neural edge predictors can effectively encode class-homophilic structure to promote intra-class edges and demote inter-class edges in given graph structure, and our main contribution introduces the GAug graph data augmentation framework, which leverages these insights to improve performance in GNN-based node classification via edge prediction. Extensive experiments on multiple benchmarks show that augmentation via GAug improves performance across GNN architectures and datasets.
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