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Register a new userRevisiting Graph Neural Networks for Link Prediction
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Added by
Muhan Zhang
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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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.
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Learning to predict missing links is important for many graph-based applications. Existing methods were designed to learn the observed association between two sets of variables: (1) the observed graph structure and (2) the existence of link between a pair of nodes. However, the causal relationship between these variables was ignored and we visit the possibility of learning it by simply asking a counterfactual question: would the link exist or not if the observed graph structure became different? To answer this question by causal inference, we consider the information of the node pair as context, global graph structural properties as treatment, and link existence as outcome. In this work, we propose a novel link prediction method that enhances graph learning by the counterfactual inference. It creates counterfactual links from the observed ones, and our method learns representations from both of them. Experiments on a number of benchmark datasets show that our proposed method achieves the state-of-the-art performance on link prediction.
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.
Molecule property prediction is a fundamental problem for computer-aided drug discovery and materials science. Quantum-chemical simulations such as density functional theory (DFT) have been widely used for calculating the molecule properties, however, because of the heavy computational cost, it is difficult to search a huge number of potential chemical compounds. Machine learning methods for molecular modeling are attractive alternatives, however, the development of expressive, accurate, and scalable graph neural networks for learning molecular representations is still challenging. In this work, we propose a simple and powerful graph neural networks for molecular property prediction. We model a molecular as a directed complete graph in which each atom has a spatial position, and introduce a recursive neural network with simple gating function. We also feed input embeddings for every layers as skip connections to accelerate the training. Experimental results show that our model achieves the state-of-the-art performance on the standard benchmark dataset for molecular property prediction.
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.
Efficient scheduling of transmissions is a key problem in wireless networks. The main challenge stems from the fact that optimal link scheduling involves solving a maximum weighted independent set (MWIS) problem, which is known to be NP-hard. For practical link scheduling schemes, centralized and distributed greedy heuristics are commonly used to approximate the solution to the MWIS problem. However, these greedy schemes mostly ignore important topological information of the wireless network. To overcome this limitation, we propose fast heuristics based on graph convolutional networks (GCNs) that can be implemented in centralized and distributed manners. Our centralized MWIS solver is based on tree search guided by a trainable GCN module and 1-step rollout. In our distributed MWIS solver, a trainable GCN module learns topology-aware node embeddings that are combined with the network weights before calling a distributed greedy solver. Test results on medium-sized wireless networks show that a GCN-based centralized MWIS solver can reach a near-optimal solution quickly. Moreover, we demonstrate that a shallow GCN-based distributed MWIS scheduler can reduce by nearly half the suboptimality gap of the distributed greedy solver with minimal increase in complexity. The proposed scheduling solutions also exhibit good generalizability across graph and weight distributions.
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