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Register a new userGoGNN: Graph of Graphs Neural Network for Predicting Structured Entity Interactions
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Hanchen Wang
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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Entity interaction prediction is essential in many important applications such as chemistry, biology, material science, and medical science. The problem becomes quite challenging when each entity is represented by a complex structure, namely structured entity, because two types of graphs are involved: local graphs for structured entities and a global graph to capture the interactions between structured entities. We observe that existing works on structured entity interaction prediction cannot properly exploit the unique graph of graphs model. In this paper, we propose a Graph of Graphs Neural Network, namely GoGNN, which extracts the features in both structured entity graphs and the entity interaction graph in a hierarchical way. We also propose the dual-attention mechanism that enables the model to preserve the neighbor importance in both levels of graphs. Extensive experiments on real-world datasets show that GoGNN outperforms the state-of-the-art methods on two representative structured entity interaction prediction tasks: chemical-chemical interaction prediction and drug-drug interaction prediction. Our code is available at Github.
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Predicting interactions between structured entities lies at the core of numerous tasks such as drug regimen and new material design. In recent years, graph neural networks have become attractive. They represent structured entities as graphs and then extract features from each individual graph using graph convolution operations. However, these methods have some limitations: i) their networks only extract features from a fix-sized subgraph structure (i.e., a fix-sized receptive field) of each node, and ignore features in substructures of different sizes, and ii) features are extracted by considering each entity independently, which may not effectively reflect the interaction between two entities. To resolve these problems, we present MR-GNN, an end-to-end graph neural network with the following features: i) it uses a multi-resolution based architecture to extract node features from different neighborhoods of each node, and, ii) it uses dual graph-state long short-term memory networks (L-STMs) to summarize local features of each graph and extracts the interaction features between pairwise graphs. Experiments conducted on real-world datasets show that MR-GNN improves the prediction of state-of-the-art methods.
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Modeling generative process of growing graphs has wide applications in social networks and recommendation systems, where cold start problem leads to new nodes isolated from existing graph. Despite the emerging literature in learning graph representation and graph generation, most of them can not handle isolated new nodes without nontrivial modifications. The challenge arises due to the fact that learning to generate representations for nodes in observed graph relies heavily on topological features, whereas for new nodes only node attributes are available. Here we propose a unified generative graph convolutional network that learns node representations for all nodes adaptively in a generative model framework, by sampling graph generation sequences constructed from observed graph data. We optimize over a variational lower bound that consists of a graph reconstruction term and an adaptive Kullback-Leibler divergence regularization term. We demonstrate the superior performance of our approach on several benchmark citation network datasets.
In graph neural networks (GNNs), message passing iteratively aggregates nodes information from their direct neighbors while neglecting the sequential nature of multi-hop node connections. Such sequential node connections e.g., metapaths, capture critical insights for downstream tasks. Concretely, in recommender systems (RSs), disregarding these insights leads to inadequate distillation of collaborative signals. In this paper, we employ collaborative subgraphs (CSGs) and metapaths to form metapath-aware subgraphs, which explicitly capture sequential semantics in graph structures. We propose metatextbf{P}ath and textbf{E}ntity-textbf{A}ware textbf{G}raph textbf{N}eural textbf{N}etwork (PEAGNN), which trains multilayer GNNs to perform metapath-aware information aggregation on such subgraphs. This aggregated information from different metapaths is then fused using attention mechanism. Finally, PEAGNN gives us the representations for node and subgraph, which can be used to train MLP for predicting score for target user-item pairs. To leverage the local structure of CSGs, we present entity-awareness that acts as a contrastive regularizer on node embedding. Moreover, PEAGNN can be combined with prominent layers such as GAT, GCN and GraphSage. Our empirical evaluation shows that our proposed technique outperforms competitive baselines on several datasets for recommendation tasks. Further analysis demonstrates that PEAGNN also learns meaningful metapath combinations from a given set of metapaths.
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