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Register a new userCoSimGNN: Towards Large-scale Graph Similarity Computation
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Added by
Ziheng Duan
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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The ability to compute similarity scores between graphs based on metrics such as Graph Edit Distance (GED) is important in many real-world applications, such as 3D action recognition and biological molecular identification. Computing exact GED values is typically an NP-hard problem and traditional algorithms usually achieve an unsatisfactory trade-off between accuracy and efficiency. Recently, Graph Neural Networks (GNNs) provide a data-driven solution for this task, which is more efficient while maintaining prediction accuracy in small graph (around 10 nodes per graph) similarity computation. Existing GNN-based methods, which either respectively embed two graphs (lack of low-level cross-graph interactions) or deploy cross-graph interactions for whole graph pairs (redundant and time-consuming), are still not able to achieve competitive results when the number of nodes in graphs increases. In this paper, we focus on similarity computation for large-scale graphs and propose the embedding-coarsening-matching framework, which first embeds and coarsens large graphs to coarsened graphs with denser local topology and then deploys fine-grained interactions on the coarsened graphs for the final similarity scores.
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Graph similarity computation aims to predict a similarity score between one pair of graphs to facilitate downstream applications, such as finding the most similar chemical compounds similar to a query compound or Fewshot 3D Action Recognition. Recently, some graph similarity computation models based on neural networks have been proposed, which are either based on graph-level interaction or node-level comparison. However, when the number of nodes in the graph increases, it will inevitably bring about reduced representation ability or high computation cost. Motivated by this observation, we propose a graph partitioning and graph neural network-based model, called PSimGNN, to effectively resolve this issue. Specifically, each of the input graphs is partitioned into a set of subgraphs to extract the local structural features directly. Next, a novel graph neural network with an attention mechanism is designed to map each subgraph into an embedding vector. Some of these subgraph pairs are automatically selected for node-level comparison to supplement the subgraph-level embedding with fine-grained information. Finally, coarse-grained interaction information among subgraphs and fine-grained comparison information among nodes in different subgraphs are integrated to predict the final similarity score. Experimental results on graph datasets with different graph sizes demonstrate that PSimGNN outperforms state-of-the-art methods in graph similarity computation tasks using approximate Graph Edit Distance (GED) as the graph similarity metric.
Graph Convolutional Networks (GCNs) have shown significant improvements in semi-supervised learning on graph-structured data. Concurrently, unsupervised learning of graph embeddings has benefited from the information contained in random walks. In this paper, we propose a model: Network of GCNs (N-GCN), which marries these two lines of work. At its core, N-GCN trains multiple instances of GCNs over node pairs discovered at different distances in random walks, and learns a combination of the instance outputs which optimizes the classification objective. Our experiments show that our proposed N-GCN model improves state-of-the-art baselines on all of the challenging node classification tasks we consider: Cora, Citeseer, Pubmed, and PPI. In addition, our proposed method has other desirable properties, including generalization to recently proposed semi-supervised learning methods such as GraphSAGE, allowing us to propose N-SAGE, and resilience to adversarial input perturbations.
Graph convolutional networks (GCNs) have recently received wide attentions, due to their successful applications in different graph tasks and different domains. Training GCNs for a large graph, however, is still a challenge. Original full-batch GCN training requires calculating the representation of all the nodes in the graph per GCN layer, which brings in high computation and memory costs. To alleviate this issue, several sampling-based methods have been proposed to train GCNs on a subset of nodes. Among them, the node-wise neighbor-sampling method recursively samples a fixed number of neighbor nodes, and thus its computation cost suffers from exponential growing neighbor size; while the layer-wise importance-sampling method discards the neighbor-dependent constraints, and thus the nodes sampled across layer suffer from sparse connection problem. To deal with the above two problems, we propose a new effective sampling algorithm called LAyer-Dependent ImportancE Sampling (LADIES). Based on the sampled nodes in the upper layer, LADIES selects their neighborhood nodes, constructs a bipartite subgraph and computes the importance probability accordingly. Then, it samples a fixed number of nodes by the calculated probability, and recursively conducts such procedure per layer to construct the whole computation graph. We prove theoretically and experimentally, that our proposed sampling algorithm outperforms the previous sampling methods in terms of both time and memory costs. Furthermore, LADIES is shown to have better generalization accuracy than original full-batch GCN, due to its stochastic nature.
While the celebrated graph neural networks yield effective representations for individual nodes of a graph, there has been relatively less success in extending to the task of graph similarity learning. Recent work on graph similarity learning has considered either global-level graph-graph interactions or low-level node-node interactions, however ignoring the rich cross-level interactions (e.g., between each node of one graph and the other whole graph). In this paper, we propose a multi-level graph matching network (MGMN) framework for computing the graph similarity between any pair of graph-structured objects in an end-to-end fashion. In particular, the proposed MGMN consists of a node-graph matching network for effectively learning cross-level interactions between each node of one graph and the other whole graph, and a siamese graph neural network to learn global-level interactions between two input graphs. Furthermore, to compensate for the lack of standard benchmark datasets, we have created and collected a set of datasets for both the graph-graph classification and graph-graph regression tasks with different sizes in order to evaluate the effectiveness and robustness of our models. Comprehensive experiments demonstrate that MGMN consistently outperforms state-of-the-art baseline models on both the graph-graph classification and graph-graph regression tasks. Compared with previous work, MGMN also exhibits stronger robustness as the sizes of the two input graphs increase.
Graph edit distance / similarity is widely used in many tasks, such as graph similarity search, binary function analysis, and graph clustering. However, computing the exact graph edit distance (GED) or maximum common subgraph (MCS) between two graphs is known to be NP-hard. In this paper, we propose the hierarchical graph matching network (HGMN), which learns to compute graph similarity from data. HGMN is motivated by the observation that two similar graphs should also be similar when they are compressed into more compact graphs. HGMN utilizes multiple stages of hierarchical clustering to organize a graph into successively more compact graphs. At each stage, the earth mover distance (EMD) is adopted to obtain a one-to-one mapping between the nodes in two graphs (on which graph similarity is to be computed), and a correlation matrix is also derived from the embeddings of the nodes in the two graphs. The correlation matrices from all stages are used as input for a convolutional neural network (CNN), which is trained to predict graph similarity by minimizing the mean squared error (MSE). Experimental evaluation on 4 datasets in different domains and 4 performance metrics shows that HGMN consistently outperforms existing baselines in the accuracy of graph similarity approximation.
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