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Representation learning enables us to automatically extract generic feature representations from a dataset to solve another machine learning task. Recently, extracted feature representations by a representation learning algorithm and a simple predictor have exhibited state-of-the-art performance on several machine learning tasks. Despite its remarkable progress, there exist various ways to evaluate representation learning algorithms depending on the application because of the flexibility of representation learning. To understand the current representation learning, we review evaluation methods of representation learning algorithms and theoretical analyses. On the basis of our evaluation survey, we also discuss the future direction of representation learning. Note that this survey is the extended version of Nozawa and Sato (2022).

This paper presents a new approach for assembling graph neural networks based on framelet transforms. The latter provides a multi-scale representation for graph-structured data. With the framelet system, we can decompose the graph feature into low-pass and high-pass frequencies as extracted features for network training, which then defines a framelet-based graph convolution. The framelet decomposition naturally induces a graph pooling strategy by aggregating the graph feature into low-pass and high-pass spectra, which considers both the feature values and geometry of the graph data and conserves the total information. The graph neural networks with the proposed framelet convolution and pooling achieve state-of-the-art performance in many types of node and graph prediction tasks. Moreover, we propose shrinkage as a new activation for the framelet convolution, which thresholds the high-frequency information at different scales. Compared to ReLU, shrinkage in framelet convolution improves the graph neural network model in terms of denoising and signal compression: noises in both node and structure can be significantly reduced by accurately cutting off the high-pass coefficients from framelet decomposition, and the signal can be compressed to less than half its original size with the prediction performance well preserved.

Deep learning methods for graphs achieve remarkable performance on many node-level and graph-level prediction tasks. However, despite the proliferation of the methods and their success, prevailing Graph Neural Networks (GNNs) neglect subgraphs, rendering subgraph prediction tasks challenging to tackle in many impactful applications. Further, subgraph prediction tasks present several unique challenges, because subgraphs can have non-trivial internal topology, but also carry a notion of position and external connectivity information relative to the underlying graph in which they exist. Here, we introduce SUB-GNN, a subgraph neural network to learn disentangled subgraph representations. In particular, we propose a novel subgraph routing mechanism that propagates neural messages between the subgraph's components and randomly sampled anchor patches from the underlying graph, yielding highly accurate subgraph representations. SUB-GNN specifies three channels, each designed to capture a distinct aspect of subgraph structure, and we provide empirical evidence that the channels encode their intended properties. We design a series of new synthetic and real-world subgraph datasets. Empirical results for subgraph classification on eight datasets show that SUB-GNN achieves considerable performance gains, outperforming strong baseline methods, including node-level and graph-level GNNs, by 12.4% over the strongest baseline. SUB-GNN performs exceptionally well on challenging biomedical datasets when subgraphs have complex topology and even comprise multiple disconnected components.

Graph Convolutional Networks (GCNs) have received increasing attention in recent machine learning. How to effectively leverage the rich structural information in complex graphs, such as knowledge graphs with heterogeneous types of entities and relations, is a primary open challenge in the field. Most GCN methods are either restricted to graphs with a homogeneous type of edges (e.g., citation links only), or focusing on representation learning for nodes only instead of jointly optimizing the embeddings of both nodes and edges for target-driven objectives. This paper addresses these limitations by proposing a novel framework, namely the GEneralized Multi-relational Graph Convolutional Networks (GEM-GCN), which combines the power of GCNs in graph-based belief propagation and the strengths of advanced knowledge-base embedding methods, and goes beyond. Our theoretical analysis shows that GEM-GCN offers an elegant unification of several well-known GCN methods as specific cases, with a new perspective of graph convolution. Experimental results on benchmark datasets show the advantageous performance of GEM-GCN over strong baseline methods in the tasks of knowledge graph alignment and entity classification.

Label Propagation (LPA) and Graph Convolutional Neural Networks (GCN) are both message passing algorithms on graphs. Both solve the task of node classification but LPA propagates node label information across the edges of the graph, while GCN propagates and transforms node feature information. However, while conceptually similar, theoretical relation between LPA and GCN has not yet been investigated. Here we study the relationship between LPA and GCN in terms of two aspects: (1) feature/label smoothing where we analyze how the feature/label of one node is spread over its neighbors; And, (2) feature/label influence of how much the initial feature/label of one node influences the final feature/label of another node. Based on our theoretical analysis, we propose an end-to-end model that unifies GCN and LPA for node classification. In our unified model, edge weights are learnable, and the LPA serves as regularization to assist the GCN in learning proper edge weights that lead to improved classification performance. Our model can also be seen as learning attention weights based on node labels, which is more task-oriented than existing feature-based attention models. In a number of experiments on real-world graphs, our model shows superiority over state-of-the-art GCN-based methods in terms of node classification accuracy.

Graph Neural Networks (GNNs), which generalize deep neural networks to graph-structured data, have drawn considerable attention and achieved state-of-the-art performance in numerous graph related tasks. However, existing GNN models mainly focus on designing graph convolution operations. The graph pooling (or downsampling) operations, that play an important role in learning hierarchical representations, are usually overlooked. In this paper, we propose a novel graph pooling operator, called Hierarchical Graph Pooling with Structure Learning (HGP-SL), which can be integrated into various graph neural network architectures. HGP-SL incorporates graph pooling and structure learning into a unified module to generate hierarchical representations of graphs. More specifically, the graph pooling operation adaptively selects a subset of nodes to form an induced subgraph for the subsequent layers. To preserve the integrity of graph's topological information, we further introduce a structure learning mechanism to learn a refined graph structure for the pooled graph at each layer. By combining HGP-SL operator with graph neural networks, we perform graph level representation learning with focus on graph classification task. Experimental results on six widely used benchmarks demonstrate the effectiveness of our proposed model.

Graph neural networks (GNNs) are a popular class of machine learning models whose major advantage is their ability to incorporate a sparse and discrete dependency structure between data points. Unfortunately, GNNs can only be used when such a graph-structure is available. In practice, however, real-world graphs are often noisy and incomplete or might not be available at all. With this work, we propose to jointly learn the graph structure and the parameters of graph convolutional networks (GCNs) by approximately solving a bilevel program that learns a discrete probability distribution on the edges of the graph. This allows one to apply GCNs not only in scenarios where the given graph is incomplete or corrupted but also in those where a graph is not available. We conduct a series of experiments that analyze the behavior of the proposed method and demonstrate that it outperforms related methods by a significant margin.

Graph convolutional networks (GCNs) have been successfully applied in node classification tasks of network mining. However, most of these models based on neighborhood aggregation are usually shallow and lack the "graph pooling" mechanism, which prevents the model from obtaining adequate global information. In order to increase the receptive field, we propose a novel deep Hierarchical Graph Convolutional Network (H-GCN) for semi-supervised node classification. H-GCN first repeatedly aggregates structurally similar nodes to hyper-nodes and then refines the coarsened graph to the original to restore the representation for each node. Instead of merely aggregating one- or two-hop neighborhood information, the proposed coarsening procedure enlarges the receptive field for each node, hence more global information can be learned. Comprehensive experiments conducted on public datasets demonstrate the effectiveness of the proposed method over the state-of-art methods. Notably, our model gains substantial improvements when only a few labeled samples are provided.

Graphs, which describe pairwise relations between objects, are essential representations of many real-world data such as social networks. In recent years, graph neural networks, which extend the neural network models to graph data, have attracted increasing attention. Graph neural networks have been applied to advance many different graph related tasks such as reasoning dynamics of the physical system, graph classification, and node classification. Most of the existing graph neural network models have been designed for static graphs, while many real-world graphs are inherently dynamic. For example, social networks are naturally evolving as new users joining and new relations being created. Current graph neural network models cannot utilize the dynamic information in dynamic graphs. However, the dynamic information has been proven to enhance the performance of many graph analytical tasks such as community detection and link prediction. Hence, it is necessary to design dedicated graph neural networks for dynamic graphs. In this paper, we propose DGNN, a new {\bf D}ynamic {\bf G}raph {\bf N}eural {\bf N}etwork model, which can model the dynamic information as the graph evolving. In particular, the proposed framework can keep updating node information by capturing the sequential information of edges, the time intervals between edges and information propagation coherently. Experimental results on various dynamic graphs demonstrate the effectiveness of the proposed framework.

Traditional methods for link prediction can be categorized into three main types: graph structure feature-based, latent feature-based, and explicit feature-based. Graph structure feature methods leverage some handcrafted node proximity scores, e.g., common neighbors, to estimate the likelihood of links. Latent feature methods rely on factorizing networks' matrix representations to learn an embedding for each node. Explicit feature methods train a machine learning model on two nodes' explicit attributes. Each of the three types of methods has its unique merits. In this paper, we propose SEAL (learning from Subgraphs, Embeddings, and Attributes for Link prediction), a new framework for link prediction which combines the power of all the three types into a single graph neural network (GNN). GNN is a new type of neural network which directly accepts graphs as input and outputs their labels. In SEAL, the input to the GNN is a local subgraph around each target link. We prove theoretically that our local subgraphs also reserve a great deal of high-order graph structure features related to link existence. Another key feature is that our GNN can naturally incorporate latent features and explicit features. It is achieved by concatenating node embeddings (latent features) and node attributes (explicit features) in the node information matrix for each subgraph, thus combining the three types of features to enhance GNN learning. Through extensive experiments, SEAL shows unprecedentedly strong performance against a wide range of baseline methods, including various link prediction heuristics and network embedding methods.