Enhancing Graph Neural Networks with Edge Features Through Sequential Representation

Graph, as an important data representation, is ubiquitous in many real world applications ranging from social network analysis to biology. How to correctly and effectively learn and extract information from graph is essential for a large number of machine learning tasks. Graph embedding is a way to transform and encode the data structure in high dimensional and non-euclidean feature space to a low dimensional and structural space, which is easily exploited by other machine learning algorithms. We have witnessed a huge surge of such embedding methods, from statistical approaches to recent deep learning methods such as the graph convolutional networks (GCN). Deep learning approaches usually outperform the traditional methods in most graph learning benchmarks by building an end-to-end learning framework to optimize the loss function directly. However, most of the existing GCN methods can only perform convolution operations with node features, while ignoring the handy information in edge features, such as relations in knowledge graphs. To address this problem, we present CensNet, Convolution with Edge-Node Switching graph neural network, for learning tasks in graph-structured data with both node and edge features. CensNet is a general graph embedding framework, which embeds both nodes and edges to a latent feature space. By using line graph of the original undirected graph, the role of nodes and edges are switched, and two novel graph convolution operations are proposed for feature propagation. Experimental results on real-world academic citation networks and quantum chemistry graphs show that our approach achieves or matches the state-of-the-art performance in four graph learning tasks, including semi-supervised node classification, multi-task graph classification, graph regression, and link prediction.

We investigate works under the propagation-based fake news detection domain, which recently seeks to improve performance through the use of Graph Neural Networks (GNNs). Generally, existing works argue that using GNNs can give results superior to what was obtained using classic graph-based methods. We agree with this argument given that GNNs are capable of gaining superior performance by leveraging node features. But we argue that existing works haven't identified the fact that the expressivity of GNNs is limited and bounded by node features. Existing works do not acknowledge that, by utilizing GNNs, they implicitly assume node features are strongly correlated to node labels. There are evidence that node features that have been employed do not necessarily correlate to node label. Instead of having a profound theoretical motivation, they have empirically observed that focusing on nodes features with strong feature-label correlation can increase predictive capability. This is a sub-optimal approach to view this problem, in fact, we argue that finding node features based on correlation is not practical or effective. Our first contribution is shifting readers from a node-level view i.e correlating node features with labels, to a graph-level view. In the graph-level view, we exploit the relationship between graph isomorphism and GNNs' expressivity which can be utilized to well understand and interpret the relation between node features and GNNs' expressivity. We conduct a wide range of experiments on basis of both node-level view and graph-level view and found graph-level view is more interpretable and strongly matches with results. Further, we gained insights on node features that wouldn't be obtainable by a node-level view. In order to have a fair and comprehensive analysis of node features, we built a unified dataset that includes a wide range of node features. Our results indicate, as we improve model accuracy on basis of the graph level view, models' generalizability decreases. We provide our hypothesis for this performance trade-off on the basis of the graph-level view. Our results and insights call for a much broader discussion on whether any sort of filtering method is effective. So, we conclude our work by providing readers with possible solutions that can be helpful to find harmony between node features and GNNs' expressivity.

Graph neural networks(GNNs) have been developed to solve challenging resource allocation (RA) problems, which leads to hopeful results in small and simple communication networks. Due to the inevitable heterogeneity of modern networks, it motivated researchers to develop the heterogeneous graph neural networks (HetGNNs) model for the RA problem of heterogeneous networks. However, node features and edge features are usually ignored by the most extant deep models, limited the performance when the size of the hidden layer in the network is larger than that of the node and edge features. In this paper, the power control or beamforming (PC/BF) in heterogeneous device-to-device (D2D) networks is focused, and proposed a HetGNN for the issue. Extensive simulations show that the proposed approach, matching or even outperforming state-of-the-art learning-based benchmarks.

Recent studies have shown that the problems of cold processing and data sparsity in recommender systems can be well alleviated with the help of knowledge graph information. Meanwhile, since the information in recommender systems can be represented by graph data structure, graph neural network has great advantages in recommendatory system. Therefore, graph neural network can better mine the deep relationship between objects in the recommender systems which combines with information from knowledge graph. This paper reviews the application of graph neural network in knowledge graph aided recommendation systems. Specifically, this paper firstly sorts out the related knowledge of knowledge graph, recommendation system and graph neural network, including the cold processing and data sparsity, the structure of knowledge graph, and the basic modules of graph neural network. This paper also summarizes the methods such as KGAT and CKAN used in knowledge graph aided recommendation systems in recent years, and gives some discussion on the development of this field.

Graph Neural Networks (GNNs) have demonstrated significant success in various graph-related tasks. However, their performance is highly dependent on the availability of sufficient, class-balanced annotated data and an accurate graph structure. GNNs are vulnerable to substantial performance degradation when confronted with limited annotated samples, class imbalance, or noisy graph structures. First, a Dual GNN learning framework is introduced for semi-supervised node classification under limited supervision. The framework comprises two GNN-based node prediction modules: a primary module, which uses the input graph structure to induce standard node embeddings and predictions, and an auxiliary module, which leverages spectral clustering to construct a new graph structure and learn new node embeddings and predictions. These modules collaborate to enable end-to-end learning of discriminative node representations. Next, a graph augmentation method called Graph Dual Mixup (GDM) is proposed for graph classification with scarce labels. GDM employs a graph structural auto-encoder to learn structural embeddings, applying mixup in the learned structural embedding space to generate new graph structures. Additionally, mixup is applied to input node features, generating node features for new graph instances. Together, these generated node features and graph structures contribute new graphs that increase the size and diversity of the labeled dataset, improving classification performance. To enhance robustness against adversarial attacks on graph structures, an Efficient Low-Rank GNN is introduced. This approach learns robust low-rank sparse graph structures through a two-stage process. In the first stage, Singular Value Decomposition is used to estimate a low-rank approximation of the graph structure. This estimate is refined in the second stage by jointly learning a low-rank sparse graph structure alongside the GNN model, resulting in enhanced robustness. Finally, to address class-imbalanced node classification, a Unified GNN Learning (Uni-GNN) framework is proposed. Uni-GNN integrates structural and semantic connectivity representations to extend the propagation of embeddings to non-adjacent structural neighbors and semantically similar nodes, facilitating the diffusion of discriminative information. Additionally, it incorporates a balanced pseudo-label generation mechanism to improve the representations of minority classes. Comprehensive evaluations on benchmark datasets demonstrate that these methods outperform state-of-the-art approaches and hold significant potential for advancing GNN learning with limited supervision.

At present, the urban traffic system is faced with the problems of congestion and low efficiency, and the traditional methods have certain limitations when dealing with the complex urban road network. This paper aims to explore a new method of capacity Optimization of Road Networks in a Smart City environment and proposes a method based on a Graph Neural network, named “Smart City Road optimization Graph Neural Network” (SCRO-GNN). SCRO-GNN first collects and preprocesses multi-source data, including road network data, traffic flow, accident records, environmental factors, etc. The key node and edge features, including the number of lanes at the intersection, the traffic flow of the section, and the adjacency matrix of the road network are defined to characterize the structure of the road network. Then, the graph neural network model is constructed and trained to predict the traffic flow of different sections and evaluate the road capacity by using the graph structure of the road network. This paper tests the performance of SCRO-GNN on real road networks in multiple cities. The results show that, compared with the traditional traffic flow prediction model, SCRO-GNN can significantly improve the prediction accuracy, especially when dealing with the highly complex urban road network structure. Based on these predictions, the proposed optimization strategy performed well in reducing traffic congestion and improving the efficiency of road use. The research in this paper not only demonstrates the potential of graph neural networks in smart city road network optimization, but also provides a new direction for future traffic system research. The successful implementation of the SCRO-GNN approach is expected to provide more efficient and intelligent solutions for urban traffic management and planning.

Graph Neural Networks (GNNs) have achieved remarkable success in graph-related tasks by combining node features and graph topology elegantly. Most GNNs assume that the networks are homophilous, which is not always true in the real world, i.e., structure noise or disassortative graphs. Only a few works focus on generalizing graph neural networks to heterophilous or low homophilous networks, where connected nodes may have different labels. In this paper, we design a simple and effective Graph Structure Learning strategy based on Feature and Label consistency (GSLFL) to increase the homophilous level of networks for generalizing any existing GNNs to heterophilous networks. Specifically, we first introduce a method to learn graph structure based on node features and then modify the graph structure based on label consistency. Further, we combine the GSLFL with three existing GNNs to learn node representations and graph structure together. And we design a self-training method to iteratively train models and modify graph structure with pseudo-labels. Finally, our empirical results on 6 public networks with homophily or heterophily, and structure attacks show that our methods outperform the state-of-the-art methods in most cases.

Graph neural networks (GNNs) have recently gained much attention for node and graph classification tasks on graph-structured data. However, multiple recent works showed that an attacker can easily make GNNs predict incorrectly via perturbing the graph structure, i.e., adding or deleting edges in the graph. We aim to defend against such attacks via developing certifiably robust GNNs. Specifically, we prove the first certified robustness guarantee of any GNN for both node and graph classifications against structural perturbation. Moreover, we show that our certified robustness guarantee is tight. Our results are based on a recently proposed technique called randomized smoothing, which we extend to graph data. We also empirically evaluate our method for both node and graph classifications on multiple GNNs and multiple benchmark datasets. For instance, on the Cora dataset, Graph Convolutional Network with our randomized smoothing can achieve a certified accuracy of 0.49 when the attacker can arbitrarily add/delete at most 15 edges in the graph.

Graph neural networks (GNNs) with missing node features have recently received increasing interest. Such missing node features seriously hurt the performance of the existing GNNs. Some recent methods have been proposed to reconstruct the missing node features by the information propagation among nodes with known and unknown attributes. Although these methods have achieved superior performance, how to exactly exploit the complex data correlations among nodes to reconstruct missing node features is still a great challenge. To solve the above problem, we propose a self-supervised guided hypergraph feature propagation (SGHFP). Specifically, the feature hypergraph is first generated according to the node features with missing information. And then, the reconstructed node features produced by the previous iteration are fed to a two-layer GNNs to construct a pseudo-label hypergraph. Before each iteration, the constructed feature hypergraph and pseudo-label hypergraph are fused effectively, which can better preserve the higher-order data correlations among nodes. After then, we apply the fused hypergraph to the feature propagation for reconstructing missing features. Finally, the reconstructed node features by multi-iteration optimization are applied to the downstream semi-supervised classification task. Extensive experiments demonstrate that the proposed SGHFP outperforms the existing semi-supervised classification with missing node feature methods.

The automatic identification of the topology of power networks is important for the data-driven and situation-aware operation of power grids. Traditional methods of topology identification lack a data-tolerant mechanism, and the accuracy of their performance in terms of identification is thus affected by the quality of data. Topology identification is related to the link prediction problem. The graph neural network can be used to predict the state of unlabeled nodes (lines) through training on features of labeled nodes (lines) with fault tolerance. Inspired by the characteristics of the graph neural network, we applied it to topology identification in this study. We propose a method to identify the topology of a power network based on a knowledge graph and the graph neural network. Traditional knowledge graphs can quickly mine possible connections between entities and generate graph structure data, but in the case of errors or informational conflicts in the data, they cannot accurately determine whether the relationships between the entities really exist. The graph neural network can use data mining to determine whether a connection obtained between entities is based on their eigenvalues, and has a fault tolerance mechanism to adapt to errors and informational conflicts in the graph data, but needs the graph data as database. The combination of the knowledge graph and the graph neural network can compensate for the deficiency of the single knowledge graph method. We tested the proposed method by using the IEEE 118-bus system and a provincial network system. The results showed that our approach is feasible and highly fault tolerant. It can accurately identify network topology even in the presence of conflicting and missing measurement-related information.

Molecular graphs are one of the established representations for small molecules, and even steric or electronic information can be encoded as node and edge features. Naturally, graph neural networks have been intensively investigated to solve various chemical problems at molecular levels. However, it remains unclear how to encode relevant chemical information into graphs. We investigate this problem by proposing three models of graph neural networks with self-attention mechanisms at different levels to adaptively select relevant chemical information for each input. Using neural graph fingerprint (NFP) as a baseline, we introduce three types of attention mechanisms on the top of NFPs. Our experimental evaluations suggest that introducing these self-attention mechanisms contributes to not only improving the prediction accuracy but also providing quantitative interpretation using obtained attention coefficients.

Graphs help to define the relationships between entities in the data. These relationships, represented by edges, often provide additional context information which can be utilised to discover patterns in the data. Graph Neural Networks (GNNs) employ the inductive bias of the graph structure to learn and predict on various tasks. The primary operation of graph neural networks is the feature aggregation step performed over neighbours of the node based on the structure of the graph. In addition to its own features, for each hop, the node gets additional combined features from its neighbours. These aggregated features help define the similarity or dissimilarity of the nodes with respect to the labels and are useful for tasks like node classification. However, in real‐world data, features of neighbours at different hops may not correlate with the node's features. Thus, any indiscriminate feature aggregation by GNN might cause the addition of noisy features leading to degradation in model's performance. In this work, we show that selective aggregation of node features from various hops leads to better performance than default aggregation on the node classification task. Furthermore, we propose a Dual‐Net GNN architecture with a classifier model and a selector model. The classifier model trains over a subset of input node features to predict node labels while the selector model learns to provide optimal input subset to the classifier for the best performance. These two models are trained jointly to learn the best subset of features that give higher accuracy in node label predictions. With extensive experiments, we show that our proposed model outperforms both feature selection methods and state‐of‐the‐art GNN models with remarkable improvements up to 27.8%.

Real data collected from different applications that have additional topological structures and connection information are amenable to be represented as a weighted graph. Considering the node labeling problem, Graph Neural Networks (GNNs) is a powerful tool, which can mimic experts’ decision on node labeling. GNNs combine node features, connection patterns, and graph structure by using a neural network to embed node information and pass it through edges in the graph. We want to identify the patterns in the input data used by the GNN model to make a decision and examine if the model works as we desire. However, due to the complex data representation and non-linear transformations, explaining decisions made by GNNs is challenging. In this work, we propose new graph features’ explanation methods to identify the informative components and important node features. Besides, we propose a pipeline to identify the critical factors used for node classification. We use four datasets (two synthetic and two real) to validate our methods. Our results demonstrate that our explanation approach can mimic data patterns used for node classification by human interpretation and disentangle different features in the graphs. Furthermore, our explanation methods can be used for understanding data, debugging GNN models, and examine model decisions.

GNN-MgrPool: Enhanced graph neural networks with multi-granularity pooling for graph classification

Graph neural networks (GNNs) have known an increasing success recently, with many GNN variants achieving state-of-the-art results on node and graph classification tasks. The proposed GNNs, however, often implement complex node and graph embedding schemes, which makes it challenging to explain their performance. In this paper, we investigate the link between a GNN’s expressiveness, that is, its ability to map different graphs to different representations, and its generalization performance in a graph classification setting. In particular, we propose a principled experimental procedure where we (i) define a practical measure for expressiveness, (ii) introduce an expressiveness-based loss function that we use to train a simple yet practical GNN that is permutation-invariant, (iii) illustrate our procedure on benchmark graph classification problems and on an original real-world application. Our results reveal that expressiveness alone does not guarantee a better performance, and that a powerful GNN should be able to produce graph representations that are well separated with respect to the class of the corresponding graphs.