The task of inferring the missing links in a graph based on its current structure is referred to as link prediction. Link prediction methods that are based on pairwise node similarity are well-established approaches in the literature. They show good prediction performance in many real-world graphs though they are heuristics and lack of universal applicability. On the other hand, the success of neural networks for classification tasks in various domains leads researchers to study them in graphs. When a neural network can operate directly on the graph, then it is termed as the graph neural network (GNN). GNN is able to learn hidden features from graphs which can be used for link prediction task in graphs. Link predictions based on GNNs have gained much attention of researchers due to their convincing high performance in many real-world graphs. This appraisal paper studies some similarity and GNN-based link prediction approaches in the domain of homogeneous graphs that consists of a single type of (attributed) nodes and single type of pairwise links. We evaluate the studied approaches against several benchmark graphs with different properties from various domains.
Graph neural networks (GNNs) learn node representations by passing and aggregating messages between neighboring nodes. GNNs have been applied successfully in several application domains and achieved promising performance. However, GNNs could be vulnerable to structural noise because of the message passing mechanism where noise may be propagated through the entire graph. Although a series of robust GNNs have been proposed, they are evaluated with different structural noises, and it lacks a systematic comparison with consistent settings. In this work, we conduct a comprehensive and systematical …
Graz University of Technology（格拉茨工业大学）；Know Center GmbH（知识中心有限公司）；RWTH Aachen（亚琛工业大学）；GESIS - Leibniz Institute for the Social Sciences（GESIS-莱布尼茨社会科学研究所）
Recent work has shown that graph neural networks (GNNs) are vulnerable to adversarial attacks on graph data. Common attack approaches are typically informed, i.e. they have access to information about node attributes such as labels and feature vectors. In this work, we study adversarial attacks that are uninformed, where an attacker only has access to the graph structure, but no information about node attributes. Here the attacker aims to exploit structural knowledge and assumptions, which GNN models make about graph data. In particular, literature has shown that structural node centrality and…
Graph Neural Networks (GNNs) achieve state-of-the-art performance on graph-structured data across numerous domains. Their underlying ability to represent nodes as summaries of their vicinities has proven effective for homophilous graphs in particular, in which same-type nodes tend to connect. On heterophilous graphs, in which different-type nodes are likely connected, GNNs perform less consistently, as neighborhood information might be less representative or even misleading. On the other hand, GNN performance is not inferior on all heterophilous graphs, and there is a lack of understanding of …
Graph Neural Networks (GNNs), which generalize the deep neural networks to graph-structured data, have achieved great success in modeling graphs. However, as an extension of deep learning for graphs, GNNs lack explainability, which largely limits their adoption in scenarios that demand the transparency of models. Though many efforts are taken to improve the explainability of deep learning, they mainly focus on i.i.d data, which cannot be directly applied to explain the predictions of GNNs because GNNs utilize both node features and graph topology to make predictions. There are only very few wo…
American International University-Bangladesh (AIUB)（孟加拉国美国国际大学（AIUB））
Fake news on social media is increasingly regarded as one of the most concerning issues. Low cost, simple accessibility via social platforms, and a plethora of low-budget online news sources are some of the factors that contribute to the spread of false news. Most of the existing fake news detection algorithms are solely focused on the news content only but engaged users prior posts or social activities provide a wealth of information about their views on news and have significant ability to improve fake news identification. Graph Neural Networks are a form of deep learning approach that condu…
Leibniz University Hannover（汉诺威莱布尼茨大学）；Fudan University（复旦大学）；Microsoft Research（微软研究院）
Networks are ubiquitous in the real world. Link prediction, as one of the key problems for network-structured data, aims to predict whether there exists a link between two nodes. The traditional approaches are based on the explicit similarity computation between the compact node representation by embedding each node into a low-dimensional space. In order to efficiently handle the intensive similarity computation in link prediction, the hashing technique has been successfully used to produce the node representation in the Hamming space. However, the hashing-based link prediction algorithms face…
Michigan State University（密歇根州立大学）；Vanderbilt University（范德堡大学）；TAL Education Group（好未来教育集团）
Graph Neural Networks (GNNs) have achieved tremendous success in various real-world applications due to their strong ability in graph representation learning. GNNs explore the graph structure and node features by aggregating and transforming information within node neighborhoods. However, through theoretical and empirical analysis, we reveal that the aggregation process of GNNs tends to destroy node similarity in the original feature space. There are many scenarios where node similarity plays a crucial role. Thus, it has motivated the proposed framework SimP-GCN that can effectively and effici…
Dynamic Graph with Similarity-Aware Attention Graph Neural Network for Recommender Systems
Department of Computer Science and Engineering（计算机科学与工程系）；SRM University Andhra Pradesh（安得拉邦SRM大学）；Mangalagiri, Andhra Pradesh 522502, India（安得拉邦马加拉加里522502, 印度）
Explaining the Explainers in Graph Neural Networks: a Comparative Study
University of Trento（特伦托大学）；Fondazione Bruno Kessler（布鲁诺·凯塞勒基金会）；University of Venice（威尼斯大学）；CNRS, Centre de Physique Theorique（国家科学研究中心，理论物理中心）；University of Cambridge（剑桥大学）
Amazon Science（亚马逊科学）；IBM Research（IBM研究院）；Indian Institute of Science（印度科学院）
Graph neural networks (GNNs) are able to achieve promising performance on multiple graph downstream tasks such as node classification and link prediction. Comparatively lesser work has been done to design GNNs which can operate directly for community detection on graphs. Traditionally, GNNs are trained on a semi-supervised or self-supervised loss function and then clustering algorithms are applied to detect communities. However, such decoupled approaches are inherently sub-optimal. Designing an unsupervised loss function to train a GNN and extract communities in an integrated manner is a funda…
University of Illinois at Chicago（伊利诺伊大学芝加哥分校）；Beihang University（北京航空航天大学）；Lehigh University（理海大学）
Mining Electronic Health Records (EHRs) becomes a promising topic because of the rich information they contain. By learning from EHRs, machine learning models can be built to help human experts to make medical decisions and thus improve healthcare quality. Recently, many models based on sequential or graph models are proposed to achieve this goal. EHRs contain multiple entities and relations and can be viewed as a heterogeneous graph. However, previous studies ignore the heterogeneity in EHRs. On the other hand, current heterogeneous graph neural networks cannot be simply used on an EHR graph …
In recent years, Graph Neural Network (GNN) has bloomly progressed for its power in processing graph-based data. Most GNNs follow a message passing scheme, and their expressive power is mathematically limited by the discriminative ability of the Weisfeiler-Lehman (WL) test. Following Tinhofer's research on compact graphs, we propose a variation of the message passing scheme, called the Weisfeiler-Lehman-Tinhofer GNN (WLT-GNN), that theoretically breaks through the limitation of the WL test. In addition, we conduct comparative experiments and ablation studies on several well-known datasets. The…
The ability to compute similarity scores between graphs based on metrics such as Graph Edit Distance (GED) is important in many real-world applications. 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 embeds two graph…
Graph neural networks have emerged as a promising approach for the analysis of non-Euclidean data such as meshes. In medical imaging, mesh-like data plays an important role for modelling anatomical structures, and shape classification can be used in computer aided diagnosis and disease detection. However, with a plethora of options, the best architectural choices for medical shape analysis using GNNs remain unclear. We conduct a comparative analysis to provide practitioners with an overview of the current state-of-the-art in geometric deep learning for shape classification in neuroimaging. Usi…
Explaining Graph Neural Networks for Node Similarity on Graphs
Vrije Universiteit Amsterdam（瓦赫宁根大学阿姆斯特丹）；Bosch Center for Artificial Intelligence（博世人工智能中心）；Abo Akademi University（阿博阿卡迪米大学）；Elsevier discovery lab（埃斯勒弗发现实验室）；University of Amsterdam（阿姆斯特丹大学）
Graph Neural Networks (GNNs) extend basic Neural Networks (NNs) by using the graph structures based on the relational inductive bias (homophily assumption). Though GNNs are believed to outperform NNs in real-world tasks, performance advantages of GNNs over graph-agnostic NNs seem not generally satisfactory. Heterophily has been considered as a main cause and numerous works have been put forward to address it. In this paper, we first show that not all cases of heterophily are harmful for GNNs with aggregation operation. Then, we propose new metrics based on a similarity matrix which considers t…
Recent research on graph neural network (GNN) models successfully applied GNNs to classical graph algorithms and combinatorial optimisation problems. This has numerous benefits, such as allowing applications of algorithms when preconditions are not satisfied, or reusing learned models when sufficient training data is not available or can't be generated. Unfortunately, a key hindrance of these approaches is their lack of explainability, since GNNs are black-box models that cannot be interpreted directly. In this work, we address this limitation by applying existing work on concept-based explana…
Graph Neural Networks (GNNs) have achieved unprecedented success in identifying categorical labels of graphs. However, most existing graph classification problems with GNNs follow the protocol of balanced data splitting, which misaligns with many real-world scenarios in which some classes have much fewer labels than others. Directly training GNNs under this imbalanced scenario may lead to uninformative representations of graphs in minority classes, and compromise the overall classification performance, which signifies the importance of developing effective GNNs towards handling imbalanced grap…
Harvard T.H. Chan School of Public Health（哈佛大学陈曾熙公共卫生学院）；IQVIA（艾昆纬）；Harvard University（哈佛大学）；University of Illinois at Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）
Molecular interaction networks are powerful resources for the discovery. They are increasingly used with machine learning methods to predict biologically meaningful interactions. While deep learning on graphs has dramatically advanced the prediction prowess, current graph neural network (GNN) methods are optimized for prediction on the basis of direct similarity between interacting nodes. In biological networks, however, similarity between nodes that do not directly interact has proved incredibly useful in the last decade across a variety of interaction networks. Here, we present SkipGNN, a gr…
DeepMind（深度思维）；Mila（米拉研究所）；Université de Montréal（蒙特利尔大学）
Effectively and efficiently deploying graph neural networks (GNNs) at scale remains one of the most challenging aspects of graph representation learning. Many powerful solutions have only ever been validated on comparatively small datasets, often with counter-intuitive outcomes -- a barrier which has been broken by the Open Graph Benchmark Large-Scale Challenge (OGB-LSC). We entered the OGB-LSC with two large-scale GNNs: a deep transductive node classifier powered by bootstrapping, and a very deep (up to 50-layer) inductive graph regressor regularised by denoising objectives. Our models achiev…
University of Illinois at Chicago（伊利诺伊大学芝加哥分校）；Beijing University of Posts and Telecommunications（北京邮电大学）；Beihang University（北京航空航天大学）
Graph Neural Networks (GNNs) have been widely applied to fraud detection problems in recent years, revealing the suspiciousness of nodes by aggregating their neighborhood information via different relations. However, few prior works have noticed the camouflage behavior of fraudsters, which could hamper the performance of GNN-based fraud detectors during the aggregation process. In this paper, we introduce two types of camouflages based on recent empirical studies, i.e., the feature camouflage and the relation camouflage. Existing GNNs have not addressed these two camouflages, which results in …
In this paper we show that simple noise regularisation can be an effective way to address GNN oversmoothing. First we argue that regularisers addressing oversmoothing should both penalise node latent similarity and encourage meaningful node representations. From this observation we derive "Noisy Nodes", a simple technique in which we corrupt the input graph with noise, and add a noise correcting node-level loss. The diverse node level loss encourages latent node diversity, and the denoising objective encourages graph manifold learning. Our regulariser applies well-studied methods in simple, st…
The rapid evolution of Graph Neural Networks (GNNs) has led to a growing number of new architectures as well as novel applications. However, current research focuses on proposing and evaluating specific architectural designs of GNNs, as opposed to studying the more general design space of GNNs that consists of a Cartesian product of different design dimensions, such as the number of layers or the type of the aggregation function. Additionally, GNN designs are often specialized to a single task, yet few efforts have been made to understand how to quickly find the best GNN design for a novel tas…
Tsinghua University（清华大学）；Tencent AI Lab（腾讯人工智能实验室）
Graph instance contrastive learning has been proved as an effective task for Graph Neural Network (GNN) pre-training. However, one key issue may seriously impede the representative power in existing works: Positive instances created by current methods often miss crucial information of graphs or even yield illegal instances (such as non-chemically-aware graphs in molecular generation). To remedy this issue, we propose to select positive graph instances directly from existing graphs in the training set, which ultimately maintains the legality and similarity to the target graphs. Our selection is…
University of Pennsylvania（宾夕法尼亚大学）；Duke University（杜克大学）
We introduce an architecture for processing signals supported on hypergraphs via graph neural networks (GNNs), which we call a Hyper-graph Expansion Neural Network (HENN), and provide the first bounds on the stability and transferability error of a hypergraph signal processing model. To do so, we provide a framework for bounding the stability and transferability error of GNNs across arbitrary graphs via spectral similarity. By bounding the difference between two graph shift operators (GSOs) in the positive semi-definite sense via their eigenvalue spectrum, we show that this error depends only …
Hierarchy-Aware Neural Subgraph Matching with Enhanced Similarity Measure
College of Computer Science and Technology, National University of Defense Technology（计算机科学与技术学院，国防科技大学）；College of Information and Communication, National University of Defense Technology（信息与通信学院，国防科技大学）
One of the key problems of GNNs is how to describe the importance of neighbor nodes in the aggregation process for learning node representations. A class of GNNs solves this problem by learning implicit weights to represent the importance of neighbor nodes, which we call implicit GNNs such as Graph Attention Network. The basic idea of implicit GNNs is to introduce graph information with special properties followed by Learnable Transformation Structures (LTS) which encode the importance of neighbor nodes via a data-driven way. In this paper, we argue that LTS makes the special properties of gra…
GNNX-BENCH: Unravelling the Utility of Perturbation-based GNN Explainers through In-depth Benchmarking
University of California Santa Barbara（加州大学圣巴巴拉分校）；Indian Institute of Technology Delhi（印度理工学院德里分校）；Rice University（莱斯大学）；University of Illinois Chicago（芝加哥大学伊利诺伊分校）
Graph Similarity Regularized Softmax for Semi-Supervised Node Classification
School of Mathematics and Physics, North China Electric Power University（华北电力大学数理学院）；School of Mathematical Sciences, Beijing Normal University（北京师范大学数学科学学院）
A Comprehensive Survey of Dynamic Graph Neural Networks: Models, Frameworks, Benchmarks, Experiments and Challenges
Zhejiang University（浙江大学）；Hangzhou High-Tech Zone (Binjiang) Institute of Blockchain and Data Security（杭州高新区（滨江）区块链与数据安全研究院）；Shanghai Institute for Advanced Study, Zhejiang University（浙江大学上海高等研究院）
Nanjing University of Posts and Telecommunications（南京邮电大学）；Nanjing Normal University（南京师范大学）
Graph neural networks (GNNs) have been widely applied to numerous fields. A recent work which combines layered structure and residual connection proposes an improved deep architecture to extend CAmouflage-REsistant GNN (CARE-GNN) to deep models named as Residual Layered CARE-GNN (RLC-GNN), which forms self-correcting and incremental learning mechanism, and achieves significant performance improvements on fraud detection task. However, we spot three issues of RLC-GNN, which are the usage of neighboring information reaching limitation, the training difficulty which is inherent problem to deep mo…
Microsoft Research Asia（微软亚洲研究院）；Beijing University of Technology（北京工业大学）；Peking University（北京大学）；Northeastern University（东北大学）
Graph Neural Networks (GNNs) are widely used on a variety of graph-based machine learning tasks. For node-level tasks, GNNs have strong power to model the homophily property of graphs (i.e., connected nodes are more similar) while their ability to capture the heterophily property is often doubtful. This is partially caused by the design of the feature transformation with the same kernel for the nodes in the same hop and the followed aggregation operator. One kernel cannot model the similarity and the dissimilarity (i.e., the positive and negative correlation) between node features simultaneous…
Graph Neural Networks for Heart Failure Prediction on an EHR-Based Patient Similarity Graph
Institute of Informatics, Universidade Federal do Rio Grande do Sul (UFRGS)（信息学院，巴西联邦大学里约格兰德杜斯圣路易斯分校）；School of Information Technology, Halmstad University（信息科技学院，哈姆斯塔德大学）；Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA)（生物信息学核心，波尔图阿莱格雷医院）
Hefei University of Technology（合肥工业大学）；Institute of Automation, Chinese Academy of Sciences（中国科学院自动化研究所）；University of Chinese Academy of Sciences（中国科学院大学）
In this paper, we present GRecX, an open-source TensorFlow framework for benchmarking GNN-based recommendation models in an efficient and unified way. GRecX consists of core libraries for building GNN-based recommendation benchmarks, as well as the implementations of popular GNN-based recommendation models. The core libraries provide essential components for building efficient and unified benchmarks, including FastMetrics (efficient metrics computation libraries), VectorSearch (efficient similarity search libraries for dense vectors), BatchEval (efficient mini-batch evaluation libraries), and …
