Despite the enormous success of graph neural networks (GNNs), most existing GNNs can only be applicable to undirected graphs where relationships among connected nodes are two-way symmetric (i.e., information can be passed back and forth). However, there is a vast amount of applications where the information flow is asymmetric, leading to directed graphs where information can only be passed in one direction. For example, a directed edge indicates that the information can only be conveyed forwardly from the start node to the end node, but not backwardly. To accommodate such an asymmetric structure of directed graphs within the framework of GNNs, we propose a simple yet remarkably effective framework for directed graph analysis to incorporate such one-way information passing. We define an incoming embedding and an outgoing embedding for each node to model its sending and receiving features respectively. We further develop two steps in our directed GNN model with the first one to aggregate/update the incoming features of nodes and the second one to aggregate/update the outgoing features. By imposing the two roles for each node, the likelihood of a directed edge can be calculated based on the outgoing embedding of the start node and the incoming embedding of the end node. The log-likelihood of all edges plays a natural role of regularization for the proposed model, which can alleviate the over-smoothing problem of the deep GNNs. Extensive experiments on multiple real-world directed graphs demonstrate outstanding performances of the proposed model in both node-level and graph-level tasks.
Recent advancements in Graph Neural Networks have led to state-of-the-art performance on graph representation learning. However, the majority of existing works process directed graphs by symmetrization, which causes loss of directional information. To address this issue, we introduce the magnetic Laplacian, a discrete Schr\"odinger operator with magnetic field, which preserves edge directionality by encoding it into a complex phase with an electric charge parameter. By adopting a truncated variant of PageRank named Linear- Rank, we design and build a low-pass filter for homogeneous graphs and a high-pass filter for heterogeneous graphs. In this work, we propose a complex-valued graph convolutional network named Magnetic Graph Convolutional network (MGC). With the corresponding complex-valued techniques, we ensure our model will be degenerated into real-valued when the charge parameter is in specific values. We test our model on several graph datasets including directed homogeneous and heterogeneous graphs. The experimental results demonstrate that MGC is fast, powerful, and widely applicable.
Graph neural network (GNN) has achieved great success on graph representation learning. Challenged by large scale private data collected from user-side, GNN may not be able to reflect the excellent performance, without rich features and complete adjacent relationships. Addressing the problem, vertical federated learning (VFL) is proposed to implement local data protection through training a global model collaboratively. Consequently, for graph-structured data, it is a natural idea to construct a GNN based VFL framework, denoted as GVFL. However, GNN has been proved vulnerable to adversarial attacks. Whether the vulnerability will be brought into the GVFL has not been studied. This is the first study of adversarial attacks on GVFL. A novel adversarial attack method is proposed, named Graph-Fraudster. It generates adversarial perturbations based on the noise-added global node embeddings via the privacy leakage and the gradient of pairwise node. Specifically, first, Graph-Fraudster steals the global node embeddings and sets up a shadow model of the server for the attack generator. Second, noise is added into node embeddings to confuse the shadow model. At last, the gradient of pairwise node is used to generate attacks with the guidance of noise-added node embeddings. Extensive experiments on five benchmark datasets demonstrate that Graph-Fraudster achieves the state-of-the-art attack performance compared with baselines in different GNN based GVFLs. Furthermore, Graph-Fraudster can remain a threat to GVFL even if two possible defense mechanisms are applied. Additionally, some suggestions are put forward for the future work to improve the robustness of GVFL. The code and datasets can be downloaded at https://github.com/hgh0545/Graph-Fraudster.
Graph Representation Learning (GRL) methods opened new avenues for addressing complex, real-world problems represented by graphs. However, many graphs used in these applications comprise millions of nodes and billions of edges and are beyond the capabilities of current methods and software implementations. We present GRAPE, a software resource for graph processing and embedding that can scale with big graphs by using specialized and smart data structures, algorithms, and a fast parallel implementation of random walk-based methods. Compared with state-of-the-art software resources, GRAPE shows an improvement of orders of magnitude in empirical space and time complexity, as well as a competitive edge and node label prediction performance. GRAPE comprises about 1.7 million well-documented lines of Python and Rust code and provides 69 node embedding methods, 25 inference models, a collection of efficient graph processing utilities and over 80,000 graphs from the literature and other sources. Standardized interfaces allow seamless integration of third-party libraries, while ready-to-use and modular pipelines permit an easy-to-use evaluation of GRL methods, therefore also positioning GRAPE as a software resource to perform a fair comparison between methods and libraries for graph processing and embedding.
Graph Convolutional Networks (GCNs) are a popular method from graph representation learning that have proved effective for tasks like node classification tasks. Although typical GCN models focus on classifying nodes within a static graph, several recent variants propose node classification in dynamic graphs whose topologies and node attributes change over time, e.g., social networks with dynamic relationships, or literature citation networks with changing co-authorships. These works, however, do not fully address the challenge of flexibly assigning different importance to snapshots of the graph at different times, which depending on the graph dynamics may have more or less predictive power on the labels. We address this challenge by proposing a new method, GCN-SE, that attaches a set of learnable attention weights to graph snapshots at different times, inspired by Squeeze and Excitation Net (SE-Net). We show that GCN-SE outperforms previously proposed node classification methods on a variety of graph datasets. To verify the effectiveness of the attention weight in determining the importance of different graph snapshots, we adapt perturbation-based methods from the field of explainable machine learning to graphical settings and evaluate the correlation between the attention weights learned by GCN-SE and the importance of different snapshots over time. These experiments demonstrate that GCN-SE can in fact identify different snapshots' predictive power for dynamic node classification.
Graph Representation Learning (GRL) is an upcoming and promising area in recommendation systems. In this paper, we revisit the Singular Value Decomposition (SVD) of adjacency matrix for embedding generation of users and items and use a two-layer neural network on top of these embeddings to learn relevance between user-item pairs. Inspired by the success of higher-order learning in GRL, we further propose an extension of this method to include two-hop neighbors for SVD through the second order of the adjacency matrix and demonstrate improved performance compared with the simple SVD method which only uses one-hop neighbors. Empirical validation on three publicly available datasets of recommendation system demonstrates that the proposed methods, despite being simple, beat many state-of-the-art methods and for two of three datasets beats all of them up to a margin of 10%. Through our research, we want to shed light on the effectiveness of matrix factorization approaches, specifically SVD, in the deep learning era and show that these methods still contribute as important baselines in recommendation systems.
In recent years, algebraic topology and its modern development, the theory of persistent homology, has shown great potential in graph representation learning. In this paper, based on the mathematics of algebraic topology, we propose a novel solution for inductive relation prediction, an important learning task for knowledge graph completion. To predict the relation between two entities, one can use the existence of rules, namely a sequence of relations. Previous works view rules as paths and primarily focus on the searching of paths between entities. The space of rules is huge, and one has to sacrifice either efficiency or accuracy. In this paper, we consider rules as cycles and show that the space of cycles has a unique structure based on the mathematics of algebraic topology. By exploring the linear structure of the cycle space, we can improve the searching efficiency of rules. We propose to collect cycle bases that span the space of cycles. We build a novel GNN framework on the collected cycles to learn the representations of cycles, and to predict the existence/non-existence of a relation. Our method achieves state-of-the-art performance on benchmarks.
Learning good representations on multi-relational graphs is essential to knowledge base completion (KBC). In this paper, we propose a new self-supervised training objective for multi-relational graph representation learning, via simply incorporating relation prediction into the commonly used 1vsAll objective. The new training objective contains not only terms for predicting the subject and object of a given triple, but also a term for predicting the relation type. We analyse how this new objective impacts multi-relational learning in KBC: experiments on a variety of datasets and models show that relation prediction can significantly improve entity ranking, the most widely used evaluation task for KBC, yielding a 6.1% increase in MRR and 9.9% increase in Hits@1 on FB15k-237 as well as a 3.1% increase in MRR and 3.4% in Hits@1 on Aristo-v4. Moreover, we observe that the proposed objective is especially effective on highly multi-relational datasets, i.e. datasets with a large number of predicates, and generates better representations when larger embedding sizes are used.
We consider the problem of binary power control, or link scheduling, in wireless interference networks, where the power control policy is trained using graph representation learning. We leverage the interference graph of the wireless network as an underlying topology for a graph neural network (GNN) backbone, which converts the channel matrix to a set of node embeddings for all transmitter-receiver pairs. We show how the node embeddings can be trained in several ways, including via supervised, unsupervised, and self-supervised learning, and we compare the impact of different supervision levels on the performance of these methods in terms of the system-level throughput, convergence behavior, sample efficiency, and generalization capability.
In this paper, we introduce a graph representation learning architecture for spatial image steganalysis, which is motivated by the assumption that steganographic modifications unavoidably distort the statistical characteristics of the hidden graph features derived from cover images. In the detailed architecture, we translate each image to a graph, where nodes represent the patches of the image and edges indicate the local relationships between the patches. Each node is associated with a feature vector determined from the corresponding patch by a shallow convolutional neural network (CNN) structure. By feeding the graph to an attention network, the discriminative features can be learned for efficient steganalysis. Experiments indicate that the reported architecture achieves a competitive performance compared to the benchmark CNN model, which has shown the potential of graph learning for steganalysis.
A central goal in deep learning is to learn compact representations of features at every layer of a neural network, which is useful for both unsupervised representation learning and structured network pruning. While there is a growing body of work in structured pruning, current state-of-the-art methods suffer from two key limitations: (i) instability during training, and (ii) need for an additional step of fine-tuning, which is resource-intensive. At the core of these limitations is the lack of a systematic approach that jointly prunes and refines weights during training in a single stage, and does not require any fine-tuning upon convergence to achieve state-of-the-art performance. We present a novel single-stage structured pruning method termed DiscriminAtive Masking (DAM). The key intuition behind DAM is to discriminatively prefer some of the neurons to be refined during the training process, while gradually masking out other neurons. We show that our proposed DAM approach has remarkably good performance over various applications, including dimensionality reduction, recommendation system, graph representation learning, and structured pruning for image classification. We also theoretically show that the learning objective of DAM is directly related to minimizing the L0 norm of the masking layer.
Graph neural networks (GNNs) have limited expressive power, failing to represent many graph classes correctly. While more expressive graph representation learning (GRL) alternatives can distinguish some of these classes, they are significantly harder to implement, may not scale well, and have not been shown to outperform well-tuned GNNs in real-world tasks. Thus, devising simple, scalable, and expressive GRL architectures that also achieve real-world improvements remains an open challenge. In this work, we show the extent to which graph reconstruction -- reconstructing a graph from its subgraphs -- can mitigate the theoretical and practical problems currently faced by GRL architectures. First, we leverage graph reconstruction to build two new classes of expressive graph representations. Secondly, we show how graph reconstruction boosts the expressive power of any GNN architecture while being a (provably) powerful inductive bias for invariances to vertex removals. Empirically, we show how reconstruction can boost GNN's expressive power -- while maintaining its invariance to permutations of the vertices -- by solving seven graph property tasks not solvable by the original GNN. Further, we demonstrate how it boosts state-of-the-art GNN's performance across nine real-world benchmark datasets.
The microstructure is an essential part of materials, storing the genes of materials and having a decisive influence on materials' physical and chemical properties. The material genetic engineering program aims to establish the relationship between material composition/process, organization, and performance to realize the reverse design of materials, thereby accelerating the research and development of new materials. However, tissue analysis methods of materials science, such as metallographic analysis, XRD analysis, and EBSD analysis, cannot directly establish a complete quantitative relationship between tissue structure and performance. Therefore, this paper proposes a novel data-knowledge-driven organization representation and performance prediction method to obtain a quantitative structure-performance relationship. First, a knowledge graph based on EBSD is constructed to describe the material's mesoscopic microstructure. Then a graph representation learning network based on graph attention is constructed, and the EBSD organizational knowledge graph is input into the network to obtain graph-level feature embedding. Finally, the graph-level feature embedding is input to a graph feature mapping network to obtain the material's mechanical properties. The experimental results show that our method is superior to traditional machine learning and machine vision methods.
Graph neural networks have emerged as a powerful model for graph representation learning to undertake graph-level prediction tasks. Various graph pooling methods have been developed to coarsen an input graph into a succinct graph-level representation through aggregating node embeddings obtained via graph convolution. However, most graph pooling methods are heavily node-centric and are unable to fully leverage the crucial information contained in global graph structure. This paper presents a cross-view graph pooling (Co-Pooling) method to better exploit crucial graph structure information. The proposed Co-Pooling fuses pooled representations learnt from both node view and edge view. Through cross-view interaction, edge-view pooling and node-view pooling seamlessly reinforce each other to learn more informative graph-level representations. Co-Pooling has the advantage of handling various graphs with different types of node attributes. Extensive experiments on a total of 15 graph benchmark datasets validate the effectiveness of our proposed method, demonstrating its superior performance over state-of-the-art pooling methods on both graph classification and graph regression tasks.
Contrastive learning has been widely applied to graph representation learning, where the view generators play a vital role in generating effective contrastive samples. Most of the existing contrastive learning methods employ pre-defined view generation methods, e.g., node drop or edge perturbation, which usually cannot adapt to input data or preserve the original semantic structures well. To address this issue, we propose a novel framework named Automated Graph Contrastive Learning (AutoGCL) in this paper. Specifically, AutoGCL employs a set of learnable graph view generators orchestrated by an auto augmentation strategy, where every graph view generator learns a probability distribution of graphs conditioned by the input. While the graph view generators in AutoGCL preserve the most representative structures of the original graph in generation of every contrastive sample, the auto augmentation learns policies to introduce adequate augmentation variances in the whole contrastive learning procedure. Furthermore, AutoGCL adopts a joint training strategy to train the learnable view generators, the graph encoder, and the classifier in an end-to-end manner, resulting in topological heterogeneity yet semantic similarity in the generation of contrastive samples. Extensive experiments on semi-supervised learning, unsupervised learning, and transfer learning demonstrate the superiority of our AutoGCL framework over the state-of-the-arts in graph contrastive learning. In addition, the visualization results further confirm that the learnable view generators can deliver more compact and semantically meaningful contrastive samples compared against the existing view generation methods.
Precisely defining the terminology is the first step in scientific communication. Developing neural text generation models for definition generation can circumvent the labor-intensity curation, further accelerating scientific discovery. Unfortunately, the lack of large-scale terminology definition dataset hinders the process toward definition generation. In this paper, we present a large-scale terminology definition dataset Graphine covering 2,010,648 terminology definition pairs, spanning 227 biomedical subdisciplines. Terminologies in each subdiscipline further form a directed acyclic graph, opening up new avenues for developing graph-aware text generation models. We then proposed a novel graph-aware definition generation model Graphex that integrates transformer with graph neural network. Our model outperforms existing text generation models by exploiting the graph structure of terminologies. We further demonstrated how Graphine can be used to evaluate pretrained language models, compare graph representation learning methods and predict sentence granularity. We envision Graphine to be a unique resource for definition generation and many other NLP tasks in biomedicine.
Graphs are powerful representations for relations among objects, which have attracted plenty of attention. A fundamental challenge for graph learning is how to train an effective Graph Neural Network (GNN) encoder without labels, which are expensive and time consuming to obtain. Contrastive Learning (CL) is one of the most popular paradigms to address this challenge, which trains GNNs by discriminating positive and negative node pairs. Despite the success of recent CL methods, there are still two under-explored problems. First, how to reduce the semantic error introduced by random topology based data augmentations. Traditional CL defines positive and negative node pairs via the node-level topological proximity, which is solely based on the graph topology regardless of the semantic information of node attributes, and thus some semantically similar nodes could be wrongly treated as negative pairs. Second, how to effectively model the multiplexity of the real-world graphs, where nodes are connected by various relations and each relation could form a homogeneous graph layer. To solve these problems, we propose a novel multiplex heterogeneous graph prototypical contrastive leaning (X-GOAL) framework to extract node embeddings. X-GOAL is comprised of two components: the GOAL framework, which learns node embeddings for each homogeneous graph layer, and an alignment regularization, which jointly models different layers by aligning layer-specific node embeddings. Specifically, the GOAL framework captures the node-level information by a succinct graph transformation technique, and captures the cluster-level information by pulling nodes within the same semantic cluster closer in the embedding space. The alignment regularization aligns embeddings across layers at both node and cluster levels. We evaluate X-GOAL on various real-world datasets and downstream tasks to demonstrate its effectiveness.
Graph Representation Learning (GRL) has become essential for modern graph data mining and learning tasks. GRL aims to capture the graph's structural information and exploit it in combination with node and edge attributes to compute low-dimensional representations. While Graph Neural Networks (GNNs) have been used in state-of-the-art GRL architectures, they have been shown to suffer from over smoothing when many GNN layers need to be stacked. In a different GRL approach, spectral methods based on graph filtering have emerged addressing over smoothing; however, up to now, they employ traditional neural networks that cannot efficiently exploit the structure of graph data. Motivated by this, we propose PointSpectrum, a spectral method that incorporates a set equivariant network to account for a graph's structure. PointSpectrum enhances the efficiency and expressiveness of spectral methods, while it outperforms or competes with state-of-the-art GRL methods. Overall, PointSpectrum addresses over smoothing by employing a graph filter and captures a graph's structure through set equivariance, lying on the intersection of GNNs and spectral methods. Our findings are promising for the benefits and applicability of this architectural shift for spectral methods and GRL.
As online service systems continue to grow in terms of complexity and volume, how service incidents are managed will significantly impact company revenue and user trust. Due to the cascading effect, cloud failures often come with an overwhelming number of incidents from dependent services and devices. To pursue efficient incident management, related incidents should be quickly aggregated to narrow down the problem scope. To this end, in this paper, we propose GRLIA, an incident aggregation framework based on graph representation learning over the cascading graph of cloud failures. A representation vector is learned for each unique type of incident in an unsupervised and unified manner, which is able to simultaneously encode the topological and temporal correlations among incidents. Thus, it can be easily employed for online incident aggregation. In particular, to learn the correlations more accurately, we try to recover the complete scope of failures' cascading impact by leveraging fine-grained system monitoring data, i.e., Key Performance Indicators (KPIs). The proposed framework is evaluated with real-world incident data collected from a large-scale online service system of Huawei Cloud. The experimental results demonstrate that GRLIA is effective and outperforms existing methods. Furthermore, our framework has been successfully deployed in industrial practice.
Travel-time prediction constitutes a task of high importance in transportation networks, with web mapping services like Google Maps regularly serving vast quantities of travel time queries from users and enterprises alike. Further, such a task requires accounting for complex spatiotemporal interactions (modelling both the topological properties of the road network and anticipating events -- such as rush hours -- that may occur in the future). Hence, it is an ideal target for graph representation learning at scale. Here we present a graph neural network estimator for estimated time of arrival (ETA) which we have deployed in production at Google Maps. While our main architecture consists of standard GNN building blocks, we further detail the usage of training schedule methods such as MetaGradients in order to make our model robust and production-ready. We also provide prescriptive studies: ablating on various architectural decisions and training regimes, and qualitative analyses on real-world situations where our model provides a competitive edge. Our GNN proved powerful when deployed, significantly reducing negative ETA outcomes in several regions compared to the previous production baseline (40+% in cities like Sydney).