Graph representation learning has achieved great success in many areas, including e-commerce, chemistry, biology, etc. However, the fundamental problem of choosing the appropriate dimension of node embedding for a given graph still remains unsolved. The commonly used strategies for Node Embedding Dimension Selection (NEDS) based on grid search or empirical knowledge suffer from heavy computation and poor model performance. In this paper, we revisit NEDS from the perspective of minimum entropy principle. Subsequently, we propose a novel Minimum Graph Entropy (MinGE) algorithm for NEDS with graph data. To be specific, MinGE considers both feature entropy and structure entropy on graphs, which are carefully designed according to the characteristics of the rich information in them. The feature entropy, which assumes the embeddings of adjacent nodes to be more similar, connects node features and link topology on graphs. The structure entropy takes the normalized degree as basic unit to further measure the higher-order structure of graphs. Based on them, we design MinGE to directly calculate the ideal node embedding dimension for any graph. Finally, comprehensive experiments with popular Graph Neural Networks (GNNs) on benchmark datasets demonstrate the effectiveness and generalizability of our proposed MinGE.
The task of natural language table retrieval (NLTR) seeks to retrieve semantically relevant tables based on natural language queries. Existing learning systems for this task often treat tables as plain text based on the assumption that tables are structured as dataframes. However, tables can have complex layouts which indicate diverse dependencies between subtable structures, such as nested headers. As a result, queries may refer to different spans of relevant content that is distributed across these structures. Moreover, such systems fail to generalize to novel scenarios beyond those seen in the training set. Prior methods are still distant from a generalizable solution to the NLTR problem, as they fall short in handling complex table layouts or queries over multiple granularities. To address these issues, we propose Graph-based Table Retrieval (GTR), a generalizable NLTR framework with multi-granular graph representation learning. In our framework, a table is first converted into a tabular graph, with cell nodes, row nodes and column nodes to capture content at different granularities. Then the tabular graph is input to a Graph Transformer model that can capture both table cell content and the layout structures. To enhance the robustness and generalizability of the model, we further incorporate a self-supervised pre-training task based on graph-context matching. Experimental results on two benchmarks show that our method leads to significant improvements over the current state-of-the-art systems. Further experiments demonstrate promising performance of our method on cross-dataset generalization, and enhanced capability of handling complex tables and fulfilling diverse query intents. Code and data are available at https://github.com/FeiWang96/GTR.
Graph pooling that summaries the information in a large graph into a compact form is essential in hierarchical graph representation learning. Existing graph pooling methods either suffer from high computational complexity or cannot capture the global dependencies between graphs before and after pooling. To address the problems of existing graph pooling methods, we propose Coarsened Graph Infomax Pooling (CGIPool) that maximizes the mutual information between the input and the coarsened graph of each pooling layer to preserve graph-level dependencies. To achieve mutual information neural maximization, we apply contrastive learning and propose a self-attention-based algorithm for learning positive and negative samples. Extensive experimental results on seven datasets illustrate the superiority of CGIPool comparing to the state-of-the-art methods.
Hypergraph, an expressive structure with flexibility to model the higher-order correlations among entities, has recently attracted increasing attention from various research domains. Despite the success of Graph Neural Networks (GNNs) for graph representation learning, how to adapt the powerful GNN-variants directly into hypergraphs remains a challenging problem. In this paper, we propose UniGNN, a unified framework for interpreting the message passing process in graph and hypergraph neural networks, which can generalize general GNN models into hypergraphs. In this framework, meticulously-designed architectures aiming to deepen GNNs can also be incorporated into hypergraphs with the least effort. Extensive experiments have been conducted to demonstrate the effectiveness of UniGNN on multiple real-world datasets, which outperform the state-of-the-art approaches with a large margin. Especially for the DBLP dataset, we increase the accuracy from 77.4\% to 88.8\% in the semi-supervised hypernode classification task. We further prove that the proposed message-passing based UniGNN models are at most as powerful as the 1-dimensional Generalized Weisfeiler-Leman (1-GWL) algorithm in terms of distinguishing non-isomorphic hypergraphs. Our code is available at \url{https://github.com/OneForward/UniGNN}.
Graph Neural Networks (GNNs) have received significant attention due to their state-of-the-art performance on various graph representation learning tasks. However, recent studies reveal that GNNs are vulnerable to adversarial attacks, i.e. an attacker is able to fool the GNNs by perturbing the graph structure or node features deliberately. While being able to successfully decrease the performance of GNNs, most existing attacking algorithms require access to either the model parameters or the training data, which is not practical in the real world. In this paper, we develop deeper insights into the Mettack algorithm, which is a representative grey-box attacking method, and then we propose a gradient-based black-box attacking algorithm. Firstly, we show that the Mettack algorithm will perturb the edges unevenly, thus the attack will be highly dependent on a specific training set. As a result, a simple yet useful strategy to defense against Mettack is to train the GNN with the validation set. Secondly, to overcome the drawbacks, we propose the Black-Box Gradient Attack (BBGA) algorithm. Extensive experiments demonstrate that out proposed method is able to achieve stable attack performance without accessing the training sets of the GNNs. Further results shows that our proposed method is also applicable when attacking against various defense methods.
Graph representation learning has become a ubiquitous component in many scenarios, ranging from social network analysis to energy forecasting in smart grids. In several applications, ensuring the fairness of the node (or graph) representations with respect to some protected attributes is crucial for their correct deployment. Yet, fairness in graph deep learning remains under-explored, with few solutions available. In particular, the tendency of similar nodes to cluster on several real-world graphs (i.e., homophily) can dramatically worsen the fairness of these procedures. In this paper, we propose a novel biased edge dropout algorithm (FairDrop) to counter-act homophily and improve fairness in graph representation learning. FairDrop can be plugged in easily on many existing algorithms, is efficient, adaptable, and can be combined with other fairness-inducing solutions. After describing the general algorithm, we demonstrate its application on two benchmark tasks, specifically, as a random walk model for producing node embeddings, and to a graph convolutional network for link prediction. We prove that the proposed algorithm can successfully improve the fairness of all models up to a small or negligible drop in accuracy, and compares favourably with existing state-of-the-art solutions. In an ablation study, we demonstrate that our algorithm can flexibly interpolate between biasing towards fairness and an unbiased edge dropout. Furthermore, to better evaluate the gains, we propose a new dyadic group definition to measure the bias of a link prediction task when paired with group-based fairness metrics. In particular, we extend the metric used to measure the bias in the node embeddings to take into account the graph structure.
Social Media Platforms (SMPs) like Facebook, Twitter, Instagram etc. have large user base all around the world that generates huge amount of data every second. This includes a lot of posts by fake and spam users, typically used by many organisations around the globe to have competitive edge over others. In this work, we aim at detecting such user accounts in Twitter using a novel approach. We show how to distinguish between Genuine and Spam accounts in Twitter using a combination of Graph Representation Learning and Natural Language Processing techniques.
Unsupervised attributed graph representation learning is challenging since both structural and feature information are required to be represented in the latent space. Existing methods concentrate on learning latent representation via reconstruction tasks, but cannot directly optimize representation and are prone to oversmoothing, thus limiting the applications on downstream tasks. To alleviate these issues, we propose a novel graph embedding framework named Deep Manifold Attributed Graph Embedding (DMAGE). A node-to-node geodesic similarity is proposed to compute the inter-node similarity between the data space and the latent space and then use Bergman divergence as loss function to minimize the difference between them. We then design a new network structure with fewer aggregation to alleviate the oversmoothing problem and incorporate graph structure augmentation to improve the representation's stability. Our proposed DMAGE surpasses state-of-the-art methods by a significant margin on three downstream tasks: unsupervised visualization, node clustering, and link prediction across four popular datasets.
Blockchain technology and, in particular, blockchain-based transaction offers us information that has never been seen before in the financial world. In contrast to fiat currencies, transactions through virtual currencies like Bitcoin are completely public. And these transactions of cryptocurrencies are permanently recorded on Blockchain and are available at any time. Therefore, this allows us to build transaction networks (TN) to analyze illegal phenomenons such as phishing scams in blockchain from a network perspective. In this paper, we propose a Transaction SubGraph Network (TSGN) based classification model to identify phishing accounts in Ethereum. Firstly we extract transaction subgraphs for each address and then expand these subgraphs into corresponding TSGNs based on the different mapping mechanisms. We find that TSGNs can provide more potential information to benefit the identification of phishing accounts. Moreover, Directed-TSGNs, by introducing direction attributes, can retain the transaction flow information that captures the significant topological pattern of phishing scams. By comparing with the TSGN, Directed-TSGN indeed has much lower time complexity, benefiting the graph representation learning. Experimental results demonstrate that, combined with network representation algorithms, the TSGN model can capture more features to enhance the classification algorithm and improve phishing nodes' identification accuracy in the Ethereum networks.
The problem of answering questions using knowledge from pre-trained language models (LMs) and knowledge graphs (KGs) presents two challenges: given a QA context (question and answer choice), methods need to (i) identify relevant knowledge from large KGs, and (ii) perform joint reasoning over the QA context and KG. In this work, we propose a new model, QA-GNN, which addresses the above challenges through two key innovations: (i) relevance scoring, where we use LMs to estimate the importance of KG nodes relative to the given QA context, and (ii) joint reasoning, where we connect the QA context and KG to form a joint graph, and mutually update their representations through graph neural networks. We evaluate our model on QA benchmarks in the commonsense (CommonsenseQA, OpenBookQA) and biomedical (MedQA-USMLE) domains. QA-GNN outperforms existing LM and LM+KG models, and exhibits capabilities to perform interpretable and structured reasoning, e.g., correctly handling negation in questions.
Graph representation learning has long been an important yet challenging task for various real-world applications. However, their downstream tasks are mainly performed in the settings of supervised or semi-supervised learning. Inspired by recent advances in unsupervised contrastive learning, this paper is thus motivated to investigate how the node-wise contrastive learning could be performed. Particularly, we respectively resolve the class collision issue and the imbalanced negative data distribution issue. Extensive experiments are performed on three real-world datasets and the proposed approach achieves the SOTA model performance.
Graph neural networks (GNN) have been proven to be mature enough for handling graph-structured data on node-level graph representation learning tasks. However, the graph pooling technique for learning expressive graph-level representation is critical yet still challenging. Existing pooling methods either struggle to capture the local substructure or fail to effectively utilize high-order dependency, thus diminishing the expression capability. In this paper we propose HAP, a hierarchical graph-level representation learning framework, which is adaptively sensitive to graph structures, i.e., HAP clusters local substructures incorporating with high-order dependencies. HAP utilizes a novel cross-level attention mechanism MOA to naturally focus more on close neighborhood while effectively capture higher-order dependency that may contain crucial information. It also learns a global graph content GCont that extracts the graph pattern properties to make the pre- and post-coarsening graph content maintain stable, thus providing global guidance in graph coarsening. This novel innovation also facilitates generalization across graphs with the same form of features. Extensive experiments on fourteen datasets show that HAP significantly outperforms twelve popular graph pooling methods on graph classification task with an maximum accuracy improvement of 22.79%, and exceeds the performance of state-of-the-art graph matching and graph similarity learning algorithms by over 3.5% and 16.7%.
Biomedical networks (or graphs) are universal descriptors for systems of interacting elements, from molecular interactions and disease co-morbidity to healthcare systems and scientific knowledge. Advances in artificial intelligence, specifically deep learning, have enabled us to model, analyze, and learn with such networked data. In this review, we put forward an observation that long-standing principles of systems biology and medicine -- while often unspoken in machine learning research -- provide the conceptual grounding for representation learning on graphs, explain its current successes and limitations, and even inform future advancements. We synthesize a spectrum of algorithmic approaches that, at their core, leverage graph topology to embed networks into compact vector spaces. We also capture the breadth of ways in which representation learning has dramatically improved the state-of-the-art in biomedical machine learning. Exemplary domains covered include identifying variants underlying complex traits, disentangling behaviors of single cells and their effects on health, assisting in diagnosis and treatment of patients, and developing safe and effective medicines.
With the ubiquitous graph-structured data in various applications, models that can learn compact but expressive vector representations of nodes have become highly desirable. Recently, bearing the message passing paradigm, graph neural networks (GNNs) have greatly advanced the performance of node representation learning on graphs. However, a majority class of GNNs are only designed for homogeneous graphs, leading to inferior adaptivity to the more informative heterogeneous graphs with various types of nodes and edges. Also, despite the necessity of inductively producing representations for completely new nodes (e.g., in streaming scenarios), few heterogeneous GNNs can bypass the transductive learning scheme where all nodes must be known during training. Furthermore, the training efficiency of most heterogeneous GNNs has been hindered by their sophisticated designs for extracting the semantics associated with each meta path or relation. In this paper, we propose WIde and DEep message passing Network (WIDEN) to cope with the aforementioned problems about heterogeneity, inductiveness, and efficiency that are rarely investigated together in graph representation learning. In WIDEN, we propose a novel inductive, meta path-free message passing scheme that packs up heterogeneous node features with their associated edges from both low- and high-order neighbor nodes. To further improve the training efficiency, we innovatively present an active downsampling strategy that drops unimportant neighbor nodes to facilitate faster information propagation. Experiments on three real-world heterogeneous graphs have further validated the efficacy of WIDEN on both transductive and inductive node representation learning, as well as the superior training efficiency against state-of-the-art baselines.
Much data with graph structures satisfy the principle of homophily, meaning that connected nodes tend to be similar with respect to a specific attribute. As such, ubiquitous datasets for graph machine learning tasks have generally been highly homophilous, rewarding methods that leverage homophily as an inductive bias. Recent work has pointed out this particular focus, as new non-homophilous datasets have been introduced and graph representation learning models better suited for low-homophily settings have been developed. However, these datasets are small and poorly suited to truly testing the effectiveness of new methods in non-homophilous settings. We present a series of improved graph datasets with node label relationships that do not satisfy the homophily principle. Along with this, we introduce a new measure of the presence or absence of homophily that is better suited than existing measures in different regimes. We benchmark a range of simple methods and graph neural networks across our proposed datasets, drawing new insights for further research. Data and codes can be found at https://github.com/CUAI/Non-Homophily-Benchmarks.
As one of the most fundamental tasks in graph theory, subgraph matching is a crucial task in many fields, ranging from information retrieval, computer vision, biology, chemistry and natural language processing. Yet subgraph matching problem remains to be an NP-complete problem. This study proposes an end-to-end learning-based approximate method for subgraph matching task, called subgraph matching network (Sub-GMN). The proposed Sub-GMN firstly uses graph representation learning to map nodes to node-level embedding. It then combines metric learning and attention mechanisms to model the relationship between matched nodes in the data graph and query graph. To test the performance of the proposed method, we applied our method on two databases. We used two existing methods, GNN and FGNN as baseline for comparison. Our experiment shows that, on dataset 1, on average the accuracy of Sub-GMN are 12.21\% and 3.2\% higher than that of GNN and FGNN respectively. On average running time Sub-GMN runs 20-40 times faster than FGNN. In addition, the average F1-score of Sub-GMN on all experiments with dataset 2 reached 0.95, which demonstrates that Sub-GMN outputs more correct node-to-node matches. Comparing with the previous GNNs-based methods for subgraph matching task, our proposed Sub-GMN allows varying query and data graphes in the test/application stage, while most previous GNNs-based methods can only find a matched subgraph in the data graph during the test/application for the same query graph used in the training stage. Another advantage of our proposed Sub-GMN is that it can output a list of node-to-node matches, while most existing end-to-end GNNs based methods cannot provide the matched node pairs.
This paper presents a new Network Intrusion Detection System (NIDS) based on Graph Neural Networks (GNNs). GNNs are a relatively new sub-field of deep neural networks, which can leverage the inherent structure of graph-based data. Training and evaluation data for NIDSs are typically represented as flow records, which can naturally be represented in a graph format. In this paper, we propose E-GraphSAGE, a GNN approach that allows capturing both the edge features of a graph as well as the topological information for network intrusion detection in IoT networks. To the best of our knowledge, our proposal is the first successful, practical, and extensively evaluated approach of applying GNNs on the problem of network intrusion detection for IoT using flow-based data. Our extensive experimental evaluation on four recent NIDS benchmark datasets shows that our approach outperforms the state-of-the-art in terms of key classification metrics, which demonstrates the potential of GNNs in network intrusion detection, and provides motivation for further research.
In this paper, we introduce a self-supervised learning method to enhance the graph-level representations with the help of a set of subgraphs. For this purpose, we propose a universal framework to generate subgraphs in an auto-regressive way and then using these subgraphs to guide the learning of graph representation by Graph Neural Networks. Under this framework, we can get a comprehensive understanding of the graph structure in a learnable way. And to fully capture enough information of original graphs, we design three information aggregators: \textbf{attribute-conv}, \textbf{layer-conv} and \textbf{subgraph-conv} to gather information from different aspects. And to achieve efficient and effective contrastive learning, a Head-Tail contrastive construction is proposed to provide abundant negative samples. Under all proposed components which can be generalized to any Graph Neural Networks, in the unsupervised case, we achieve new state-of-the-art results in several benchmarks. We also evaluate our model on semi-supervised learning tasks and make a fair comparison to state-of-the-art semi-supervised methods.
In this work, we study the phenomenon of catastrophic forgetting in the graph representation learning scenario. The primary objective of the analysis is to understand whether classical continual learning techniques for flat and sequential data have a tangible impact on performances when applied to graph data. To do so, we experiment with a structure-agnostic model and a deep graph network in a robust and controlled environment on three different datasets. The benchmark is complemented by an investigation on the effect of structure-preserving regularization techniques on catastrophic forgetting. We find that replay is the most effective strategy in so far, which also benefits the most from the use of regularization. Our findings suggest interesting future research at the intersection of the continual and graph representation learning fields. Finally, we provide researchers with a flexible software framework to reproduce our results and carry out further experiments.
Graph representation learning for static graphs is a well studied topic. Recently, a few studies have focused on learning temporal information in addition to the topology of a graph. Most of these studies have relied on learning to represent nodes and substructures in dynamic graphs. However, the representation learning problem for entire graphs in a dynamic context is yet to be addressed. In this paper, we propose an unsupervised representation learning architecture for dynamic graphs, designed to learn both the topological and temporal features of the graphs that evolve over time. The approach consists of a sequence-to-sequence encoder-decoder model embedded with gated graph neural networks (GGNNs) and long short-term memory networks (LSTMs). The GGNN is able to learn the topology of the graph at each time step, while LSTMs are leveraged to propagate the temporal information among the time steps. Moreover, an encoder learns the temporal dynamics of an evolving graph and a decoder reconstructs the dynamics over the same period of time using the encoded representation provided by the encoder. We demonstrate that our approach is capable of learning the representation of a dynamic graph through time by applying the embeddings to dynamic graph classification using a real world dataset of animal behaviour. Graph representation learning for static graphs is a well studied topic. Recently, a few studies have focused on learning temporal information in addition to the topology of a graph. Most of these studies have relied on learning to represent nodes and substructures in dynamic graphs. However, the representation learning problem for entire graphs in a dynamic context is yet to be addressed. In this paper, we propose an unsupervised representation learning architecture for dynamic graphs, designed to learn both the topological and temporal features of the graphs that evolve over time. The approach consists of a sequence-to-sequence encoder-decoder model embedded with gated graph neural networks (GGNNs) and long short-term memory networks (LSTMs). The GGNN is able to learn the topology of the graph at each time step, while LSTMs are leveraged to propagate the temporal information among the time steps. Moreover, an encoder learns the temporal dynamics of an evolving graph and a decoder reconstructs the dynamics over the same period of time using the encoded representation provided by the encoder. We demonstrate that our approach is capable of learning the representation of a dynamic graph through time by applying the embeddings to dynamic graph classification using a real world dataset of animal behaviour.