Knowledge graphs (KGs) consisting of a large number of triples have become widespread recently, and many knowledge graph embedding (KGE) methods are proposed to embed entities and relations of a KG into continuous vector spaces. Such embedding methods simplify the operations of conducting various in-KG tasks (e.g., link prediction) and out-of-KG tasks (e.g., question answering). They can be viewed as general solutions for representing KGs. However, existing KGE methods are not applicable to inductive settings, where a model trained on source KGs will be tested on target KGs with entities unseen during model training. Existing works focusing on KGs in inductive settings can only solve the inductive relation prediction task. They can not handle other out-of-KG tasks as general as KGE methods since they don't produce embeddings for entities. In this paper, to achieve inductive knowledge graph embedding, we propose a model MorsE, which does not learn embeddings for entities but learns transferable meta-knowledge that can be used to produce entity embeddings. Such meta-knowledge is modeled by entity-independent modules and learned by meta-learning. Experimental results show that our model significantly outperforms corresponding baselines for in-KG and out-of-KG tasks in inductive settings.
Graph embedding based on random-walks supports effective solutions for many graph-related downstream tasks. However, the abundance of embedding literature has made it increasingly difficult to compare existing methods and to identify opportunities to advance the state-of-the-art. Meanwhile, existing work has left several fundamental questions -- such as how embeddings capture different structural scales and how they should be applied for effective link prediction -- unanswered. This paper addresses these challenges with an analytical framework for random-walk based graph embedding that consists of three components: a random-walk process, a similarity function, and an embedding algorithm. Our framework not only categorizes many existing approaches but naturally motivates new ones. With it, we illustrate novel ways to incorporate embeddings at multiple scales to improve downstream task performance. We also show that embeddings based on autocovariance similarity, when paired with dot product ranking for link prediction, outperform state-of-the-art methods based on Pointwise Mutual Information similarity by up to 100%.
Graphs are ubiquitous, and they can model unique characteristics and complex relations of real-life systems. Although using machine learning (ML) on graphs is promising, their raw representation is not suitable for ML algorithms. Graph embedding represents each node of a graph as a d-dimensional vector which is more suitable for ML tasks. However, the embedding process is expensive, and CPU-based tools do not scale to real-world graphs. In this work, we present GOSH, a GPU-based tool for embedding large-scale graphs with minimum hardware constraints. GOSH employs a novel graph coarsening algorithm to enhance the impact of updates and minimize the work for embedding. It also incorporates a decomposition schema that enables any arbitrarily large graph to be embedded with a single GPU. As a result, GOSH sets a new state-of-the-art in link prediction both in accuracy and speed, and delivers high-quality embeddings for node classification at a fraction of the time compared to the state-of-the-art. For instance, it can embed a graph with over 65 million vertices and 1.8 billion edges in less than 30 minutes on a single GPU.
Unsupervised feature learning often finds low-dimensional embeddings that capture the structure of complex data. For tasks for which prior expert topological knowledge is available, incorporating this into the learned representation may lead to higher quality embeddings. For example, this may help one to embed the data into a given number of clusters, or to accommodate for noise that prevents one from deriving the distribution of the data over the model directly, which can then be learned more effectively. However, a general tool for integrating different prior topological knowledge into embeddings is lacking. Although differentiable topology layers have been recently developed that can (re)shape embeddings into prespecified topological models, they have two important limitations for representation learning, which we address in this paper. First, the currently suggested topological losses fail to represent simple models such as clusters and flares in a natural manner. Second, these losses neglect all original structural (such as neighborhood) information in the data that is useful for learning. We overcome these limitations by introducing a new set of topological losses, and proposing their usage as a way for topologically regularizing data embeddings to naturally represent a prespecified model. We include thorough experiments on synthetic and real data that highlight the usefulness and versatility of this approach, with applications ranging from modeling high-dimensional single-cell data, to graph embedding.
Predicting the next place to visit is a key in human mobility behavior modeling, which plays a significant role in various fields, such as epidemic control, urban planning, traffic management, and travel recommendation. To achieve this, one typical solution is designing modules based on RNN to capture their preferences to various locations. Although these RNN-based methods can effectively learn individual's hidden personalized preferences to her visited places, the interactions among users can only be weakly learned through the representations of locations. Targeting this, we propose an end-to-end framework named personalized and group preference guided network (PG$^2$Net), considering the users' preferences to various places at both individual and collective levels. Specifically, PG$^2$Net concatenates Bi-LSTM and attention mechanism to capture each user's long-term mobility tendency. To learn population's group preferences, we utilize spatial and temporal information of the visitations to construct a spatio-temporal dependency module. We adopt a graph embedding method to map users' trajectory into a hidden space, capturing their sequential relation. In addition, we devise an auxiliary loss to learn the vectorial representation of her next location. Experiment results on two Foursquare check-in datasets and one mobile phone dataset indicate the advantages of our model compared to the state-of-the-art baselines. Source codes are available at https://github.com/urbanmobility/PG2Net.
Graph embedding maps a graph into a convenient vector-space representation for graph analysis and machine learning applications. Many graph embedding methods hinge on a sampling of context nodes based on random walks. However, random walks can be a biased sampler due to the structural properties of graphs. Most notably, random walks are biased by the degree of each node, where a node is sampled proportionally to its degree. The implication of such biases has not been clear, particularly in the context of graph representation learning. Here, we investigate the impact of the random walks' bias on graph embedding and propose residual2vec, a general graph embedding method that can debias various structural biases in graphs by using random graphs. We demonstrate that this debiasing not only improves link prediction and clustering performance but also allows us to explicitly model salient structural properties in graph embedding.
Identifying vulnerabilities in the source code is essential to protect the software systems from cyber security attacks. It, however, is also a challenging step that requires specialized expertise in security and code representation. To this end, we aim to develop a general, practical, and programming language-independent model capable of running on various source codes and libraries without difficulty. Therefore, we consider vulnerability detection as an inductive text classification problem and propose ReGVD, a simple yet effective graph neural network-based model for the problem. In particular, ReGVD views each raw source code as a flat sequence of tokens to build a graph, wherein node features are initialized by only the token embedding layer of a pre-trained programming language (PL) model. ReGVD then leverages residual connection among GNN layers and examines a mixture of graph-level sum and max poolings to return a graph embedding for the source code. ReGVD outperforms the existing state-of-the-art models and obtains the highest accuracy on the real-world benchmark dataset from CodeXGLUE for vulnerability detection. Our code is available at: \url{https://github.com/daiquocnguyen/GNN-ReGVD}.
Given a node-attributed graph, how can we efficiently represent it with few numerical features that expressively reflect its topology and attribute information? We propose A-DOGE, for Attributed DOS-based Graph Embedding, based on density of states (DOS, a.k.a. spectral density) to tackle this problem. A-DOGE is designed to fulfill a long desiderata of desirable characteristics. Most notably, it capitalizes on efficient approximation algorithms for DOS, that we extend to blend in node labels and attributes for the first time, making it fast and scalable for large attributed graphs and graph databases. Being based on the entire eigenspectrum of a graph, A-DOGE can capture structural and attribute properties at multiple ("glocal") scales. Moreover, it is unsupervised (i.e. agnostic to any specific objective) and lends itself to various interpretations, which makes it is suitable for exploratory graph mining tasks. Finally, it processes each graph independent of others, making it amenable for streaming settings as well as parallelization. Through extensive experiments, we show the efficacy and efficiency of A-DOGE on exploratory graph analysis and graph classification tasks, where it significantly outperforms unsupervised baselines and achieves competitive performance with modern supervised GNNs, while achieving the best trade-off between accuracy and runtime.
Knowledge graph embedding involves learning representations of entities -- the vertices of the graph -- and relations -- the edges of the graph -- such that the resulting representations encode the known factual information represented by the knowledge graph and can be used in the inference of new relations. We show that knowledge graph embedding is naturally expressed in the topological and categorical language of \textit{cellular sheaves}: a knowledge graph embedding can be described as an approximate global section of an appropriate \textit{knowledge sheaf} over the graph, with consistency constraints induced by the knowledge graph's schema. This approach provides a generalized framework for reasoning about knowledge graph embedding models and allows for the expression of a wide range of prior constraints on embeddings. Further, the resulting embeddings can be easily adapted for reasoning over composite relations without special training. We implement these ideas to highlight the benefits of the extensions inspired by this new perspective.
In this work, a novel idea is presented for combinatorial optimization problems, a hybrid network, which results in a superior outcome. We applied this method to graph pointer networks [1], expanding its capabilities to a higher level. We proposed a hybrid pointer network (HPN) to solve the travelling salesman problem trained by reinforcement learning. Furthermore, HPN builds upon graph pointer networks which is an extension of pointer networks with an additional graph embedding layer. HPN outperforms the graph pointer network in solution quality due to the hybrid encoder, which provides our model with a verity encoding type, allowing our model to converge to a better policy. Our network significantly outperforms the original graph pointer network for small and large-scale problems increasing its performance for TSP50 from 5.959 to 5.706 without utilizing 2opt, Pointer networks, Attention model, and a wide range of models, producing results comparable to highly tuned and specialized algorithms. We make our data, models, and code publicly available [2].
Graph is an important data representation ubiquitously existing in the real world. However, analyzing the graph data is computationally difficult due to its non-Euclidean nature. Graph embedding is a powerful tool to solve the graph analytics problem by transforming the graph data into low-dimensional vectors. These vectors could also be shared with third parties to gain additional insights of what is behind the data. While sharing graph embedding is intriguing, the associated privacy risks are unexplored. In this paper, we systematically investigate the information leakage of the graph embedding by mounting three inference attacks. First, we can successfully infer basic graph properties, such as the number of nodes, the number of edges, and graph density, of the target graph with up to 0.89 accuracy. Second, given a subgraph of interest and the graph embedding, we can determine with high confidence that whether the subgraph is contained in the target graph. For instance, we achieve 0.98 attack AUC on the DD dataset. Third, we propose a novel graph reconstruction attack that can reconstruct a graph that has similar graph structural statistics to the target graph. We further propose an effective defense mechanism based on graph embedding perturbation to mitigate the inference attacks without noticeable performance degradation for graph classification tasks. Our code is available at https://github.com/Zhangzhk0819/GNN-Embedding-Leaks.
Machine learning on graph-structured data has recently become a major topic in industry and research, finding many exciting applications such as recommender systems and automated theorem proving. We propose an energy-based graph embedding algorithm to characterize industrial automation systems, integrating knowledge from different domains like industrial automation, communications and cybersecurity. By combining knowledge from multiple domains, the learned model is capable of making context-aware predictions regarding novel system events and can be used to evaluate the severity of anomalies that might be indicative of, e.g., cybersecurity breaches. The presented model is mappable to a biologically-inspired neural architecture, serving as a first bridge between graph embedding methods and neuromorphic computing - uncovering a promising edge application for this upcoming technology.
Dynamic graph embedding has gained great attention recently due to its capability of learning low dimensional graph representations for complex temporal graphs with high accuracy. However, recent advances mostly focus on learning node embeddings as deterministic "vectors" for static graphs yet disregarding the key graph temporal dynamics and the evolving uncertainties associated with node embedding in the latent space. In this work, we propose an efficient stochastic dynamic graph embedding method (DynG2G) that applies an inductive feed-forward encoder trained with node triplet-based contrastive loss. Every node per timestamp is encoded as a time-dependent probabilistic multivariate Gaussian distribution in the latent space, hence we can quantify the node embedding uncertainty on-the-fly. We adopted eight different benchmarks that represent diversity in size (from 96 nodes to 87,626 and from 13,398 edges to 4,870,863) and diversity in dynamics. We demonstrate via extensive experiments on these eight dynamic graph benchmarks that DynG2G achieves new state-of-the-art performance in capturing the underlying temporal node embeddings. We also demonstrate that DynG2G can predict the evolving node embedding uncertainty, which plays a crucial role in quantifying the intrinsic dimensionality of the dynamical system over time. We obtain a universal relation of the optimal embedding dimension, $L_o$, versus the effective dimensionality of uncertainty, $D_u$, and we infer that $L_o=D_u$ for all cases. This implies that the uncertainty quantification approach we employ in the DynG2G correctly captures the intrinsic dimensionality of the dynamics of such evolving graphs despite the diverse nature and composition of the graphs at each timestamp. Moreover, this $L_0 - D_u$ correlation provides a clear path to select adaptively the optimum embedding size at each timestamp by setting $L \ge D_u$.
In this paper we propose a lightning fast graph embedding method called one-hot graph encoder embedding. It has a linear computational complexity and the capacity to process billions of edges within minutes on standard PC -- making it an ideal candidate for huge graph processing. It is applicable to either adjacency matrix or graph Laplacian, and can be viewed as a transformation of the spectral embedding. Under random graph models, the graph encoder embedding is approximately normally distributed per vertex, and asymptotically converges to its mean. We showcase three applications: vertex classification, vertex clustering, and graph bootstrap. In every case, the graph encoder embedding exhibits unrivalled computational advantages.
Knowledge Graph Embedding (KGE) aims to learn representations for entities and relations. Most KGE models have gained great success, especially on extrapolation scenarios. Specifically, given an unseen triple (h, r, t), a trained model can still correctly predict t from (h, r, ?), or h from (?, r, t), such extrapolation ability is impressive. However, most existing KGE works focus on the design of delicate triple modeling function, which mainly tells us how to measure the plausibility of observed triples, but offers limited explanation of why the methods can extrapolate to unseen data, and what are the important factors to help KGE extrapolate. Therefore in this work, we attempt to study the KGE extrapolation of two problems: 1. How does KGE extrapolate to unseen data? 2. How to design the KGE model with better extrapolation ability? For the problem 1, we first discuss the impact factors for extrapolation and from relation, entity and triple level respectively, propose three Semantic Evidences (SEs), which can be observed from train set and provide important semantic information for extrapolation. Then we verify the effectiveness of SEs through extensive experiments on several typical KGE methods. For the problem 2, to make better use of the three levels of SE, we propose a novel GNN-based KGE model, called Semantic Evidence aware Graph Neural Network (SE-GNN). In SE-GNN, each level of SE is modeled explicitly by the corresponding neighbor pattern, and merged sufficiently by the multi-layer aggregation, which contributes to obtaining more extrapolative knowledge representation. Finally, through extensive experiments on FB15k-237 and WN18RR datasets, we show that SE-GNN achieves state-of-the-art performance on Knowledge Graph Completion task and performs a better extrapolation ability. Our code is available at https://github.com/renli1024/SE-GNN.
As a pivotal tool to alleviate the information overload problem, recommender systems aim to predict user's preferred items from millions of candidates by analyzing observed user-item relations. As for alleviating the sparsity and cold start problems encountered by recommender systems, researchers resort to employing side information or knowledge in recommendation as a strategy for uncovering hidden (indirect) user-item relations, aiming to enrich observed information (or data) for recommendation. However, in the face of the high complexity and large scale of side information and knowledge, this strategy relies for efficient implementation on the scalability of recommendation models. Not until after the prevalence of machine learning did graph embedding techniques be a concentration, which can efficiently utilize complex and large-scale data. In light of that, equipping recommender systems with graph embedding techniques has been widely studied these years, appearing to outperform conventional recommendation implemented directly based on graph topological analysis. As the focus, this article retrospects graph embedding-based recommendation from embedding techniques for bipartite graphs, general graphs and knowledge graphs, and proposes a general design pipeline of that. In addition, after comparing several representative graph embedding-based recommendation models with the most common-used conventional recommendation models on simulations, this article manifests that the conventional models can overall outperform the graph embedding-based ones in predicting implicit user-item interactions, revealing the comparative weakness of graph embedding-based recommendation in these tasks. To foster future research, this article proposes suggestions on making a trade-off between graph embedding-based recommendation and conventional recommendation in different tasks, and puts forward open questions.
This paper introduces a novel approach to learn visually grounded meaning representations of words as low-dimensional node embeddings on an underlying graph hierarchy. The lower level of the hierarchy models modality-specific word representations through dedicated but communicating graphs, while the higher level puts these representations together on a single graph to learn a representation jointly from both modalities. The topology of each graph models similarity relations among words, and is estimated jointly with the graph embedding. The assumption underlying this model is that words sharing similar meaning correspond to communities in an underlying similarity graph in a low-dimensional space. We named this model Hierarchical Multi-Modal Similarity Graph Embedding (HM-SGE). Experimental results validate the ability of HM-SGE to simulate human similarity judgements and concept categorization, outperforming the state of the art.
Community detection, aiming to group the graph nodes into clusters with dense inner-connection, is a fundamental graph mining task. Recently, it has been studied on the heterogeneous graph, which contains multiple types of nodes and edges, posing great challenges for modeling the high-order relationship between nodes. With the surge of graph embedding mechanism, it has also been adopted to community detection. A remarkable group of works use the meta-path to capture the high-order relationship between nodes and embed them into nodes' embedding to facilitate community detection. However, defining meaningful meta-paths requires much domain knowledge, which largely limits their applications, especially on schema-rich heterogeneous graphs like knowledge graphs. To alleviate this issue, in this paper, we propose to exploit the context path to capture the high-order relationship between nodes, and build a Context Path-based Graph Neural Network (CP-GNN) model. It recursively embeds the high-order relationship between nodes into the node embedding with attention mechanisms to discriminate the importance of different relationships. By maximizing the expectation of the co-occurrence of nodes connected by context paths, the model can learn the nodes' embeddings that both well preserve the high-order relationship between nodes and are helpful for community detection. Extensive experimental results on four real-world datasets show that CP-GNN outperforms the state-of-the-art community detection methods.
Recently, road scene-graph representations used in conjunction with graph learning techniques have been shown to outperform state-of-the-art deep learning techniques in tasks including action classification, risk assessment, and collision prediction. To enable the exploration of applications of road scene-graph representations, we introduce roadscene2vec: an open-source tool for extracting and embedding road scene-graphs. The goal of roadscene2vec is to enable research into the applications and capabilities of road scene-graphs by providing tools for generating scene-graphs, graph learning models to generate spatio-temporal scene-graph embeddings, and tools for visualizing and analyzing scene-graph-based methodologies. The capabilities of roadscene2vec include (i) customized scene-graph generation from either video clips or data from the CARLA simulator, (ii) multiple configurable spatio-temporal graph embedding models and baseline CNN-based models, (iii) built-in functionality for using graph and sequence embeddings for risk assessment and collision prediction applications, (iv) tools for evaluating transfer learning, and (v) utilities for visualizing scene-graphs and analyzing the explainability of graph learning models. We demonstrate the utility of roadscene2vec for these use cases with experimental results and qualitative evaluations for both graph learning models and CNN-based models. roadscene2vec is available at https://github.com/AICPS/roadscene2vec.
In this work, we present a Boundary Oriented Graph Embedding (BOGE) approach for the Graph Neural Network (GNN) to serve as a general surrogate model for regressing physical fields and solving boundary value problems. Providing shortcuts for both boundary elements and local neighbor elements, the BOGE approach can embed structured mesh elements into the graph and performs an efficient regression on large-scale triangular-mesh-based FEA results, which cannot be realized by other machine-learning-based surrogate methods. Focusing on the cantilever beam problem, our BOGE approach cannot only fit the distribution of stress fields but also regresses the topological optimization results, which show its potential of realizing abstract decision-making design process. The BOGE approach with 3-layer DeepGCN model \textcolor{blue}{achieves the regression with MSE of 0.011706 (2.41\% MAPE) for stress field prediction and 0.002735 MSE (with 1.58\% elements having error larger than 0.01) for topological optimization.} The overall concept of the BOGE approach paves the way for a general and efficient deep-learning-based FEA simulator that will benefit both industry and design-related areas.