Graph neural networks are powerful architectures for structured datasets. However, current methods struggle to represent long-range dependencies. Scaling the depth or width of GNNs is insufficient to broaden receptive fields as larger GNNs encounter optimization instabilities such as vanishing gradients and representation oversmoothing, while pooling-based approaches have yet to become as universally useful as in computer vision. In this work, we propose the use of Transformer-based self-attention to learn long-range pairwise relationships, with a novel "readout" mechanism to obtain a global graph embedding. Inspired by recent computer vision results that find position-invariant attention performant in learning long-range relationships, our method, which we call GraphTrans, applies a permutation-invariant Transformer module after a standard GNN module. This simple architecture leads to state-of-the-art results on several graph classification tasks, outperforming methods that explicitly encode graph structure. Our results suggest that purely-learning-based approaches without graph structure may be suitable for learning high-level, long-range relationships on graphs. Code for GraphTrans is available at https://github.com/ucbrise/graphtrans.
Graph representation learning (also called graph embeddings) is a popular technique for incorporating network structure into machine learning models. Unsupervised graph embedding methods aim to capture graph structure by learning a low-dimensional vector representation (the embedding) for each node. Despite the widespread use of these embeddings for a variety of downstream transductive machine learning tasks, there is little principled analysis of the effectiveness of this approach for common tasks. In this work, we provide an empirical and theoretical analysis for the performance of a class of embeddings on the common task of pairwise community labeling. This is a binary variant of the classic community detection problem, which seeks to build a classifier to determine whether a pair of vertices participate in a community. In line with our goal of foundational understanding, we focus on a popular class of unsupervised embedding techniques that learn low rank factorizations of a vertex proximity matrix (this class includes methods like GraRep, DeepWalk, node2vec, NetMF). We perform detailed empirical analysis for community labeling over a variety of real and synthetic graphs with ground truth. In all cases we studied, the models trained from embedding features perform poorly on community labeling. In constrast, a simple logistic model with classic graph structural features handily outperforms the embedding models. For a more principled understanding, we provide a theoretical analysis for the (in)effectiveness of these embeddings in capturing the community structure. We formally prove that popular low-dimensional factorization methods either cannot produce community structure, or can only produce ``unstable" communities. These communities are inherently unstable under small perturbations.
Graph contrastive learning attracts/disperses node representations for similar/dissimilar node pairs under some notion of similarity. It may be combined with a low-dimensional embedding of nodes to preserve intrinsic and structural properties of a graph. In this paper, we extend the celebrated Laplacian Eigenmaps with contrastive learning, and call them COntrastive Laplacian EigenmapS (COLES). Starting from a GAN-inspired contrastive formulation, we show that the Jensen-Shannon divergence underlying many contrastive graph embedding models fails under disjoint positive and negative distributions, which may naturally emerge during sampling in the contrastive setting. In contrast, we demonstrate analytically that COLES essentially minimizes a surrogate of Wasserstein distance, which is known to cope well under disjoint distributions. Moreover, we show that the loss of COLES belongs to the family of so-called block-contrastive losses, previously shown to be superior compared to pair-wise losses typically used by contrastive methods. We show on popular benchmarks/backbones that COLES offers favourable accuracy/scalability compared to DeepWalk, GCN, Graph2Gauss, DGI and GRACE baselines.
Previous knowledge graph embedding approaches usually map entities to representations and utilize score functions to predict the target entities, yet they typically struggle to reason rare or emerging unseen entities. In this paper, we propose kNN-KGE, a new knowledge graph embedding approach with pre-trained language models, by linearly interpolating its entity distribution with k-nearest neighbors. We compute the nearest neighbors based on the distance in the entity embedding space from the knowledge store. Our approach can allow rare or emerging entities to be memorized explicitly rather than implicitly in model parameters. Experimental results demonstrate that our approach can improve inductive and transductive link prediction results and yield better performance for low-resource settings with only a few triples, which might be easier to reason via explicit memory. Code is available at https://github.com/zjunlp/KNN-KG.
Knowledge graphs (KGs) are typically incomplete and we often wish to infer new facts given the existing ones. This can be thought of as a binary classification problem; we aim to predict if new facts are true or false. Unfortunately, we generally only have positive examples (the known facts) but we also need negative ones to train a classifier. To resolve this, it is usual to generate negative examples using a negative sampling strategy. However, this can produce false negatives which may reduce performance, is computationally expensive, and does not produce calibrated classification probabilities. In this paper, we propose a training procedure that obviates the need for negative sampling by adding a novel regularization term to the loss function. Our results for two relational embedding models (DistMult and SimplE) show the merit of our proposal both in terms of performance and speed.
We present an effective graph neural network (GNN)-based knowledge graph embedding model, which we name WGE, to capture entity- and relation-focused graph structures. Given a knowledge graph, WGE builds a single undirected entity-focused graph that views entities as nodes. WGE also constructs another single undirected graph from relation-focused constraints, which views entities and relations as nodes. WGE then proposes a GNN-based architecture to better learn vector representations of entities and relations from these two single entity- and relation-focused graphs. WGE feeds the learned entity and relation representations into a weighted score function to return the triple scores for knowledge graph completion. Experimental results show that WGE outperforms strong baselines on seven benchmark datasets for knowledge graph completion.
Graphs can model complicated interactions between entities, which naturally emerge in many important applications. These applications can often be cast into standard graph learning tasks, in which a crucial step is to learn low-dimensional graph representations. Graph neural networks (GNNs) are currently the most popular model in graph embedding approaches. However, standard GNNs in the neighborhood aggregation paradigm suffer from limited discriminative power in distinguishing \emph{high-order} graph structures as opposed to \emph{low-order} structures. To capture high-order structures, researchers have resorted to motifs and developed motif-based GNNs. However, existing motif-based GNNs still often suffer from less discriminative power on high-order structures. To overcome the above limitations, we propose Motif Graph Neural Network (MGNN), a novel framework to better capture high-order structures, hinging on our proposed motif redundancy minimization operator and injective motif combination. First, MGNN produces a set of node representations w.r.t. each motif. The next phase is our proposed redundancy minimization among motifs which compares the motifs with each other and distills the features unique to each motif. Finally, MGNN performs the updating of node representations by combining multiple representations from different motifs. In particular, to enhance the discriminative power, MGNN utilizes an injective function to combine the representations w.r.t. different motifs. We further show that our proposed architecture increases the expressive power of GNNs with a theoretical analysis. We demonstrate that MGNN outperforms state-of-the-art methods on seven public benchmarks on both node classification and graph classification tasks.
Event analysis from news and social networks is very useful for a wide range of social studies and real-world applications. Recently, event graphs have been explored to model event datasets and their complex relationships, where events are vertices connected to other vertices representing locations, people's names, dates, and various other event metadata. Graph representation learning methods are promising for extracting latent features from event graphs to enable the use of different classification algorithms. However, existing methods fail to meet essential requirements for event graphs, such as (i) dealing with semi-supervised graph embedding to take advantage of some labeled events, (ii) automatically determining the importance of the relationships between event vertices and their metadata vertices, as well as (iii) dealing with the graph heterogeneity. This paper presents GNEE (GAT Neural Event Embeddings), a method that combines Graph Attention Networks and Graph Regularization. First, an event graph regularization is proposed to ensure that all graph vertices receive event features, thereby mitigating the graph heterogeneity drawback. Second, semi-supervised graph embedding with self-attention mechanism considers existing labeled events, as well as learns the importance of relationships in the event graph during the representation learning process. A statistical analysis of experimental results with five real-world event graphs and six graph embedding methods shows that our GNEE outperforms state-of-the-art semi-supervised graph embedding methods.
We propose a novel software service recommendation model to help users find their suitable repositories in GitHub. Our model first designs a novel context-induced repository graph embedding method to leverage rich contextual information of repositories to alleviate the difficulties caused by the data sparsity issue. It then leverages sequence information of user-repository interactions for the first time in the software service recommendation field. Specifically, a deep-learning based sequential recommendation technique is adopted to capture the dynamics of user preferences. Comprehensive experiments have been conducted on a large dataset collected from GitHub against a list of existing methods. The results illustrate the superiority of our method in various aspects.
Unsupervised graph-level representation learning plays a crucial role in a variety of tasks such as molecular property prediction and community analysis, especially when data annotation is expensive. Currently, most of the best-performing graph embedding methods are based on Infomax principle. The performance of these methods highly depends on the selection of negative samples and hurt the performance, if the samples were not carefully selected. Inter-graph similarity-based methods also suffer if the selected set of graphs for similarity matching is low in quality. To address this, we focus only on utilizing the current input graph for embedding learning. We are motivated by an observation from real-world graph generation processes where the graphs are formed based on one or more global factors which are common to all elements of the graph (e.g., topic of a discussion thread, solubility level of a molecule). We hypothesize extracting these common factors could be highly beneficial. Hence, this work proposes a new principle for unsupervised graph representation learning: Graph-wise Common latent Factor EXtraction (GCFX). We further propose a deep model for GCFX, deepGCFX, based on the idea of reversing the above-mentioned graph generation process which could explicitly extract common latent factors from an input graph and achieve improved results on downstream tasks to the current state-of-the-art. Through extensive experiments and analysis, we demonstrate that, while extracting common latent factors is beneficial for graph-level tasks to alleviate distractions caused by local variations of individual nodes or local neighbourhoods, it also benefits node-level tasks by enabling long-range node dependencies, especially for disassortative graphs.
Many real-world graphs (networks) are heterogeneous with different types of nodes and edges. Heterogeneous graph embedding, aiming at learning the low-dimensional node representations of a heterogeneous graph, is vital for various downstream applications. Many meta-path based embedding methods have been proposed to learn the semantic information of heterogeneous graphs in recent years. However, most of the existing techniques overlook the graph structure information when learning the heterogeneous graph embeddings. This paper proposes a novel Structure-Aware Heterogeneous Graph Neural Network (SHGNN) to address the above limitations. In detail, we first utilize a feature propagation module to capture the local structure information of intermediate nodes in the meta-path. Next, we use a tree-attention aggregator to incorporate the graph structure information into the aggregation module on the meta-path. Finally, we leverage a meta-path aggregator to fuse the information aggregated from different meta-paths. We conducted experiments on node classification and clustering tasks and achieved state-of-the-art results on the benchmark datasets, which shows the effectiveness of our proposed method.
Adoption of recently developed methods from machine learning has given rise to creation of drug-discovery knowledge graphs (KG) that utilize the interconnected nature of the domain. Graph-based modelling of the data, combined with KG embedding (KGE) methods, are promising as they provide a more intuitive representation and are suitable for inference tasks such as predicting missing links. One common application is to produce ranked lists of genes for a given disease, where the rank is based on the perceived likelihood of association between the gene and the disease. It is thus critical that these predictions are not only pertinent but also biologically meaningful. However, KGs can be biased either directly due to the underlying data sources that are integrated or due to modeling choices in the construction of the graph, one consequence of which is that certain entities can get topologically overrepresented. We demonstrate the effect of these inherent structural imbalances, resulting in densely-connected entities being highly ranked no matter the context. We provide support for this observation across different datasets, models as well as predictive tasks. Further, we present various graph perturbation experiments which yield more support to the observation that KGE models can be more influenced by the frequency of entities rather than any biological information encoded within the relations. Our results highlight the importance of data modeling choices, and emphasizes the need for practitioners to be mindful of these issues when interpreting model outputs and during KG composition.
Learning the embeddings of knowledge graphs (KG) is vital in artificial intelligence, and can benefit various downstream applications, such as recommendation and question answering. In recent years, many research efforts have been proposed for knowledge graph embedding (KGE). However, most previous KGE methods ignore the semantic similarity between the related entities and entity-relation couples in different triples since they separately optimize each triple with the scoring function. To address this problem, we propose a simple yet efficient contrastive learning framework for tensor decomposition based (TDB) KGE, which can shorten the semantic distance of the related entities and entity-relation couples in different triples and thus improve the performance of KGE. We evaluate our proposed method on three standard KGE datasets: WN18RR, FB15k-237 and YAGO3-10. Our method can yield some new state-of-the-art results, achieving 51.2% MRR, 46.8% Hits@1 on the WN18RR dataset, 37.8% MRR, 28.6% Hits@1 on FB15k-237 dataset, and 59.1% MRR, 51.8% Hits@1 on the YAGO3-10 dataset.
We have created a knowledge graph based on major data sources used in ecotoxicological risk assessment. We have applied this knowledge graph to an important task in risk assessment, namely chemical effect prediction. We have evaluated nine knowledge graph embedding models from a selection of geometric, decomposition, and convolutional models on this prediction task. We show that using knowledge graph embeddings can increase the accuracy of effect prediction with neural networks. Furthermore, we have implemented a fine-tuning architecture that adapts the knowledge graph embeddings to the effect prediction task and leads to better performance. Finally, we evaluate certain characteristics of the knowledge graph embedding models to shed light on the individual model performance.
Graph embedding is a transformation of nodes of a network into a set of vectors. A good embedding should capture the underlying graph topology and structure, node-to-node relationship, and other relevant information about the graph, its subgraphs, and nodes themselves. If these objectives are achieved, an embedding is a meaningful, understandable, and often compressed representation of a network. Unfortunately, selecting the best embedding is a challenging task and very often requires domain experts. In this paper, we extend the framework for evaluating graph embeddings that was recently introduced by the authors. Now, the framework assigns two scores, local and global, to each embedding that measure the quality of an evaluated embedding for tasks that require good representation of local and, respectively, global properties of the network. The best embedding, if needed, can be selected in an unsupervised way, or the framework can identify a few embeddings that are worth further investigation. The framework is flexible, scalable, and can deal with undirected/directed, weighted/unweighted graphs.
Object encoding and identification are vital for robotic tasks such as autonomous exploration, semantic scene understanding, and re-localization. Previous approaches have attempted to either track objects or generate descriptors for object identification. However, such systems are limited to a "fixed" partial object representation from a single viewpoint. In a robot exploration setup, there is a requirement for a temporally "evolving" global object representation built as the robot observes the object from multiple viewpoints. Furthermore, given the vast distribution of unknown novel objects in the real world, the object identification process must be class-agnostic. In this context, we propose a novel temporal 3D object encoding approach, dubbed AirObject, to obtain global keypoint graph-based embeddings of objects. Specifically, the global 3D object embeddings are generated using a temporal convolutional network across structural information of multiple frames obtained from a graph attention-based encoding method. We demonstrate that AirObject achieves the state-of-the-art performance for video object identification and is robust to severe occlusion, perceptual aliasing, viewpoint shift, deformation, and scale transform, outperforming the state-of-the-art single-frame and sequential descriptors. To the best of our knowledge, AirObject is one of the first temporal object encoding methods. Source code is available at https://github.com/Nik-V9/AirObject.
We study the problem of generating data poisoning attacks against Knowledge Graph Embedding (KGE) models for the task of link prediction in knowledge graphs. To poison KGE models, we propose to exploit their inductive abilities which are captured through the relationship patterns like symmetry, inversion and composition in the knowledge graph. Specifically, to degrade the model's prediction confidence on target facts, we propose to improve the model's prediction confidence on a set of decoy facts. Thus, we craft adversarial additions that can improve the model's prediction confidence on decoy facts through different inference patterns. Our experiments demonstrate that the proposed poisoning attacks outperform state-of-art baselines on four KGE models for two publicly available datasets. We also find that the symmetry pattern based attacks generalize across all model-dataset combinations which indicates the sensitivity of KGE models to this pattern.
In autonomous vehicles (AVs), early warning systems rely on collision prediction to ensure occupant safety. However, state-of-the-art methods using deep convolutional networks either fail at modeling collisions or are too expensive/slow, making them less suitable for deployment on AV edge hardware. To address these limitations, we propose sg2vec, a spatio-temporal scene-graph embedding methodology that uses Graph Neural Network (GNN) and Long Short-Term Memory (LSTM) layers to predict future collisions via visual scene perception. We demonstrate that sg2vec predicts collisions 8.11% more accurately and 39.07% earlier than the state-of-the-art method on synthesized datasets, and 29.47% more accurately on a challenging real-world collision dataset. We also show that sg2vec is better than the state-of-the-art at transferring knowledge from synthetic datasets to real-world driving datasets. Finally, we demonstrate that sg2vec performs inference 9.3x faster with an 88.0% smaller model, 32.4% less power, and 92.8% less energy than the state-of-the-art method on the industry-standard Nvidia DRIVE PX 2 platform, making it more suitable for implementation on the edge.
Knowledge graph embedding models learn the representations of entities and relations in the knowledge graphs for predicting missing links (relations) between entities. Their effectiveness are deeply affected by the ability of modeling and inferring different relation patterns such as symmetry, asymmetry, inversion, composition and transitivity. Although existing models are already able to model many of these relations patterns, transitivity, a very common relation pattern, is still not been fully supported. In this paper, we first theoretically show that the transitive relations can be modeled with projections. We then propose the Rot-Pro model which combines the projection and relational rotation together. We prove that Rot-Pro can infer all the above relation patterns. Experimental results show that the proposed Rot-Pro model effectively learns the transitivity pattern and achieves the state-of-the-art results on the link prediction task in the datasets containing transitive relations.
Unsupervised representation learning (URL), which learns compact embeddings of high-dimensional data without supervision, has made remarkable progress recently. However, the development of URLs for different requirements is independent, which limits the generalization of the algorithms, especially prohibitive as the number of tasks grows. For example, dimension reduction methods, t-SNE, and UMAP optimize pair-wise data relationships by preserving the global geometric structure, while self-supervised learning, SimCLR, and BYOL focus on mining the local statistics of instances under specific augmentations. To address this dilemma, we summarize and propose a unified similarity-based URL framework, GenURL, which can smoothly adapt to various URL tasks. In this paper, we regard URL tasks as different implicit constraints on the data geometric structure that help to seek optimal low-dimensional representations that boil down to data structural modeling (DSM) and low-dimensional transformation (LDT). Specifically, DMS provides a structure-based submodule to describe the global structures, and LDT learns compact low-dimensional embeddings with given pretext tasks. Moreover, an objective function, General Kullback-Leibler divergence (GKL), is proposed to connect DMS and LDT naturally. Comprehensive experiments demonstrate that GenURL achieves consistent state-of-the-art performance in self-supervised visual learning, unsupervised knowledge distillation (KD), graph embeddings (GE), and dimension reduction.