Graph Neural Networks (GNNs) extend the success of neural networks to graph-structured data by accounting for their intrinsic geometry. While extensive research has been done on developing GNN models with superior performance according to a collection of graph representation learning benchmarks, it is currently not well understood what aspects of a given model are probed by them. For example, to what extent do they test the ability of a model to leverage graph structure vs. node features? Here, we develop a principled approach to taxonomize benchmarking datasets according to a $\textit{sensitivity profile}$ that is based on how much GNN performance changes due to a collection of graph perturbations. Our data-driven analysis provides a deeper understanding of which benchmarking data characteristics are leveraged by GNNs. Consequently, our taxonomy can aid in selection and development of adequate graph benchmarks, and better informed evaluation of future GNN methods. Finally, our approach and implementation in $\texttt{GTaxoGym}$ package are extendable to multiple graph prediction task types and future datasets.
Graph contrastive learning (GCL) improves graph representation learning, leading to SOTA on various downstream tasks. The graph augmentation step is a vital but scarcely studied step of GCL. In this paper, we show that the node embedding obtained via the graph augmentations is highly biased, somewhat limiting contrastive models from learning discriminative features for downstream tasks. Thus, instead of investigating graph augmentation in the input space, we alternatively propose to perform augmentations on the hidden features (feature augmentation). Inspired by so-called matrix sketching, we propose COSTA, a novel COvariance-preServing feaTure space Augmentation framework for GCL, which generates augmented features by maintaining a "good sketch" of original features. To highlight the superiority of feature augmentation with COSTA, we investigate a single-view setting (in addition to multi-view one) which conserves memory and computations. We show that the feature augmentation with COSTA achieves comparable/better results than graph augmentation based models.
Many modern deep-learning techniques do not work without enormous datasets. At the same time, several fields demand methods working in scarcity of data. This problem is even more complex when the samples have varying structures, as in the case of graphs. Graph representation learning techniques have recently proven successful in a variety of domains. Nevertheless, the employed architectures perform miserably when faced with data scarcity. On the other hand, few-shot learning allows employing modern deep learning models in scarce data regimes without waiving their effectiveness. In this work, we tackle the problem of few-shot graph classification, showing that equipping a simple distance metric learning baseline with a state-of-the-art graph embedder allows to obtain competitive results on the task. While the simplicity of the architecture is enough to outperform more complex ones, it also allows straightforward additions. To this end, we show that additional improvements may be obtained by encouraging a task-conditioned embedding space. Finally, we propose a MixUp-based online data augmentation technique acting in the latent space and show its effectiveness on the task.
Designing accurate deep learning models for molecular property prediction plays an increasingly essential role in drug and material discovery. Recently, due to the scarcity of labeled molecules, self-supervised learning methods for learning generalizable and transferable representations of molecular graphs have attracted lots of attention. In this paper, we argue that there exist two major issues hindering current self-supervised learning methods from obtaining desired performance on molecular property prediction, that is, the ill-defined pre-training tasks and the limited model capacity. To this end, we introduce Knowledge-guided Pre-training of Graph Transformer (KPGT), a novel self-supervised learning framework for molecular graph representation learning, to alleviate the aforementioned issues and improve the performance on the downstream molecular property prediction tasks. More specifically, we first introduce a high-capacity model, named Line Graph Transformer (LiGhT), which emphasizes the importance of chemical bonds and is mainly designed to model the structural information of molecular graphs. Then, a knowledge-guided pre-training strategy is proposed to exploit the additional knowledge of molecules to guide the model to capture the abundant structural and semantic information from large-scale unlabeled molecular graphs. Extensive computational tests demonstrated that KPGT can offer superior performance over current state-of-the-art methods on several molecular property prediction tasks.
Capsule networks were proposed as an alternative approach to Convolutional Neural Networks (CNNs) for learning object-centric representations, which can be leveraged for improved generalization and sample complexity. Unlike CNNs, capsule networks are designed to explicitly model part-whole hierarchical relationships by using groups of neurons to encode visual entities, and learn the relationships between those entities. Promising early results achieved by capsule networks have motivated the deep learning community to continue trying to improve their performance and scalability across several application areas. However, a major hurdle for capsule network research has been the lack of a reliable point of reference for understanding their foundational ideas and motivations. The aim of this survey is to provide a comprehensive overview of the capsule network research landscape, which will serve as a valuable resource for the community going forward. To that end, we start with an introduction to the fundamental concepts and motivations behind capsule networks, such as equivariant inference in computer vision. We then cover the technical advances in the capsule routing mechanisms and the various formulations of capsule networks, e.g. generative and geometric. Additionally, we provide a detailed explanation of how capsule networks relate to the popular attention mechanism in Transformers, and highlight non-trivial conceptual similarities between them in the context of representation learning. Afterwards, we explore the extensive applications of capsule networks in computer vision, video and motion, graph representation learning, natural language processing, medical imaging and many others. To conclude, we provide an in-depth discussion regarding the main hurdles in capsule network research, and highlight promising research directions for future work.
The human proteome contains a vast network of interacting kinases and substrates. Even though some kinases have proven to be immensely useful as therapeutic targets, a majority are still understudied. In this work, we present a novel knowledge graph representation learning approach to predict novel interaction partners for understudied kinases. Our approach uses a phosphoproteomic knowledge graph constructed by integrating data from iPTMnet, Protein Ontology, Gene Ontology and BioKG. The representation of kinases and substrates in this knowledge graph are learned by performing directed random walks on triples coupled with a modified SkipGram or CBOW model. These representations are then used as an input to a supervised classification model to predict novel interactions for understudied kinases. We also present a post-predictive analysis of the predicted interactions and an ablation study of the phosphoproteomic knowledge graph to gain an insight into the biology of the understudied kinases.
Graph contrastive learning (GCL) alleviates the heavy reliance on label information for graph representation learning (GRL) via self-supervised learning schemes. The core idea is to learn by maximising mutual information for similar instances, which requires similarity computation between two node instances. However, GCL is inefficient in both time and memory consumption. In addition, GCL normally requires a large number of training epochs to be well-trained on large-scale datasets. Inspired by an observation of a technical defect (i.e., inappropriate usage of Sigmoid function) commonly used in two representative GCL works, DGI and MVGRL, we revisit GCL and introduce a new learning paradigm for self-supervised graph representation learning, namely, Group Discrimination (GD), and propose a novel GD-based method called Graph Group Discrimination (GGD). Instead of similarity computation, GGD directly discriminates two groups of node samples with a very simple binary cross-entropy loss. In addition, GGD requires much fewer training epochs to obtain competitive performance compared with GCL methods on large-scale datasets. These two advantages endow GGD with very efficient property. Extensive experiments show that GGD outperforms state-of-the-art self-supervised methods on eight datasets. In particular, GGD can be trained in 0.18 seconds (6.44 seconds including data preprocessing) on ogbn-arxiv, which is orders of magnitude (10,000+) faster than GCL baselines while consuming much less memory. Trained with 9 hours on ogbn-papers100M with billion edges, GGD outperforms its GCL counterparts in both accuracy and efficiency.
Graph Neural Networks (GNNs) are effective tools for graph representation learning. Most GNNs rely on a recursive neighborhood aggregation scheme, named message passing, thereby their theoretical expressive power is limited to the first-order Weisfeiler-Lehman test (1-WL). An effective approach to this challenge is to explicitly retrieve some annotated examples used to enhance GNN models. While retrieval-enhanced models have been proved to be effective in many language and vision domains, it remains an open question how effective retrieval-enhanced GNNs are when applied to graph datasets. Motivated by this, we want to explore how the retrieval idea can help augment the useful information learned in the graph neural networks, and we design a retrieval-enhanced scheme called GRAPHRETRIEVAL, which is agnostic to the choice of graph neural network models. In GRAPHRETRIEVAL, for each input graph, similar graphs together with their ground-true labels are retrieved from an existing database. Thus they can act as a potential enhancement to complete various graph property predictive tasks. We conduct comprehensive experiments over 13 datasets, and we observe that GRAPHRETRIEVAL is able to reach substantial improvements over existing GNNs. Moreover, our empirical study also illustrates that retrieval enhancement is a promising remedy for alleviating the long-tailed label distribution problem.
Unsupervised/self-supervised graph representation learning is critical for downstream node- and graph-level classification tasks. Global structure of graphs helps discriminating representations and existing methods mainly utilize the global structure by imposing additional supervisions. However, their global semantics are usually invariant for all nodes/graphs and they fail to explicitly embed the global semantics to enrich the representations. In this paper, we propose Omni-Granular Ego-Semantic Propagation for Self-Supervised Graph Representation Learning (OEPG). Specifically, we introduce instance-adaptive global-aware ego-semantic descriptors, leveraging the first- and second-order feature differences between each node/graph and hierarchical global clusters of the entire graph dataset. The descriptors can be explicitly integrated into local graph convolution as new neighbor nodes. Besides, we design an omni-granular normalization on the whole scales and hierarchies of the ego-semantic to assign attentional weight to each descriptor from an omni-granular perspective. Specialized pretext tasks and cross-iteration momentum update are further developed for local-global mutual adaptation. In downstream tasks, OEPG consistently achieves the best performance with a 2%~6% accuracy gain on multiple datasets cross scales and domains. Notably, OEPG also generalizes to quantity- and topology-imbalance scenarios.
Recent years have witnessed a rapid growth of applying deep spatiotemporal methods in traffic forecasting. However, the prediction of origin-destination (OD) demands is still a challenging problem since the number of OD pairs is usually quadratic to the number of stations. In this case, most of the existing spatiotemporal methods fail to handle spatial relations on such a large scale. To address this problem, this paper provides a dynamic graph representation learning framework for OD demands prediction. In particular, a hierarchical memory updater is first proposed to maintain a time-aware representation for each node, and the representations are updated according to the most recently observed OD trips in continuous-time and multiple discrete-time ways. Second, a spatiotemporal propagation mechanism is provided to aggregate representations of neighbor nodes along a random spatiotemporal route which treats origin and destination as two different semantic entities. Last, an objective function is designed to derive the future OD demands according to the most recent node representations, and also to tackle the data sparsity problem in OD prediction. Extensive experiments have been conducted on two real-world datasets, and the experimental results demonstrate the superiority of the proposed method. The code and data are available at https://github.com/Rising0321/HMOD.
Learning efficient graph representation is the key to favorably addressing downstream tasks on graphs, such as node or graph property prediction. Given the non-Euclidean structural property of graphs, preserving the original graph data's similarity relationship in the embedded space needs specific tools and a similarity metric. This paper develops a new graph representation learning scheme, namely EGG, which embeds approximated second-order graph characteristics into a Grassmann manifold. The proposed strategy leverages graph convolutions to learn hidden representations of the corresponding subspace of the graph, which is then mapped to a Grassmann point of a low dimensional manifold through truncated singular value decomposition (SVD). The established graph embedding approximates denoised correlationship of node attributes, as implemented in the form of a symmetric matrix space for Euclidean calculation. The effectiveness of EGG is demonstrated using both clustering and classification tasks at the node level and graph level. It outperforms baseline models on various benchmarks.
This paper is concerned with the complex task of identifying the type and cause of the events that are captured by distribution-level phasor measurement units (D-PMUs) in order to enhance situational awareness in power distribution systems. Our goal is to address two fundamental challenges in this field: a) scarcity in measurement locations due to the high cost of purchasing, installing, and streaming data from D-PMUs; b) limited prior knowledge about the event signatures due to the fact that the events are diverse, infrequent, and inherently unscheduled. To tackle these challenges, we propose an unsupervised graph-representation learning method, called GraphPMU, to significantly improve the performance in event clustering under locationally-scarce data availability by proposing the following two new directions: 1) using the topological information about the relative location of the few available phasor measurement units on the graph of the power distribution network; 2) utilizing not only the commonly used fundamental phasor measurements, bus also the less explored harmonic phasor measurements in the process of analyzing the signatures of various events. Through a detailed analysis of several case studies, we show that GraphPMU can highly outperform the prevalent methods in the literature.
We propose a recipe on how to build a general, powerful, scalable (GPS) graph Transformer with linear complexity and state-of-the-art results on a diverse set of benchmarks. Graph Transformers (GTs) have gained popularity in the field of graph representation learning with a variety of recent publications but they lack a common foundation about what constitutes a good positional or structural encoding, and what differentiates them. In this paper, we summarize the different types of encodings with a clearer definition and categorize them as being $\textit{local}$, $\textit{global}$ or $\textit{relative}$. The prior GTs are constrained to small graphs with a few hundred nodes, here we propose the first architecture with a complexity linear in the number of nodes and edges $O(N+E)$ by decoupling the local real-edge aggregation from the fully-connected Transformer. We argue that this decoupling does not negatively affect the expressivity, with our architecture being a universal function approximator on graphs. Our GPS recipe consists of choosing 3 main ingredients: (i) positional/structural encoding, (ii) local message-passing mechanism, and (iii) global attention mechanism. We provide a modular framework $\textit{GraphGPS}$ that supports multiple types of encodings and that provides efficiency and scalability both in small and large graphs. We test our architecture on 16 benchmarks and show highly competitive results in all of them, show-casing the empirical benefits gained by the modularity and the combination of different strategies.
Leveraging graphs on recommender systems has gained popularity with the development of graph representation learning (GRL). In particular, knowledge graph embedding (KGE) and graph neural networks (GNNs) are representative GRL approaches, which have achieved the state-of-the-art performance on several recommendation tasks. Furthermore, combination of KGE and GNNs (KG-GNNs) has been explored and found effective in many academic literatures. One of the main characteristics of GNNs is their ability to retain structural properties among neighbors in the resulting dense representation, which is usually coined as smoothing. The smoothing is specially desired in the presence of homophilic graphs, such as the ones we find on recommender systems. In this paper, we propose a new model for recommender systems named Knowledge Query-based Graph Convolution (KQGC). In contrast to exisiting KG-GNNs, KQGC focuses on the smoothing, and leverages a simple linear graph convolution for smoothing KGE. A pre-trained KGE is fed into KQGC, and it is smoothed by aggregating neighbor knowledge queries, which allow entity-embeddings to be aligned on appropriate vector points for smoothing KGE effectively. We apply the proposed KQGC to a recommendation task that aims prospective users for specific products. Extensive experiments on a real E-commerce dataset demonstrate the effectiveness of KQGC.
Sequential recommendation (SR) learns users' preferences by capturing the sequential patterns from users' behaviors evolution. As discussed in many works, user-item interactions of SR generally present the intrinsic power-law distribution, which can be ascended to hierarchy-like structures. Previous methods usually handle such hierarchical information by making user-item sectionalization empirically under Euclidean space, which may cause distortion of user-item representation in real online scenarios. In this paper, we propose a Poincar\'{e}-based heterogeneous graph neural network named PHGR to model the sequential pattern information as well as hierarchical information contained in the data of SR scenarios simultaneously. Specifically, for the purpose of explicitly capturing the hierarchical information, we first construct a weighted user-item heterogeneous graph by aliening all the user-item interactions to improve the perception domain of each user from a global view. Then the output of the global representation would be used to complement the local directed item-item homogeneous graph convolution. By defining a novel hyperbolic inner product operator, the global and local graph representation learning are directly conducted in Poincar\'{e} ball instead of commonly used projection operation between Poincar\'{e} ball and Euclidean space, which could alleviate the cumulative error issue of general bidirectional translation process. Moreover, for the purpose of explicitly capturing the sequential dependency information, we design two types of temporal attention operations under Poincar\'{e} ball space. Empirical evaluations on datasets from the public and financial industry show that PHGR outperforms several comparison methods.
Transformers have achieved remarkable performance in widespread fields, including natural language processing, computer vision and graph mining. However, vanilla Transformer architectures have not yielded promising improvements in the Knowledge Graph (KG) representations, where the translational distance paradigm dominates this area. Note that vanilla Transformer architectures struggle to capture the intrinsically heterogeneous structural and semantic information of knowledge graphs. To this end, we propose a new variant of Transformer for knowledge graph representations dubbed Relphormer. Specifically, we introduce Triple2Seq which can dynamically sample contextualized sub-graph sequences as the input to alleviate the heterogeneity issue. We propose a novel structure-enhanced self-attention mechanism to encode the relational information and keep the semantic information within entities and relations. Moreover, we utilize masked knowledge modeling for general knowledge graph representation learning, which can be applied to various KG-based tasks including knowledge graph completion, question answering, and recommendation. Experimental results on six datasets show that Relphormer can obtain better performance compared with baselines. Code is available in https://github.com/zjunlp/Relphormer.
Graph representation learning aim at integrating node contents with graph structure to learn nodes/graph representations. Nevertheless, it is found that many existing graph learning methods do not work well on data with high heterophily level that accounts for a large proportion of edges between different class labels. Recent efforts to this problem focus on improving the message passing mechanism. However, it remains unclear whether heterophily truly does harm to the performance of graph neural networks (GNNs). The key is to unfold the relationship between a node and its immediate neighbors, e.g., are they heterophilous or homophilious? From this perspective, here we study the role of heterophily in graph representation learning before/after the relationships between connected nodes are disclosed. In particular, we propose an end-to-end framework that both learns the type of edges (i.e., heterophilous/homophilious) and leverage edge type information to improve the expressiveness of graph neural networks. We implement this framework in two different ways. Specifically, to avoid messages passing through heterophilous edges, we can optimize the graph structure to be homophilious by dropping heterophilous edges identified by an edge classifier. Alternatively, it is possible to exploit the information about the presence of heterophilous neighbors for feature learning, so a hybrid message passing approach is devised to aggregate homophilious neighbors and diversify heterophilous neighbors based on edge classification. Extensive experiments demonstrate the remarkable performance improvement of GNNs with the proposed framework on multiple datasets across the full spectrum of homophily level.
The growing popularity of Graph Representation Learning (GRL) methods has resulted in the development of a large number of models applied to a miscellany of domains. Behind this diversity of domains, there is a strong heterogeneity of graphs, making it difficult to estimate the expected performance of a model on a new graph, especially when the graph has distinctive characteristics that have not been encountered in the benchmark yet. To address this, we have developed an experimental pipeline, to assess the impact of a given property on the models performances. In this paper, we use this pipeline to study the effect of two specificities encountered on banks transactional graphs resulting from the partial view a bank has on all the individuals and transactions carried out on the market. These specific features are graph sparsity and asymmetric node information. This study demonstrates the robustness of GRL methods to these distinctive characteristics. We believe that this work can ease the evaluation of GRL methods to specific characteristics and foster the development of such methods on transactional graphs.
Dual embodied-symbolic concept representations are the foundation for deep learning and symbolic AI integration. We discuss the use of dual embodied-symbolic concept representations for molecular graph representation learning, specifically with exemplar-based contrastive self-supervised learning (SSL). The embodied representations are learned from molecular graphs, and the symbolic representations are learned from the corresponding Chemical knowledge graph (KG). We use the Chemical KG to enhance molecular graphs with symbolic (semantic) knowledge and generate their augmented molecular graphs. We treat a molecular graph and its semantically augmented molecular graph as exemplars of the same semantic class, and use the pairs as positive pairs in exemplar-based contrastive SSL.
The real-time transient stability assessment (TSA) plays a critical role in the secure operation of the power system. Although the classic numerical integration method, \textit{i.e.} time-domain simulation (TDS), has been widely used in industry practice, it is inevitably trapped in a high computational complexity due to the high latitude sophistication of the power system. In this work, a data-driven power system estimation method is proposed to quickly predict the stability of the power system before TDS reaches the end of simulating time windows, which can reduce the average simulation time of stability assessment without loss of accuracy. As the topology of the power system is in the form of graph structure, graph neural network based representation learning is naturally suitable for learning the status of the power system. Motivated by observing the distribution information of crucial active power and reactive power on the power system's bus nodes, we thus propose a distribution-aware learning~(DAL) module to explore an informative graph representation vector for describing the status of a power system. Then, TSA is re-defined as a binary classification task, and the stability of the system is determined directly from the resulting graph representation without numerical integration. Finally, we apply our method to the online TSA task. The case studies on the IEEE 39-bus system and Polish 2383-bus system demonstrate the effectiveness of our proposed method.