The classical Weisfeiler-Leman algorithm aka color refinement is fundamental for graph learning with kernels and neural networks. Originally developed for graph isomorphism testing, the algorithm iteratively refines vertex colors. On many datasets, the stable coloring is reached after a few iterations and the optimal number of iterations for machine learning tasks is typically even lower. This suggests that the colors diverge too fast, defining a similarity that is too coarse. We generalize the concept of color refinement and propose a framework for gradual neighborhood refinement, which allows a slower convergence to the stable coloring and thus provides a more fine-grained refinement hierarchy and vertex similarity. We assign new colors by clustering vertex neighborhoods, replacing the original injective color assignment function. Our approach is used to derive new variants of existing graph kernels and to approximate the graph edit distance via optimal assignments regarding vertex similarity. We show that in both tasks, our method outperforms the original color refinement with only a moderate increase in running time advancing the state of the art.
Although previous graph-based multi-view clustering algorithms have gained significant progress, most of them are still faced with three limitations. First, they often suffer from high computational complexity, which restricts their applications in large-scale scenarios. Second, they usually perform graph learning either at the single-view level or at the view-consensus level, but often neglect the possibility of the joint learning of single-view and consensus graphs. Third, many of them rely on the k-means for discretization of the spectral embeddings, which lack the ability to directly learn the graph with discrete cluster structure. In light of this, this paper presents an efficient multi-view clustering approach via unified and discrete bipartite graph learning (UDBGL). Specifically, the anchor-based subspace learning is incorporated to learn the view-specific bipartite graphs from multiple views, upon which the bipartite graph fusion is leveraged to learn a view-consensus bipartite graph with adaptive weight learning. Further, the Laplacian rank constraint is imposed to ensure that the fused bipartite graph has discrete cluster structures (with a specific number of connected components). By simultaneously formulating the view-specific bipartite graph learning, the view-consensus bipartite graph learning, and the discrete cluster structure learning into a unified objective function, an efficient minimization algorithm is then designed to tackle this optimization problem and directly achieve a discrete clustering solution without requiring additional partitioning, which notably has linear time complexity in data size. Experiments on a variety of multi-view datasets demonstrate the robustness and efficiency of our UDBGL approach. The code is available at https://github.com/huangdonghere/UDBGL.
As special information carriers containing both structure and feature information, graphs are widely used in graph mining, e.g., Graph Neural Networks (GNNs). However, in some practical scenarios, graph data are stored separately in multiple distributed parties, which may not be directly shared due to conflicts of interest. Hence, federated graph neural networks are proposed to address such data silo problems while preserving the privacy of each party (or client). Nevertheless, different graph data distributions among various parties, which is known as the statistical heterogeneity, may degrade the performance of naive federated learning algorithms like FedAvg. In this paper, we propose FedEgo, a federated graph learning framework based on ego-graphs to tackle the challenges above, where each client will train their local models while also contributing to the training of a global model. FedEgo applies GraphSAGE over ego-graphs to make full use of the structure information and utilizes Mixup for privacy concerns. To deal with the statistical heterogeneity, we integrate personalization into learning and propose an adaptive mixing coefficient strategy that enables clients to achieve their optimal personalization. Extensive experimental results and in-depth analysis demonstrate the effectiveness of FedEgo.
Session-based recommender systems capture the short-term interest of a user within a session. Session contexts (i.e., a user's high-level interests or intents within a session) are not explicitly given in most datasets, and implicitly inferring session context as an aggregation of item-level attributes is crude. In this paper, we propose ISCON, which implicitly contextualizes sessions. ISCON first generates implicit contexts for sessions by creating a session-item graph, learning graph embeddings, and clustering to assign sessions to contexts. ISCON then trains a session context predictor and uses the predicted contexts' embeddings to enhance the next-item prediction accuracy. Experiments on four datasets show that ISCON has superior next-item prediction accuracy than state-of-the-art models. A case study of ISCON on the Reddit dataset confirms that assigned session contexts are unique and meaningful.
Topology-imbalance is a graph-specific imbalance problem caused by the uneven topology positions of labeled nodes, which significantly damages the performance of GNNs. What topology-imbalance means and how to measure its impact on graph learning remain under-explored. In this paper, we provide a new understanding of topology-imbalance from a global view of the supervision information distribution in terms of under-reaching and over-squashing, which motivates two quantitative metrics as measurements. In light of our analysis, we propose a novel position-aware graph structure learning framework named PASTEL, which directly optimizes the information propagation path and solves the topology-imbalance issue in essence. Our key insight is to enhance the connectivity of nodes within the same class for more supervision information, thereby relieving the under-reaching and over-squashing phenomena. Specifically, we design an anchor-based position encoding mechanism, which better incorporates relative topology position and enhances the intra-class inductive bias by maximizing the label influence. We further propose a class-wise conflict measure as the edge weights, which benefits the separation of different node classes. Extensive experiments demonstrate the superior potential and adaptability of PASTEL in enhancing GNNs' power in different data annotation scenarios.
Graph Neural Networks (GNNs) have been successfully applied to many real-world static graphs. However, the success of static graphs has not fully translated to dynamic graphs due to the limitations in model design, evaluation settings, and training strategies. Concretely, existing dynamic GNNs do not incorporate state-of-the-art designs from static GNNs, which limits their performance. Current evaluation settings for dynamic GNNs do not fully reflect the evolving nature of dynamic graphs. Finally, commonly used training methods for dynamic GNNs are not scalable. Here we propose ROLAND, an effective graph representation learning framework for real-world dynamic graphs. At its core, the ROLAND framework can help researchers easily repurpose any static GNN to dynamic graphs. Our insight is to view the node embeddings at different GNN layers as hierarchical node states and then recurrently update them over time. We then introduce a live-update evaluation setting for dynamic graphs that mimics real-world use cases, where GNNs are making predictions and being updated on a rolling basis. Finally, we propose a scalable and efficient training approach for dynamic GNNs via incremental training and meta-learning. We conduct experiments over eight different dynamic graph datasets on future link prediction tasks. Models built using the ROLAND framework achieve on average 62.7% relative mean reciprocal rank (MRR) improvement over state-of-the-art baselines under the standard evaluation settings on three datasets. We find state-of-the-art baselines experience out-of-memory errors for larger datasets, while ROLAND can easily scale to dynamic graphs with 56 million edges. After re-implementing these baselines using the ROLAND training strategy, ROLAND models still achieve on average 15.5% relative MRR improvement over the baselines.
This work considers the task of representation learning on the attributed relational graph (ARG). Both the nodes and edges in an ARG are associated with attributes/features allowing ARGs to encode rich structural information widely observed in real applications. Existing graph neural networks offer limited ability to capture complex interactions within local structural contexts, which hinders them from taking advantage of the expression power of ARGs. We propose Motif Convolution Module (MCM), a new motif-based graph representation learning technique to better utilize local structural information. The ability to handle continuous edge and node features is one of MCM's advantages over existing motif-based models. MCM builds a motif vocabulary in an unsupervised way and deploys a novel motif convolution operation to extract the local structural context of individual nodes, which is then used to learn higher-level node representations via multilayer perceptron and/or message passing in graph neural networks. When compared with other graph learning approaches to classifying synthetic graphs, our approach is substantially better in capturing structural context. We also demonstrate the performance and explainability advantages of our approach by applying it to several molecular benchmarks.
The generalizability to new databases is of vital importance to Text-to-SQL systems which aim to parse human utterances into SQL statements. Existing works achieve this goal by leveraging the exact matching method to identify the lexical matching between the question words and the schema items. However, these methods fail in other challenging scenarios, such as the synonym substitution in which the surface form differs between the corresponding question words and schema items. In this paper, we propose a framework named ISESL-SQL to iteratively build a semantic enhanced schema-linking graph between question tokens and database schemas. First, we extract a schema linking graph from PLMs through a probing procedure in an unsupervised manner. Then the schema linking graph is further optimized during the training process through a deep graph learning method. Meanwhile, we also design an auxiliary task called graph regularization to improve the schema information mentioned in the schema-linking graph. Extensive experiments on three benchmarks demonstrate that ISESL-SQL could consistently outperform the baselines and further investigations show its generalizability and robustness.
Recent advances in data processing have stimulated the demand for learning graphs of very large scales. Graph Neural Networks (GNNs), being an emerging and powerful approach in solving graph learning tasks, are known to be difficult to scale up. Most scalable models apply node-based techniques in simplifying the expensive graph message-passing propagation procedure of GNN. However, we find such acceleration insufficient when applied to million- or even billion-scale graphs. In this work, we propose SCARA, a scalable GNN with feature-oriented optimization for graph computation. SCARA efficiently computes graph embedding from node features, and further selects and reuses feature computation results to reduce overhead. Theoretical analysis indicates that our model achieves sub-linear time complexity with a guaranteed precision in propagation process as well as GNN training and inference. We conduct extensive experiments on various datasets to evaluate the efficacy and efficiency of SCARA. Performance comparison with baselines shows that SCARA can reach up to 100x graph propagation acceleration than current state-of-the-art methods with fast convergence and comparable accuracy. Most notably, it is efficient to process precomputation on the largest available billion-scale GNN dataset Papers100M (111M nodes, 1.6B edges) in 100 seconds.
Active speaker detection (ASD) in videos with multiple speakers is a challenging task as it requires learning effective audiovisual features and spatial-temporal correlations over long temporal windows. In this paper, we present SPELL, a novel spatial-temporal graph learning framework that can solve complex tasks such as ASD. To this end, each person in a video frame is first encoded in a unique node for that frame. Nodes corresponding to a single person across frames are connected to encode their temporal dynamics. Nodes within a frame are also connected to encode inter-person relationships. Thus, SPELL reduces ASD to a node classification task. Importantly, SPELL is able to reason over long temporal contexts for all nodes without relying on computationally expensive fully connected graph neural networks. Through extensive experiments on the AVA-ActiveSpeaker dataset, we demonstrate that learning graph-based representations can significantly improve the active speaker detection performance owing to its explicit spatial and temporal structure. SPELL outperforms all previous state-of-the-art approaches while requiring significantly lower memory and computational resources. Our code is publicly available at https://github.com/SRA2/SPELL
Personalized PageRank (PPR) is a fundamental tool in unsupervised learning of graph representations such as node ranking, labeling, and graph embedding. However, while data privacy is one of the most important recent concerns, existing PPR algorithms are not designed to protect user privacy. PPR is highly sensitive to the input graph edges: the difference of only one edge may cause a big change in the PPR vector, potentially leaking private user data. In this work, we propose an algorithm which outputs an approximate PPR and has provably bounded sensitivity to input edges. In addition, we prove that our algorithm achieves similar accuracy to non-private algorithms when the input graph has large degrees. Our sensitivity-bounded PPR directly implies private algorithms for several tools of graph learning, such as, differentially private (DP) PPR ranking, DP node classification, and DP node embedding. To complement our theoretical analysis, we also empirically verify the practical performances of our algorithms.
This paper is focused on the statistical analysis of data consisting of a collection of multiple series of probability measures that are indexed by distinct time instants and supported over a bounded interval of the real line. By modeling these time-dependent probability measures as random objects in the Wasserstein space, we propose a new auto-regressive model for the statistical analysis of multivariate distributional time series. Using the theory of iterated random function systems, results on the existence, uniqueness and stationarity of the solution of such a model are provided. We also propose a consistent estimator for the auto-regressive coefficients of this model. Due to the simplex constraints that we impose on the model coefficients, the proposed estimator that is learned under these constraints, naturally has a sparse structure. The sparsity allows the application of the proposed model in learning a graph of temporal dependency from multivariate distributional time series. We explore the numerical performances of our estimation procedure using simulated data. To shed some light on the benefits of our approach for real data analysis, we also apply this methodology to two data sets, respectively made of observations from age distribution in different countries and those from the bike sharing network in Paris.
Molecular representation learning (MRL) is a key step to build the connection between machine learning and chemical science. In particular, it encodes molecules as numerical vectors preserving the molecular structures and features, on top of which the downstream tasks (e.g., property prediction) can be performed. Recently, MRL has achieved considerable progress, especially in methods based on deep molecular graph learning. In this survey, we systematically review these graph-based molecular representation techniques, especially the methods incorporating chemical domain knowledge. Specifically, we first introduce the features of 2D and 3D molecular graphs. Then we summarize and categorize MRL methods into three groups based on their input. Furthermore, we discuss some typical chemical applications supported by MRL. To facilitate studies in this fast-developing area, we also list the benchmarks and commonly used datasets in the paper. Finally, we share our thoughts on future research directions.
TensorFlow-GNN (TF-GNN) is a scalable library for Graph Neural Networks in TensorFlow. It is designed from the bottom up to support the kinds of rich heterogeneous graph data that occurs in today's information ecosystems. In addition to enabling machine learning researchers and advanced developers, TF-GNN offers low-code solutions to empower the broader developer community in graph learning. Many production models at Google use TF-GNN, and it has been recently released as an open source project. In this paper we describe the TF-GNN data model, its Keras message passing API, and relevant capabilities such as graph sampling and distributed training.
When dealing with tabular data, models based on decision trees are a popular choice due to their high accuracy on these data types, their ease of application, and explainability properties. However, when it comes to graph-structured data, it is not clear how to apply them effectively, in a way that incorporates the topological information with the tabular data available on the vertices of the graph. To address this challenge, we introduce TREE-G. TREE-G modifies standard decision trees, by introducing a novel split function that is specialized for graph data. Not only does this split function incorporate the node features and the topological information, but it also uses a novel pointer mechanism that allows split nodes to use information computed in previous splits. Therefore, the split function adapts to the predictive task and the graph at hand. We analyze the theoretical properties of TREE-G and demonstrate its benefits empirically on multiple graph and vertex prediction benchmarks. In these experiments, TREE-G consistently outperforms other tree-based models and often outperforms other graph-learning algorithms such as Graph Neural Networks (GNNs) and Graph Kernels, sometimes by large margins. Moreover, TREE-Gs models and their predictions can be explained and visualized
We show that standard Transformers without graph-specific modifications can lead to promising results in graph learning both in theory and practice. Given a graph, we simply treat all nodes and edges as independent tokens, augment them with token embeddings, and feed them to a Transformer. With an appropriate choice of token embeddings, we prove that this approach is theoretically at least as expressive as an invariant graph network (2-IGN) composed of equivariant linear layers, which is already more expressive than all message-passing Graph Neural Networks (GNN). When trained on a large-scale graph dataset (PCQM4Mv2), our method coined Tokenized Graph Transformer (TokenGT) achieves significantly better results compared to GNN baselines and competitive results compared to Transformer variants with sophisticated graph-specific inductive bias. Our implementation is available at https://github.com/jw9730/tokengt.
Given a graph learning task, such as link prediction, on a new graph, how can we select the best method as well as its hyperparameters (collectively called a model) without having to train or evaluate any model on the new graph? Model selection for graph learning has been largely ad hoc. A typical approach has been to apply popular methods to new datasets, but this is often suboptimal. On the other hand, systematically comparing models on the new graph quickly becomes too costly, or even impractical. In this work, we develop the first meta-learning approach for evaluation-free graph learning model selection, called MetaGL, which utilizes the prior performances of existing methods on various benchmark graph datasets to automatically select an effective model for the new graph, without any model training or evaluations. To quantify similarities across a wide variety of graphs, we introduce specialized meta-graph features that capture the structural characteristics of a graph. Then we design G-M network, which represents the relations among graphs and models, and develop a graph-based meta-learner operating on this G-M network, which estimates the relevance of each model to different graphs. Extensive experiments show that using MetaGL to select a model for the new graph greatly outperforms several existing meta-learning techniques tailored for graph learning model selection (up to 47% better), while being extremely fast at test time (~1 sec).
We all depend on mobility, and vehicular transportation affects the daily lives of most of us. Thus, the ability to forecast the state of traffic in a road network is an important functionality and a challenging task. Traffic data is often obtained from sensors deployed in a road network. Recent proposals on spatial-temporal graph neural networks have achieved great progress at modeling complex spatial-temporal correlations in traffic data, by modeling traffic data as a diffusion process. However, intuitively, traffic data encompasses two different kinds of hidden time series signals, namely the diffusion signals and inherent signals. Unfortunately, nearly all previous works coarsely consider traffic signals entirely as the outcome of the diffusion, while neglecting the inherent signals, which impacts model performance negatively. To improve modeling performance, we propose a novel Decoupled Spatial-Temporal Framework (DSTF) that separates the diffusion and inherent traffic information in a data-driven manner, which encompasses a unique estimation gate and a residual decomposition mechanism. The separated signals can be handled subsequently by the diffusion and inherent modules separately. Further, we propose an instantiation of DSTF, Decoupled Dynamic Spatial-Temporal Graph Neural Network (D2STGNN), that captures spatial-temporal correlations and also features a dynamic graph learning module that targets the learning of the dynamic characteristics of traffic networks. Extensive experiments with four real-world traffic datasets demonstrate that the framework is capable of advancing the state-of-the-art.
Graph embedding techniques are a staple of modern graph learning research. When using embeddings for downstream tasks such as classification, information about their stability and robustness, i.e., their susceptibility to sources of noise, stochastic effects, or specific parameter choices, becomes increasingly important. As one of the most prominent graph embedding schemes, we focus on node2vec and analyse its embedding quality from multiple perspectives. Our findings indicate that embedding quality is unstable with respect to parameter choices, and we propose strategies to remedy this in practice.
We introduce Hyperbard, a dataset of diverse relational data representations derived from Shakespeare's plays. Our representations range from simple graphs capturing character co-occurrence in single scenes to hypergraphs encoding complex communication settings and character contributions as hyperedges with edge-specific node weights. By making multiple intuitive representations readily available for experimentation, we facilitate rigorous representation robustness checks in graph learning, graph mining, and network analysis, highlighting the advantages and drawbacks of specific representations. Leveraging the data released in Hyperbard, we demonstrate that many solutions to popular graph mining problems are highly dependent on the representation choice, thus calling current graph curation practices into question. As an homage to our data source, and asserting that science can also be art, we present all our points in the form of a play.