Graph Neural Networks (GNNs) have achieved great success on a variety of tasks with graph-structural data, among which node classification is an essential one. Unsupervised Graph Domain Adaptation (UGDA) shows its practical value of reducing the labeling cost for node classification. It leverages knowledge from a labeled graph (i.e., source domain) to tackle the same task on another unlabeled graph (i.e., target domain). Most existing UGDA methods heavily rely on the labeled graph in the source domain. They utilize labels from the source domain as the supervision signal and are jointly trained on both the source graph and the target graph. However, in some real-world scenarios, the source graph is inaccessible because of privacy issues. Therefore, we propose a novel scenario named Source Free Unsupervised Graph Domain Adaptation (SFUGDA). In this scenario, the only information we can leverage from the source domain is the well-trained source model, without any exposure to the source graph and its labels. As a result, existing UGDA methods are not feasible anymore. To address the non-trivial adaptation challenges in this practical scenario, we propose a model-agnostic algorithm called SOGA for domain adaptation to fully exploit the discriminative ability of the source model while preserving the consistency of structural proximity on the target graph. We prove the effectiveness of the proposed algorithm both theoretically and empirically. The experimental results on four cross-domain tasks show consistent improvements in the Macro-F1 score and Macro-AUC.
Graph Neural Networks (GNNs) have achieved unprecedented success in identifying categorical labels of graphs. However, most existing graph classification problems with GNNs follow the protocol of balanced data splitting, which misaligns with many real-world scenarios in which some classes have much fewer labels than others. Directly training GNNs under this imbalanced scenario may lead to uninformative representations of graphs in minority classes, and compromise the overall classification performance, which signifies the importance of developing effective GNNs towards handling imbalanced graph classification. Existing methods are either tailored for non-graph structured data or designed specifically for imbalanced node classification while few focus on imbalanced graph classification. To this end, we introduce a novel framework, Graph-of-Graph Neural Networks (G$^2$GNN), which alleviates the graph imbalance issue by deriving extra supervision globally from neighboring graphs and locally from stochastic augmentations of graphs. Globally, we construct a graph of graphs (GoG) based on kernel similarity and perform GoG propagation to aggregate neighboring graph representations. Locally, we employ topological augmentation via masking node features or dropping edges with self-consistency regularization to generate stochastic augmentations of each graph that improve the model generalibility. Extensive graph classification experiments conducted on seven benchmark datasets demonstrate our proposed G$^2$GNN outperforms numerous baselines by roughly 5\% in both F1-macro and F1-micro scores. The implementation of G$^2$GNN is available at https://github.com/YuWVandy/G2GNN}{https://github.com/YuWVandy/G2GNN
In this work, we aim to classify nodes of unstructured peer-to-peer networks with communication uncertainty, such as users of decentralized social networks. Graph Neural Networks (GNNs) are known to improve the accuracy of simple classifiers in centralized settings by leveraging naturally occurring network links, but graph convolutional layers are challenging to implement in decentralized settings when node neighbors are not constantly available. We address this problem by employing decoupled GNNs, where base classifier predictions and errors are diffused through graphs after training. For these, we deploy pre-trained and gossip-trained base classifiers and implement peer-to-peer graph diffusion under communication uncertainty. In particular, we develop an asynchronous decentralized formulation of diffusion that converges to centralized predictions in distribution and linearly with respect to communication rates. We experiment on three real-world graphs with node features and labels and simulate peer-to-peer networks with uniformly random communication frequencies; given a portion of known labels, our decentralized graph diffusion achieves comparable accuracy to centralized GNNs with minimal communication overhead (less than 3% of what gossip training already adds).
Most graph neural networks (GNNs) use the message passing paradigm, in which node features are propagated on the input graph. Recent works pointed to the distortion of information flowing from distant nodes as a factor limiting the efficiency of message passing for tasks relying on long-distance interactions. This phenomenon, referred to as 'over-squashing', has been heuristically attributed to graph bottlenecks where the number of $k$-hop neighbors grows rapidly with $k$. We provide a precise description of the over-squashing phenomenon in GNNs and analyze how it arises from bottlenecks in the graph. For this purpose, we introduce a new edge-based combinatorial curvature and prove that negatively curved edges are responsible for the over-squashing issue. We also propose and experimentally test a curvature-based graph rewiring method to alleviate the over-squashing.
Graph Neural Networks (GNNs) have become increasingly popular and achieved impressive results in many graph-based applications. However, extensive manual work and domain knowledge are required to design effective architectures, and the results of GNN models have high variance with different training setups, which limits the application of existing GNN models. In this paper, we present AutoHEnsGNN, a framework to build effective and robust models for graph tasks without any human intervention. AutoHEnsGNN won first place in the AutoGraph Challenge for KDD Cup 2020, and achieved the best rank score of five real-life datasets in the final phase. Given a task, AutoHEnsGNN first applies a fast proxy evaluation to automatically select a pool of promising GNN models. Then it builds a hierarchical ensemble framework: 1) We propose graph self-ensemble (GSE), which can reduce the variance of weight initialization and efficiently exploit the information of local and global neighborhoods; 2) Based on GSE, a weighted ensemble of different types of GNN models is used to effectively learn more discriminative node representations. To efficiently search the architectures and ensemble weights, we propose AutoHEnsGNN$_{\text{Gradient}}$, which treats the architectures and ensemble weights as architecture parameters and uses gradient-based architecture search to obtain optimal configurations, and AutoHEnsGNN$_{\text{Adaptive}}$, which can adaptively adjust the ensemble weight based on the model accuracy. Extensive experiments on node classification, graph classification, edge prediction and KDD Cup challenge demonstrate the effectiveness and generality of AutoHEnsGNN
While Graph Neural Networks (GNNs) have recently become the de facto standard for modeling relational data, they impose a strong assumption on the availability of the node or edge features of the graph. In many real-world applications, however, features are only partially available; for example, in social networks, age and gender are available only for a small subset of users. We present a general approach for handling missing features in graph machine learning applications that is based on minimization of the Dirichlet energy and leads to a diffusion-type differential equation on the graph. The discretization of this equation produces a simple, fast and scalable algorithm which we call Feature Propagation. We experimentally show that the proposed approach outperforms previous methods on seven common node-classification benchmarks and can withstand surprisingly high rates of missing features: on average we observe only around 4% relative accuracy drop when 99% of the features are missing. Moreover, it takes only 10 seconds to run on a graph with $\sim$2.5M nodes and $\sim$123M edges on a single GPU.
Recent advances in neural networks have solved common graph problems such as link prediction, node classification, node clustering, node recommendation by developing embeddings of entities and relations into vector spaces. Graph embeddings encode the structural information present in a graph. The encoded embeddings then can be used to predict the missing links in a graph. However, obtaining the optimal embeddings for a graph can be a computationally challenging task specially in an embedded system. Two techniques which we focus on in this work are 1) node embeddings from random walk based methods and 2) knowledge graph embeddings. Random walk based embeddings are computationally inexpensive to obtain but are sub-optimal whereas knowledge graph embeddings perform better but are computationally expensive. In this work, we investigate a transformation model which converts node embeddings obtained from random walk based methods to embeddings obtained from knowledge graph methods directly without an increase in the computational cost. Extensive experimentation shows that the proposed transformation model can be used for solving link prediction in real-time.
Many applications require explainable node classification in knowledge graphs. Towards this end, a popular ``white-box'' approach is class expression learning: Given sets of positive and negative nodes, class expressions in description logics are learned that separate positive from negative nodes. Most existing approaches are search-based approaches generating many candidate class expressions and selecting the best one. However, they often take a long time to find suitable class expressions. In this paper, we cast class expression learning as a translation problem and propose a new family of class expression learning approaches which we dub neural class expression synthesizers. Training examples are ``translated'' into class expressions in a fashion akin to machine translation. Consequently, our synthesizers are not subject to the runtime limitations of search-based approaches. We study three instances of this novel family of approaches based on LSTMs, GRUs, and set transformers, respectively. An evaluation of our approach on four benchmark datasets suggests that it can effectively synthesize high-quality class expressions with respect to the input examples in approximately one second on average. Moreover, a comparison to state-of-the-art approaches suggests that we achieve better F-measures on large datasets. For reproducibility purposes, we provide our implementation as well as pretrained models in our public GitHub repository at https://github.com/dice-group/NeuralClassExpressionSynthesis
Graph neural networks (GNNs) have demonstrated superior performance for semi-supervised node classification on graphs, as a result of their ability to exploit node features and topological information simultaneously. However, most GNNs implicitly assume that the labels of nodes and their neighbors in a graph are the same or consistent, which does not hold in heterophilic graphs, where the labels of linked nodes are likely to differ. Hence, when the topology is non-informative for label prediction, ordinary GNNs may work significantly worse than simply applying multi-layer perceptrons (MLPs) on each node. To tackle the above problem, we propose a new $p$-Laplacian based GNN model, termed as $^p$GNN, whose message passing mechanism is derived from a discrete regularization framework and could be theoretically explained as an approximation of a polynomial graph filter defined on the spectral domain of $p$-Laplacians. The spectral analysis shows that the new message passing mechanism works simultaneously as low-pass and high-pass filters, thus making $^p$GNNs are effective on both homophilic and heterophilic graphs. Empirical studies on real-world and synthetic datasets validate our findings and demonstrate that $^p$GNNs significantly outperform several state-of-the-art GNN architectures on heterophilic benchmarks while achieving competitive performance on homophilic benchmarks. Moreover, $^p$GNNs can adaptively learn aggregation weights and are robust to noisy edges.
Graph Neural Networks have become one of the indispensable tools to learn from graph-structured data, and their usefulness has been shown in wide variety of tasks. In recent years, there have been tremendous improvements in architecture design, resulting in better performance on various prediction tasks. In general, these neural architectures combine node feature aggregation and feature transformation using learnable weight matrix in the same layer. This makes it challenging to analyze the importance of node features aggregated from various hops and the expressiveness of the neural network layers. As different graph datasets show varying levels of homophily and heterophily in features and class label distribution, it becomes essential to understand which features are important for the prediction tasks without any prior information. In this work, we decouple the node feature aggregation step and depth of graph neural network, and empirically analyze how different aggregated features play a role in prediction performance. We show that not all features generated via aggregation steps are useful, and often using these less informative features can be detrimental to the performance of the GNN model. Through our experiments, we show that learning certain subsets of these features can lead to better performance on wide variety of datasets. We propose to use softmax as a regularizer and "soft-selector" of features aggregated from neighbors at different hop distances; and L2-Normalization over GNN layers. Combining these techniques, we present a simple and shallow model, Feature Selection Graph Neural Network (FSGNN), and show empirically that the proposed model achieves comparable or even higher accuracy than state-of-the-art GNN models in nine benchmark datasets for the node classification task, with remarkable improvements up to 51.1%.
Graph Neural Networks (GNNs) have achieved state-of-the-art performance in node classification, regression, and recommendation tasks. GNNs work well when rich and high-quality connections are available. However, their effectiveness is often jeopardized in many real-world graphs in which node degrees have power-law distributions. The extreme case of this situation, where a node may have no neighbors, is called Strict Cold Start (SCS). SCS forces the prediction to rely completely on the node's own features. We propose Cold Brew, a teacher-student distillation approach to address the SCS and noisy-neighbor challenges for GNNs. We also introduce feature contribution ratio (FCR), a metric to quantify the behavior of inductive GNNs to solve SCS. We experimentally show that FCR disentangles the contributions of different graph data components and helps select the best architecture for SCS generalization. We further demonstrate the superior performance of Cold Brew on several public benchmark and proprietary e-commerce datasets, where many nodes have either very few or noisy connections. Our source code is available at https://github.com/amazon-research/gnn-tail-generalization.
Graph neural networks (GNNs) have emerged as a powerful tool for graph classification and representation learning. However, GNNs tend to suffer from over-smoothing problems and are vulnerable to graph perturbations. To address these challenges, we propose a novel topological neural framework of topological relational inference (TRI) which allows for integrating higher-order graph information to GNNs and for systematically learning a local graph structure. The key idea is to rewire the original graph by using the persistent homology of the small neighborhoods of nodes and then to incorporate the extracted topological summaries as the side information into the local algorithm. As a result, the new framework enables us to harness both the conventional information on the graph structure and information on the graph higher order topological properties. We derive theoretical stability guarantees for the new local topological representation and discuss their implications on the graph algebraic connectivity. The experimental results on node classification tasks demonstrate that the new TRI-GNN outperforms all 14 state-of-the-art baselines on 6 out 7 graphs and exhibit higher robustness to perturbations, yielding up to 10\% better performance under noisy scenarios.
Many widely used datasets for graph machine learning tasks have generally been homophilous, where nodes with similar labels connect to each other. Recently, new Graph Neural Networks (GNNs) have been developed that move beyond the homophily regime; however, their evaluation has often been conducted on small graphs with limited application domains. We collect and introduce diverse non-homophilous datasets from a variety of application areas that have up to 384x more nodes and 1398x more edges than prior datasets. We further show that existing scalable graph learning and graph minibatching techniques lead to performance degradation on these non-homophilous datasets, thus highlighting the need for further work on scalable non-homophilous methods. To address these concerns, we introduce LINKX -- a strong simple method that admits straightforward minibatch training and inference. Extensive experimental results with representative simple methods and GNNs across our proposed datasets show that LINKX achieves state-of-the-art performance for learning on non-homophilous graphs. Our codes and data are available at https://github.com/CUAI/Non-Homophily-Large-Scale.
Most state-of-the-art Graph Neural Networks (GNNs) can be defined as a form of graph convolution which can be realized by message passing between direct neighbors or beyond. To scale such GNNs to large graphs, various neighbor-, layer-, or subgraph-sampling techniques are proposed to alleviate the "neighbor explosion" problem by considering only a small subset of messages passed to the nodes in a mini-batch. However, sampling-based methods are difficult to apply to GNNs that utilize many-hops-away or global context each layer, show unstable performance for different tasks and datasets, and do not speed up model inference. We propose a principled and fundamentally different approach, VQ-GNN, a universal framework to scale up any convolution-based GNNs using Vector Quantization (VQ) without compromising the performance. In contrast to sampling-based techniques, our approach can effectively preserve all the messages passed to a mini-batch of nodes by learning and updating a small number of quantized reference vectors of global node representations, using VQ within each GNN layer. Our framework avoids the "neighbor explosion" problem of GNNs using quantized representations combined with a low-rank version of the graph convolution matrix. We show that such a compact low-rank version of the gigantic convolution matrix is sufficient both theoretically and experimentally. In company with VQ, we design a novel approximated message passing algorithm and a nontrivial back-propagation rule for our framework. Experiments on various types of GNN backbones demonstrate the scalability and competitive performance of our framework on large-graph node classification and link prediction benchmarks.
The interdependence between nodes in graphs is key to improve class predictions on nodes and utilized in approaches like Label Propagation (LP) or in Graph Neural Networks (GNN). Nonetheless, uncertainty estimation for non-independent node-level predictions is under-explored. In this work, we explore uncertainty quantification for node classification in three ways: (1) We derive three axioms explicitly characterizing the expected predictive uncertainty behavior in homophilic attributed graphs. (2) We propose a new model Graph Posterior Network (GPN) which explicitly performs Bayesian posterior updates for predictions on interdependent nodes. GPN provably obeys the proposed axioms. (3) We extensively evaluate GPN and a strong set of baselines on semi-supervised node classification including detection of anomalous features, and detection of left-out classes. GPN outperforms existing approaches for uncertainty estimation in the experiments.
Evolving temporal networks serve as the abstractions of many real-life dynamic systems, e.g., social network and e-commerce. The purpose of temporal network embedding is to map each node to a time-evolving low-dimension vector for downstream tasks, e.g., link prediction and node classification. The difficulty of temporal network embedding lies in how to utilize the topology and time information jointly to capture the evolution of a temporal network. In response to this challenge, we propose a temporal motif-preserving network embedding method with bicomponent neighbor aggregation, named TME-BNA. Considering that temporal motifs are essential to the understanding of topology laws and functional properties of a temporal network, TME-BNA constructs additional edge features based on temporal motifs to explicitly utilize complex topology with time information. In order to capture the topology dynamics of nodes, TME-BNA utilizes Graph Neural Networks (GNNs) to aggregate the historical and current neighbors respectively according to the timestamps of connected edges. Experiments are conducted on three public temporal network datasets, and the results show the effectiveness of TME-BNA.
Recent years have witnessed the significant success of applying graph neural networks (GNNs) in learning effective node representations for classification. However, current GNNs are mostly built under the balanced data-splitting, which is inconsistent with many real-world networks where the number of training nodes can be extremely imbalanced among the classes. Thus, directly utilizing current GNNs on imbalanced data would generate coarse representations of nodes in minority classes and ultimately compromise the classification performance. This therefore portends the importance of developing effective GNNs for handling imbalanced graph data. In this work, we propose a novel Distance-wise Prototypical Graph Neural Network (DPGNN), which proposes a class prototype-driven training to balance the training loss between majority and minority classes and then leverages distance metric learning to differentiate the contributions of different dimensions of representations and fully encode the relative position of each node to each class prototype. Moreover, we design a new imbalanced label propagation mechanism to derive extra supervision from unlabeled nodes and employ self-supervised learning to smooth representations of adjacent nodes while separating inter-class prototypes. Comprehensive node classification experiments and parameter analysis on multiple networks are conducted and the proposed DPGNN almost always significantly outperforms all other baselines, which demonstrates its effectiveness in imbalanced node classification. The implementation of DPGNN is available at \url{https://github.com/YuWVandy/DPGNN}.
While Graph Neural Networks have gained popularity in multiple domains, graph-structured input remains a major challenge due to (a) over-smoothing, (b) noisy neighbours (heterophily), and (c) the suspended animation problem. To address all these problems simultaneously, we propose a novel graph neural network FDGATII, inspired by attention mechanism's ability to focus on selective information supplemented with two feature preserving mechanisms. FDGATII combines Initial Residuals and Identity Mapping with the more expressive dynamic self-attention to handle noise prevalent from the neighbourhoods in heterophilic data sets. By using sparse dynamic attention, FDGATII is inherently parallelizable in design, whist efficient in operation; thus theoretically able to scale to arbitrary graphs with ease. Our approach has been extensively evaluated on 7 datasets. We show that FDGATII outperforms GAT and GCN based benchmarks in accuracy and performance on fully supervised tasks, obtaining state-of-the-art results on Chameleon and Cornell datasets with zero domain-specific graph pre-processing, and demonstrate its versatility and fairness.
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.
Graph Neural Networks (GNNs) are popular for graph machine learning and have shown great results on wide node classification tasks. Yet, they are less popular for practical deployments in the industry owing to their scalability challenges incurred by data dependency. Namely, GNN inference depends on neighbor nodes multiple hops away from the target, and fetching them burdens latency-constrained applications. Existing inference acceleration methods like pruning and quantization can speed up GNNs by reducing Multiplication-and-ACcumulation (MAC) operations, but the improvements are limited given the data dependency is not resolved. Conversely, multi-layer perceptrons (MLPs) have no graph dependency and infer much faster than GNNs, even though they are less accurate than GNNs for node classification in general. Motivated by these complementary strengths and weaknesses, we bring GNNs and MLPs together via knowledge distillation (KD). Our work shows that the performance of MLPs can be improved by large margins with GNN KD. We call the distilled MLPs Graph-less Neural Networks (GLNNs) as they have no inference graph dependency. We show that GLNNs with competitive accuracy infer faster than GNNs by 146X-273X and faster than other acceleration methods by 14X-27X. Under a production setting involving both transductive and inductive predictions across 7 datasets, GLNN accuracies improve over stand-alone MLPs by 12.36% on average and match GNNs on 6/7 datasets. Comprehensive analysis shows when and why GLNNs can achieve competitive accuracies to GNNs and suggests GLNN as a handy choice for latency-constrained applications.