Temporal heterogeneous information network (temporal HIN) embedding, aiming to represent various types of nodes of different timestamps into low dimensional spaces while preserving structural and semantic information, is of vital importance in diverse real-life tasks. Researchers have made great efforts on temporal HIN embedding in Euclidean spaces and got some considerable achievements. However, there is always a fundamental conflict that many real-world networks show hierarchical property and power-law distribution, and are not isometric of Euclidean spaces. Recently, representation learning in hyperbolic spaces has been proved to be valid for data with hierarchical and power-law structure. Inspired by this character, we propose a hyperbolic heterogeneous temporal network embedding ($\text{H}^2\text{TNE}$) model for temporal HINs. Specifically, we leverage a temporally and heterogeneously double-constrained random walk strategy to capture the structural and semantic information, and then calculate the embedding by exploiting hyperbolic distance in proximity measurement. Experimental results show that our method has superior performance on temporal link prediction and node classification compared with SOTA models.
Learning unbiased node representations for imbalanced samples in the graph has become a more remarkable and important topic. For the graph, a significant challenge is that the topological properties of the nodes (e.g., locations, roles) are unbalanced (topology-imbalance), other than the number of training labeled nodes (quantity-imbalance). Existing studies on topology-imbalance focus on the location or the local neighborhood structure of nodes, ignoring the global underlying hierarchical properties of the graph, i.e., hierarchy. In the real-world scenario, the hierarchical structure of graph data reveals important topological properties of graphs and is relevant to a wide range of applications. We find that training labeled nodes with different hierarchical properties have a significant impact on the node classification tasks and confirm it in our experiments. It is well known that hyperbolic geometry has a unique advantage in representing the hierarchical structure of graphs. Therefore, we attempt to explore the hierarchy-imbalance issue for node classification of graph neural networks with a novelty perspective of hyperbolic geometry, including its characteristics and causes. Then, we propose a novel hyperbolic geometric hierarchy-imbalance learning framework, named HyperIMBA, to alleviate the hierarchy-imbalance issue caused by uneven hierarchy-levels and cross-hierarchy connectivity patterns of labeled nodes.Extensive experimental results demonstrate the superior effectiveness of HyperIMBA for hierarchy-imbalance node classification tasks.
Unsupervised Representation Learning on graphs is gaining traction due to the increasing abundance of unlabelled network data and the compactness, richness, and usefulness of the representations generated. In this context, the need to consider fairness and bias constraints while generating the representations has been well-motivated and studied to some extent in prior works. One major limitation of most of the prior works in this setting is that they do not aim to address the bias generated due to connectivity patterns in the graphs, such as varied node centrality, which leads to a disproportionate performance across nodes. In our work, we aim to address this issue of mitigating bias due to inherent graph structure in an unsupervised setting. To this end, we propose CAFIN, a centrality-aware fairness-inducing framework that leverages the structural information of graphs to tune the representations generated by existing frameworks. We deploy it on GraphSAGE (a popular framework in this domain) and showcase its efficacy on two downstream tasks - Node Classification and Link Prediction. Empirically, CAFIN consistently reduces the performance disparity across popular datasets (varying from 18 to 80% reduction in performance disparity) from various domains while incurring only a minimal cost of fairness.
We introduce a new dataset named WikiVitals which contains a large graph of 48k mutually referred Wikipedia articles classified into 32 categories and connected by 2.3M edges. Our aim is to rigorously evaluate the contributions of three distinct sources of information to the label prediction in a semi-supervised node classification setting, namely the content of the articles, their connections with each other and the correlations among their labels. We perform this evaluation using a Graph Markov Neural Network which provides a theoretically principled model for this task and we conduct a detailed evaluation of the contributions of each sources of information using a clear separation of model selection and model assessment. One interesting observation is that including the effect of label dependencies is more relevant for sparse train sets than it is for dense train sets.
Efficient large-scale neural network training and inference on commodity CPU hardware is of immense practical significance in democratizing deep learning (DL) capabilities. Presently, the process of training massive models consisting of hundreds of millions to billions of parameters requires the extensive use of specialized hardware accelerators, such as GPUs, which are only accessible to a limited number of institutions with considerable financial resources. Moreover, there is often an alarming carbon footprint associated with training and deploying these models. In this paper, we take a step towards addressing these challenges by introducing BOLT, a sparse deep learning library for training large-scale search and recommendation models on standard CPU hardware. BOLT provides a flexible, high-level API for constructing models that will be familiar to users of existing popular DL frameworks. By automatically tuning specialized hyperparameters, BOLT also abstracts away the algorithmic details of sparse network training. We evaluate BOLT on a number of information retrieval tasks including product recommendations, text classification, graph neural networks, and personalization. We find that our proposed system achieves competitive performance with state-of-the-art techniques at a fraction of the cost and energy consumption and an order-of-magnitude faster inference time. BOLT has also been successfully deployed by multiple businesses to address critical problems, and we highlight one customer case study in the field of e-commerce.
A large number of real-world networks include multiple types of nodes and edges. Graph Neural Network (GNN) emerged as a deep learning framework to generate node and graph embeddings for downstream machine learning tasks. However, popular GNN-based architectures operate on single homogeneous networks. Enabling them to work on multiple networks brings additional challenges due to the heterogeneity of the networks and the multiplicity of the existing associations. In this study, we present a computational approach named GRAF (Graph Attention-aware Fusion Networks) utilizing GNN-based approaches on multiple networks with the help of attention mechanisms and network fusion. Using attention-based neighborhood aggregation, GRAF learns the importance of each neighbor per node (called node-level attention) followed by the importance of association (called association-level attention). Then, GRAF processes a network fusion step weighing each edge according to learned node- and association-level attentions. Considering that the fused network could be a highly dense network with many weak edges depending on the given input networks, we included an edge elimination step with respect to edges' weights. Finally, GRAF utilizes Graph Convolutional Network (GCN) on the fused network and incorporates node features on graph-structured data for a node classification or a similar downstream task. To demonstrate GRAF's generalizability, we applied it to four datasets from different domains and observed that GRAF outperformed or was on par with the baselines, state-of-the-art methods, and its own variations for each node classification task. Source code for our tool is publicly available at https://github.com/bozdaglab/GRAF .
Dynamic graphs arise in various real-world applications, and it is often welcomed to model the dynamics directly in continuous time domain for its flexibility. This paper aims to design an easy-to-use pipeline (termed as EasyDGL which is also due to its implementation by DGL toolkit) composed of three key modules with both strong fitting ability and interpretability. Specifically the proposed pipeline which involves encoding, training and interpreting: i) a temporal point process (TPP) modulated attention architecture to endow the continuous-time resolution with the coupled spatiotemporal dynamics of the observed graph with edge-addition events; ii) a principled loss composed of task-agnostic TPP posterior maximization based on observed events on the graph, and a task-aware loss with a masking strategy over dynamic graph, where the covered tasks include dynamic link prediction, dynamic node classification and node traffic forecasting; iii) interpretation of the model outputs (e.g., representations and predictions) with scalable perturbation-based quantitative analysis in the graph Fourier domain, which could more comprehensively reflect the behavior of the learned model. Extensive experimental results on public benchmarks show the superior performance of our EasyDGL for time-conditioned predictive tasks, and in particular demonstrate that EasyDGL can effectively quantify the predictive power of frequency content that a model learn from the evolving graph data.
Extremely skewed label distributions are common in real-world node classification tasks. If not dealt with appropriately, it significantly hurts the performance of GNNs in minority classes. Due to its practical importance, there have been a series of recent research devoted to this challenge. Existing over-sampling techniques smooth the label distribution by generating ``fake'' minority nodes and synthesizing their features and local topology, which largely ignore the rich information of unlabeled nodes on graphs. In this paper, we propose UNREAL, an iterative over-sampling method. The first key difference is that we only add unlabeled nodes instead of synthetic nodes, which eliminates the challenge of feature and neighborhood generation. To select which unlabeled nodes to add, we propose geometric ranking to rank unlabeled nodes. Geometric ranking exploits unsupervised learning in the node embedding space to effectively calibrates pseudo-label assignment. Finally, we identify the issue of geometric imbalance in the embedding space and provide a simple metric to filter out geometrically imbalanced nodes. Extensive experiments on real-world benchmark datasets are conducted, and the empirical results show that our method significantly outperforms current state-of-the-art methods consistent on different datasets with different imbalance ratios.
Graph transformers have emerged as a promising architecture for a variety of graph learning and representation tasks. Despite their successes, though, it remains challenging to scale graph transformers to large graphs while maintaining accuracy competitive with message-passing networks. In this paper, we introduce Exphormer, a framework for building powerful and scalable graph transformers. Exphormer consists of a sparse attention mechanism based on two mechanisms: virtual global nodes and expander graphs, whose mathematical characteristics, such as spectral expansion, pseduorandomness, and sparsity, yield graph transformers with complexity only linear in the size of the graph, while allowing us to prove desirable theoretical properties of the resulting transformer models. We show that incorporating Exphormer into the recently-proposed GraphGPS framework produces models with competitive empirical results on a wide variety of graph datasets, including state-of-the-art results on three datasets. We also show that Exphormer can scale to datasets on larger graphs than shown in previous graph transformer architectures. Code can be found at \url{https://github.com/hamed1375/Exphormer}.
This vision paper proposes KGNet, an on-demand graph machine learning (GML) as a service on top of RDF engines to support GML-enabled SPARQL queries. KGNet automates the training of GML models on a KG by identifying a task-specific subgraph. This helps reduce the task-irrelevant KG structure and properties for better scalability and accuracy. While training a GML model on KG, KGNet collects metadata of trained models in the form of an RDF graph called KGMeta, which is interlinked with the relevant subgraphs in KG. Finally, all trained models are accessible via a SPARQL-like query. We call it a GML-enabled query and refer to it as SPARQLML. KGNet supports SPARQLML on top of existing RDF engines as an interface for querying and inferencing over KGs using GML models. The development of KGNet poses research opportunities in several areas, including meta-sampling for identifying task-specific subgraphs, GML pipeline automation with computational constraints, such as limited time and memory budget, and SPARQLML query optimization. KGNet supports different GML tasks, such as node classification, link prediction, and semantic entity matching. We evaluated KGNet using two real KGs of different application domains. Compared to training on the entire KG, KGNet significantly reduced training time and memory usage while maintaining comparable or improved accuracy. The KGNet source-code is available for further study
Graph Neural Networks (GNNs) have achieved promising results in various tasks such as node classification and graph classification. Recent studies find that GNNs are vulnerable to adversarial attacks. However, effective backdoor attacks on graphs are still an open problem. In particular, backdoor attack poisons the graph by attaching triggers and the target class label to a set of nodes in the training graph. The backdoored GNNs trained on the poisoned graph will then be misled to predict test nodes to target class once attached with triggers. Though there are some initial efforts in graph backdoor attacks, our empirical analysis shows that they may require a large attack budget for effective backdoor attacks and the injected triggers can be easily detected and pruned. Therefore, in this paper, we study a novel problem of unnoticeable graph backdoor attacks with limited attack budget. To fully utilize the attack budget, we propose to deliberately select the nodes to inject triggers and target class labels in the poisoning phase. An adaptive trigger generator is deployed to obtain effective triggers that are difficult to be noticed. Extensive experiments on real-world datasets against various defense strategies demonstrate the effectiveness of our proposed method in conducting effective unnoticeable backdoor attacks.
Graph neural networks (GNNs) fuel diverse machine learning tasks involving graph-structured data, ranging from predicting protein structures to serving personalized recommendations. Real-world graph data must often be stored distributed across many machines not just because of capacity constraints, but because of compliance with data residency or privacy laws. In such setups, network communication is costly and becomes the main bottleneck to train GNNs. Optimizations for distributed GNN training have targeted data-level improvements so far -- via caching, network-aware partitioning, and sub-sampling -- that work for data center-like setups where graph data is accessible to a single entity and data transfer costs are ignored. We present RETEXO, the first framework which eliminates the severe communication bottleneck in distributed GNN training while respecting any given data partitioning configuration. The key is a new training procedure, lazy message passing, that reorders the sequence of training GNN elements. RETEXO achieves 1-2 orders of magnitude reduction in network data costs compared to standard GNN training, while retaining accuracy. RETEXO scales gracefully with increasing decentralization and decreasing bandwidth. It is the first framework that can be used to train GNNs at all network decentralization levels -- including centralized data-center networks, wide area networks, proximity networks, and edge networks.
Graph neural networks (GNNs) have shown high potential for a variety of real-world, challenging applications, but one of the major obstacles in GNN research is the lack of large-scale flexible datasets. Most existing public datasets for GNNs are relatively small, which limits the ability of GNNs to generalize to unseen data. The few existing large-scale graph datasets provide very limited labeled data. This makes it difficult to determine if the GNN model's low accuracy for unseen data is inherently due to insufficient training data or if the model failed to generalize. Additionally, datasets used to train GNNs need to offer flexibility to enable a thorough study of the impact of various factors while training GNN models. In this work, we introduce the Illinois Graph Benchmark (IGB), a research dataset tool that the developers can use to train, scrutinize and systematically evaluate GNN models with high fidelity. IGB includes both homogeneous and heterogeneous academic graphs of enormous sizes, with more than 40% of their nodes labeled. Compared to the largest graph datasets publicly available, the IGB provides over 162X more labeled data for deep learning practitioners and developers to create and evaluate models with higher accuracy. The IGB dataset is a collection of academic graphs designed to be flexible, enabling the study of various GNN architectures, embedding generation techniques, and analyzing system performance issues for node classification tasks. IGB is open-sourced, supports DGL and PyG frameworks, and comes with releases of the raw text that we believe foster emerging language models and GNN research projects. An early public version of IGB is available at https://github.com/IllinoisGraphBenchmark/IGB-Datasets.
Polynomial filters, a kind of Graph Neural Networks, typically use a predetermined polynomial basis and learn the coefficients from the training data. It has been observed that the effectiveness of the model is highly dependent on the property of the polynomial basis. Consequently, two natural and fundamental questions arise: Can we learn a suitable polynomial basis from the training data? Can we determine the optimal polynomial basis for a given graph and node features? In this paper, we propose two spectral GNN models that provide positive answers to the questions posed above. First, inspired by Favard's Theorem, we propose the FavardGNN model, which learns a polynomial basis from the space of all possible orthonormal bases. Second, we examine the supposedly unsolvable definition of optimal polynomial basis from Wang & Zhang (2022) and propose a simple model, OptBasisGNN, which computes the optimal basis for a given graph structure and graph signal. Extensive experiments are conducted to demonstrate the effectiveness of our proposed models. Our code is available at https://github.com/yuziGuo/FarOptBasis.
Node classification is a classical graph machine learning task on which Graph Neural Networks (GNNs) have recently achieved strong results. However, it is often believed that standard GNNs only work well for homophilous graphs, i.e., graphs where edges tend to connect nodes of the same class. Graphs without this property are called heterophilous, and it is typically assumed that specialized methods are required to achieve strong performance on such graphs. In this work, we challenge this assumption. First, we show that the standard datasets used for evaluating heterophily-specific models have serious drawbacks, making results obtained by using them unreliable. The most significant of these drawbacks is the presence of a large number of duplicate nodes in the datasets Squirrel and Chameleon, which leads to train-test data leakage. We show that removing duplicate nodes strongly affects GNN performance on these datasets. Then, we propose a set of heterophilous graphs of varying properties that we believe can serve as a better benchmark for evaluating the performance of GNNs under heterophily. We show that standard GNNs achieve strong results on these heterophilous graphs, almost always outperforming specialized models. Our datasets and the code for reproducing our experiments are available at https://github.com/yandex-research/heterophilous-graphs
Graph convolutional networks (GCNs) were a great step towards extending deep learning to unstructured data such as graphs. But GCNs still need a constructed graph to work with. To solve this problem, classical graphs such as $k$-nearest neighbor are usually used to initialize the GCN. Although it is computationally efficient to construct $k$-nn graphs, the constructed graph might not be very useful for learning. In a $k$-nn graph, points are restricted to have a fixed number of edges, and all edges in the graph have equal weights. We present a new way to construct the graph and initialize the GCN. It is based on random projection forest (rpForest). rpForest enables us to assign varying weights on edges indicating varying importance, which enhanced the learning. The number of trees is a hyperparameter in rpForest. We performed spectral analysis to help us setting this parameter in the right range. In the experiments, initializing the GCN using rpForest provides better results compared to $k$-nn initialization.
Graph Neural Networks (GNNs) are increasingly becoming the favorite method for graph learning. They exploit the semi-supervised nature of deep learning, and they bypass computational bottlenecks associated with traditional graph learning methods. In addition to the feature matrix $X$, GNNs need an adjacency matrix $A$ to perform feature propagation. In many cases, the adjacency matrix $A$ is missing. We introduce a graph construction scheme that constructs the adjacency matrix $A$ using unsupervised and supervised information. Unsupervised information characterizes the neighborhood around points. We used Principal Axis trees (PA-trees) as a source for unsupervised information, where we create edges between points falling onto the same leaf node. For supervised information, we used the concept of penalty and intrinsic graphs. A penalty graph connects points with different class labels, whereas an intrinsic graph connects points with the same class labels. We used the penalty and intrinsic graphs to remove or add edges to the graph constructed via PA-tree. We tested this graph construction scheme on two well-known GNNs: 1) Graph Convolutional Network (GCN) and 2) Simple Graph Convolution (SGC). The experiments show that it is better to use SGC because it is faster and delivers better or the same results as GCN. We also test the effect of oversmoothing on both GCN and SGC. We found out that the level of smoothing has to be carefully selected for SGC to avoid oversmoothing.
Node classification is a substantial problem in graph-based fraud detection. Many existing works adopt Graph Neural Networks (GNNs) to enhance fraud detectors. While promising, currently most GNN-based fraud detectors fail to generalize to the low homophily setting. Besides, label utilization has been proved to be significant factor for node classification problem. But we find they are less effective in fraud detection tasks due to the low homophily in graphs. In this work, we propose GAGA, a novel Group AGgregation enhanced TrAnsformer, to tackle the above challenges. Specifically, the group aggregation provides a portable method to cope with the low homophily issue. Such an aggregation explicitly integrates the label information to generate distinguishable neighborhood information. Along with group aggregation, an attempt towards end-to-end trainable group encoding is proposed which augments the original feature space with the class labels. Meanwhile, we devise two additional learnable encodings to recognize the structural and relational context. Then, we combine the group aggregation and the learnable encodings into a Transformer encoder to capture the semantic information. Experimental results clearly show that GAGA outperforms other competitive graph-based fraud detectors by up to 24.39% on two trending public datasets and a real-world industrial dataset from Anonymous. Even more, the group aggregation is demonstrated to outperform other label utilization methods (e.g., C&S, BoT/UniMP) in the low homophily setting.
Graph convolutional networks (GCNs) are currently the most promising paradigm for dealing with graph-structure data, while recent studies have also shown that GCNs are vulnerable to adversarial attacks. Thus developing GCN models that are robust to such attacks become a hot research topic. However, the structural purification learning-based or robustness constraints-based defense GCN methods are usually designed for specific data or attacks, and introduce additional objective that is not for classification. Extra training overhead is also required in their design. To address these challenges, we conduct in-depth explorations on mid-frequency signals on graphs and propose a simple yet effective Mid-pass filter GCN (Mid-GCN). Theoretical analyses guarantee the robustness of signals through the mid-pass filter, and we also shed light on the properties of different frequency signals under adversarial attacks. Extensive experiments on six benchmark graph data further verify the effectiveness of our designed Mid-GCN in node classification accuracy compared to state-of-the-art GCNs under various adversarial attack strategies.
Self-supervised node representation learning aims to learn node representations from unlabelled graphs that rival the supervised counterparts. The key towards learning informative node representations lies in how to effectively gain contextual information from the graph structure. In this work, we present simple-yet-effective self-supervised node representation learning via aligning the hidden representations of nodes and their neighbourhood. Our first idea achieves such node-to-neighbourhood alignment by directly maximizing the mutual information between their representations, which, we prove theoretically, plays the role of graph smoothing. Our framework is optimized via a surrogate contrastive loss and a Topology-Aware Positive Sampling (TAPS) strategy is proposed to sample positives by considering the structural dependencies between nodes, which enables offline positive selection. Considering the excessive memory overheads of contrastive learning, we further propose a negative-free solution, where the main contribution is a Graph Signal Decorrelation (GSD) constraint to avoid representation collapse and over-smoothing. The GSD constraint unifies some of the existing constraints and can be used to derive new implementations to combat representation collapse. By applying our methods on top of simple MLP-based node representation encoders, we learn node representations that achieve promising node classification performance on a set of graph-structured datasets from small- to large-scale.