Graph and hypergraph representation learning has attracted increasing attention from various research fields. Despite the decent performance and fruitful applications of Graph Neural Networks (GNNs), Hypergraph Neural Networks (HGNNs), and their well-designed variants, on some commonly used benchmark graphs and hypergraphs, they are outperformed by even a simple Multi-Layer Perceptron. This observation motivates a reexamination of the design paradigm of the current GNNs and HGNNs and poses challenges of extracting graph features effectively. In this work, a universal feature encoder for both graph and hypergraph representation learning is designed, called UniG-Encoder. The architecture starts with a forward transformation of the topological relationships of connected nodes into edge or hyperedge features via a normalized projection matrix. The resulting edge/hyperedge features, together with the original node features, are fed into a neural network. The encoded node embeddings are then derived from the reversed transformation, described by the transpose of the projection matrix, of the network's output, which can be further used for tasks such as node classification. The proposed architecture, in contrast to the traditional spectral-based and/or message passing approaches, simultaneously and comprehensively exploits the node features and graph/hypergraph topologies in an efficient and unified manner, covering both heterophilic and homophilic graphs. The designed projection matrix, encoding the graph features, is intuitive and interpretable. Extensive experiments are conducted and demonstrate the superior performance of the proposed framework on twelve representative hypergraph datasets and six real-world graph datasets, compared to the state-of-the-art methods. Our implementation is available online at https://github.com/MinhZou/UniG-Encoder.
Node classification is one of the core tasks on attributed graphs, but successful graph learning solutions require sufficiently labeled data. To keep annotation costs low, active graph learning focuses on selecting the most qualitative subset of nodes that maximizes label efficiency. However, deciding which heuristic is best suited for an unlabeled graph to increase label efficiency is a persistent challenge. Existing solutions either neglect aligning the learned model and the sampling method or focus only on limited selection aspects. They are thus sometimes worse or only equally good as random sampling. In this work, we introduce a novel active graph learning approach called DiffusAL, showing significant robustness in diverse settings. Toward better transferability between different graph structures, we combine three independent scoring functions to identify the most informative node samples for labeling in a parameter-free way: i) Model Uncertainty, ii) Diversity Component, and iii) Node Importance computed via graph diffusion heuristics. Most of our calculations for acquisition and training can be pre-processed, making DiffusAL more efficient compared to approaches combining diverse selection criteria and similarly fast as simpler heuristics. Our experiments on various benchmark datasets show that, unlike previous methods, our approach significantly outperforms random selection in 100% of all datasets and labeling budgets tested.
Graph neural networks (GNNs) have shown remarkable success in learning representations for graph-structured data. However, GNNs still face challenges in modeling complex phenomena that involve feature transportation. In this paper, we propose a novel GNN architecture inspired by Advection-Diffusion-Reaction systems, called ADR-GNN. Advection models feature transportation, while diffusion captures the local smoothing of features, and reaction represents the non-linear transformation between feature channels. We provide an analysis of the qualitative behavior of ADR-GNN, that shows the benefit of combining advection, diffusion, and reaction. To demonstrate its efficacy, we evaluate ADR-GNN on real-world node classification and spatio-temporal datasets, and show that it improves or offers competitive performance compared to state-of-the-art networks.
In recent years, self-supervised learning has emerged as a promising approach in addressing the issues of label dependency and poor generalization performance in traditional GNNs. However, existing self-supervised methods have limited effectiveness on heterophilic graphs, due to the homophily assumption that results in similar node representations for connected nodes. In this work, we propose a multi-view contrastive learning model for heterophilic graphs, namely, MUSE. Specifically, we construct two views to capture the information of the ego node and its neighborhood by GNNs enhanced with contrastive learning, respectively. Then we integrate the information from these two views to fuse the node representations. Fusion contrast is utilized to enhance the effectiveness of fused node representations. Further, considering that the influence of neighboring contextual information on information fusion may vary across different ego nodes, we employ an information fusion controller to model the diversity of node-neighborhood similarity at both the local and global levels. Finally, an alternating training scheme is adopted to ensure that unsupervised node representation learning and information fusion controller can mutually reinforce each other. We conduct extensive experiments to evaluate the performance of MUSE on 9 benchmark datasets. Our results show the effectiveness of MUSE on both node classification and clustering tasks.
Graph Neural Networks (GNNs) have achieved notable success in learning from graph-structured data, owing to their ability to capture intricate dependencies and relationships between nodes. They excel in various applications, including semi-supervised node classification, link prediction, and graph generation. However, it is important to acknowledge that the majority of state-of-the-art GNN models are built upon the assumption of an in-distribution setting, which hinders their performance on real-world graphs with dynamic structures. In this article, we aim to assess the impact of training GNNs on localized subsets of the graph. Such restricted training data may lead to a model that performs well in the specific region it was trained on but fails to generalize and make accurate predictions for the entire graph. In the context of graph-based semi-supervised learning (SSL), resource constraints often lead to scenarios where the dataset is large, but only a portion of it can be labeled, affecting the model's performance. This limitation affects tasks like anomaly detection or spam detection when labeling processes are biased or influenced by human subjectivity. To tackle the challenges posed by localized training data, we approach the problem as an out-of-distribution (OOD) data issue by by aligning the distributions between the training data, which represents a small portion of labeled data, and the graph inference process that involves making predictions for the entire graph. We propose a regularization method to minimize distributional discrepancies between localized training data and graph inference, improving model performance on OOD data. Extensive tests on popular GNN models show significant performance improvement on three citation GNN benchmark datasets. The regularization approach effectively enhances model adaptation and generalization, overcoming challenges posed by OOD data.
Graph domain adaptation models are widely adopted in cross-network learning tasks, with the aim of transferring labeling or structural knowledge. Currently, there mainly exist two limitations in evaluating graph domain adaptation models. On one side, they are primarily tested for the specific cross-network node classification task, leaving tasks at edge-level and graph-level largely under-explored. Moreover, they are primarily tested in limited scenarios, such as social networks or citation networks, lacking validation of model's capability in richer scenarios. As comprehensively assessing models could enhance model practicality in real-world applications, we propose a benchmark, known as OpenGDA. It provides abundant pre-processed and unified datasets for different types of tasks (node, edge, graph). They originate from diverse scenarios, covering web information systems, urban systems and natural systems. Furthermore, it integrates state-of-the-art models with standardized and end-to-end pipelines. Overall, OpenGDA provides a user-friendly, scalable and reproducible benchmark for evaluating graph domain adaptation models. The benchmark experiments highlight the challenges of applying GDA models to real-world applications with consistent good performance, and potentially provide insights to future research. As an emerging project, OpenGDA will be regularly updated with new datasets and models. It could be accessed from https://github.com/Skyorca/OpenGDA.
Clinical Practice Guidelines (CPGs) for cancer diseases evolve rapidly due to new evidence generated by active research. Currently, CPGs are primarily published in a document format that is ill-suited for managing this developing knowledge. A knowledge model of the guidelines document suitable for programmatic interaction is required. This work proposes an automated method for extraction of knowledge from National Comprehensive Cancer Network (NCCN) CPGs in Oncology and generating a structured model containing the retrieved knowledge. The proposed method was tested using two versions of NCCN Non-Small Cell Lung Cancer (NSCLC) CPG to demonstrate the effectiveness in faithful extraction and modeling of knowledge. Three enrichment strategies using Cancer staging information, Unified Medical Language System (UMLS) Metathesaurus & National Cancer Institute thesaurus (NCIt) concepts, and Node classification are also presented to enhance the model towards enabling programmatic traversal and querying of cancer care guidelines. The Node classification was performed using a Support Vector Machine (SVM) model, achieving a classification accuracy of 0.81 with 10-fold cross-validation.
Despite a surge in interest in GNN development, homogeneity in benchmarking datasets still presents a fundamental issue to GNN research. GraphWorld is a recent solution which uses the Stochastic Block Model (SBM) to generate diverse populations of synthetic graphs for benchmarking any GNN task. Despite its success, the SBM imposed fundamental limitations on the kinds of graph structure GraphWorld could create. In this work we examine how two additional synthetic graph generators can improve GraphWorld's evaluation; LFR, a well-established model in the graph clustering literature and CABAM, a recent adaptation of the Barabasi-Albert model tailored for GNN benchmarking. By integrating these generators, we significantly expand the coverage of graph space within the GraphWorld framework while preserving key graph properties observed in real-world networks. To demonstrate their effectiveness, we generate 300,000 graphs to benchmark 11 GNN models on a node classification task. We find GNN performance variations in response to homophily, degree distribution and feature signal. Based on these findings, we classify models by their sensitivity to the new generators under these properties. Additionally, we release the extensions made to GraphWorld on the GitHub repository, offering further evaluation of GNN performance on new graphs.
Graph convolutional networks (GCNs) enable end-to-end learning on graph structured data. However, many works assume a given graph structure. When the input graph is noisy or unavailable, one approach is to construct or learn a latent graph structure. These methods typically fix the choice of node degree for the entire graph, which is suboptimal. Instead, we propose a novel end-to-end differentiable graph generator which builds graph topologies where each node selects both its neighborhood and its size. Our module can be readily integrated into existing pipelines involving graph convolution operations, replacing the predetermined or existing adjacency matrix with one that is learned, and optimized, as part of the general objective. As such it is applicable to any GCN. We integrate our module into trajectory prediction, point cloud classification and node classification pipelines resulting in improved accuracy over other structure-learning methods across a wide range of datasets and GCN backbones.
A curriculum is a planned sequence of learning materials and an effective one can make learning efficient and effective for both humans and machines. Recent studies developed effective data-driven curriculum learning approaches for training graph neural networks in language applications. However, existing curriculum learning approaches often employ a single criterion of difficulty in their training paradigms. In this paper, we propose a new perspective on curriculum learning by introducing a novel approach that builds on graph complexity formalisms (as difficulty criteria) and model competence during training. The model consists of a scheduling scheme which derives effective curricula by accounting for different views of sample difficulty and model competence during training. The proposed solution advances existing research in curriculum learning for graph neural networks with the ability to incorporate a fine-grained spectrum of graph difficulty criteria in their training paradigms. Experimental results on real-world link prediction and node classification tasks illustrate the effectiveness of the proposed approach.
Many real-world datasets have an underlying dynamic graph structure, where entities and their interactions evolve over time. Machine learning models should consider these dynamics in order to harness their full potential in downstream tasks. Previous approaches for graph representation learning have focused on either sampling k-hop neighborhoods, akin to breadth-first search, or random walks, akin to depth-first search. However, these methods are computationally expensive and unsuitable for real-time, low-latency inference on dynamic graphs. To overcome these limitations, we propose graph-sprints a general purpose feature extraction framework for continuous-time-dynamic-graphs (CTDGs) that has low latency and is competitive with state-of-the-art, higher latency models. To achieve this, a streaming, low latency approximation to the random-walk based features is proposed. In our framework, time-aware node embeddings summarizing multi-hop information are computed using only single-hop operations on the incoming edges. We evaluate our proposed approach on three open-source datasets and two in-house datasets, and compare with three state-of-the-art algorithms (TGN-attn, TGN-ID, Jodie). We demonstrate that our graph-sprints features, combined with a machine learning classifier, achieve competitive performance (outperforming all baselines for the node classification tasks in five datasets). Simultaneously, graph-sprints significantly reduce inference latencies, achieving close to an order of magnitude speed-up in our experimental setting.
We present PolyGNN, a polyhedron-based graph neural network for 3D building reconstruction from point clouds. PolyGNN learns to assemble primitives obtained by polyhedral decomposition via graph node classification, achieving a watertight and compact reconstruction. To effectively represent arbitrary-shaped polyhedra in the neural network, we propose a skeleton-based sampling strategy to generate polyhedron-wise queries. These queries are then incorporated with inter-polyhedron adjacency to enhance the classification. PolyGNN is end-to-end optimizable and is designed to accommodate variable-size input points, polyhedra, and queries with an index-driven batching technique. To address the abstraction gap between existing city-building models and the underlying instances, and provide a fair evaluation of the proposed method, we develop our method on a large-scale synthetic dataset with well-defined ground truths of polyhedral labels. We further conduct a transferability analysis across cities and on real-world point clouds. Both qualitative and quantitative results demonstrate the effectiveness of our method, particularly its efficiency for large-scale reconstructions. The source code and data are available at https://github.com/chenzhaiyu/polygnn.
Utilizing long-range dependency, a concept extensively studied in homogeneous graphs, remains underexplored in heterogeneous graphs, especially on large ones, posing two significant challenges: Reducing computational costs while maximizing effective information utilization in the presence of heterogeneity, and overcoming the over-smoothing issue in graph neural networks. To address this gap, we investigate the importance of different meta-paths and introduce an automatic framework for utilizing long-range dependency on heterogeneous graphs, denoted as Long-range Meta-path Search through Progressive Sampling (LMSPS). Specifically, we develop a search space with all meta-paths related to the target node type. By employing a progressive sampling algorithm, LMSPS dynamically shrinks the search space with hop-independent time complexity. Through a sampling evaluation strategy, LMSPS conducts a specialized and effective meta-path selection, leading to retraining with only effective meta-paths, thus mitigating costs and over-smoothing. Extensive experiments across diverse heterogeneous datasets validate LMSPS's capability in discovering effective long-range meta-paths, surpassing state-of-the-art methods. Our code is available at https://github.com/JHL-HUST/LMSPS.
Graph neural networks have become the standard approach for dealing with learning problems on graphs. Among the different variants of graph neural networks, graph attention networks (GATs) have been applied with great success to different tasks. In the GAT model, each node assigns an importance score to its neighbors using an attention mechanism. However, similar to other graph neural networks, GATs aggregate messages from nodes that belong to different classes, and therefore produce node representations that are not well separated with respect to the different classes, which might hurt their performance. In this work, to alleviate this problem, we propose a new technique that can be incorporated into any graph attention model to encourage higher attention scores between nodes that share the same class label. We evaluate the proposed method on several node classification datasets demonstrating increased performance over standard baseline models.
Graph neural networks have shown great ability in representation (GNNs) learning on graphs, facilitating various tasks. Despite their great performance in modeling graphs, recent works show that GNNs tend to inherit and amplify the bias from training data, causing concerns of the adoption of GNNs in high-stake scenarios. Hence, many efforts have been taken for fairness-aware GNNs. However, most existing fair GNNs learn fair node representations by adopting statistical fairness notions, which may fail to alleviate bias in the presence of statistical anomalies. Motivated by causal theory, there are several attempts utilizing graph counterfactual fairness to mitigate root causes of unfairness. However, these methods suffer from non-realistic counterfactuals obtained by perturbation or generation. In this paper, we take a causal view on fair graph learning problem. Guided by the casual analysis, we propose a novel framework CAF, which can select counterfactuals from training data to avoid non-realistic counterfactuals and adopt selected counterfactuals to learn fair node representations for node classification task. Extensive experiments on synthetic and real-world datasets show the effectiveness of CAF. Our code is available at https://github.com/TimeLovercc/CAF-GNN.
Graph neural network (GNN) has gained increasing popularity in recent years owing to its capability and flexibility in modeling complex graph structure data. Among all graph learning methods, hypergraph learning is a technique for exploring the implicit higher-order correlations when training the embedding space of the graph. In this paper, we propose a hypergraph learning framework named LFH that is capable of dynamic hyperedge construction and attentive embedding update utilizing the heterogeneity attributes of the graph. Specifically, in our framework, the high-quality features are first generated by the pairwise fusion strategy that utilizes explicit graph structure information when generating initial node embedding. Afterwards, a hypergraph is constructed through the dynamic grouping of implicit hyperedges, followed by the type-specific hypergraph learning process. To evaluate the effectiveness of our proposed framework, we conduct comprehensive experiments on several popular datasets with eleven state-of-the-art models on both node classification and link prediction tasks, which fall into categories of homogeneous pairwise graph learning, heterogeneous pairwise graph learning, and hypergraph learning. The experiment results demonstrate a significant performance gain (average 12.5% in node classification and 13.3% in link prediction) compared with recent state-of-the-art methods.
Learning on Graphs has attracted immense attention due to its wide real-world applications. The most popular pipeline for learning on graphs with textual node attributes primarily relies on Graph Neural Networks (GNNs), and utilizes shallow text embedding as initial node representations, which has limitations in general knowledge and profound semantic understanding. In recent years, Large Language Models (LLMs) have been proven to possess extensive common knowledge and powerful semantic comprehension abilities that have revolutionized existing workflows to handle text data. In this paper, we aim to explore the potential of LLMs in graph machine learning, especially the node classification task, and investigate two possible pipelines: LLMs-as-Enhancers and LLMs-as-Predictors. The former leverages LLMs to enhance nodes' text attributes with their massive knowledge and then generate predictions through GNNs. The latter attempts to directly employ LLMs as standalone predictors. We conduct comprehensive and systematical studies on these two pipelines under various settings. From comprehensive empirical results, we make original observations and find new insights that open new possibilities and suggest promising directions to leverage LLMs for learning on graphs. Our codes and datasets are available at https://github.com/CurryTang/Graph-LLM.
Dynamic graph embedding has emerged as a very effective technique for addressing diverse temporal graph analytic tasks (i.e., link prediction, node classification, recommender systems, anomaly detection, and graph generation) in various applications. Such temporal graphs exhibit heterogeneous transient dynamics, varying time intervals, and highly evolving node features throughout their evolution. Hence, incorporating long-range dependencies from the historical graph context plays a crucial role in accurately learning their temporal dynamics. In this paper, we develop a graph embedding model with uncertainty quantification, TransformerG2G, by exploiting the advanced transformer encoder to first learn intermediate node representations from its current state ($t$) and previous context (over timestamps [$t-1, t-l$], $l$ is the length of context). Moreover, we employ two projection layers to generate lower-dimensional multivariate Gaussian distributions as each node's latent embedding at timestamp $t$. We consider diverse benchmarks with varying levels of ``novelty" as measured by the TEA (Temporal Edge Appearance) plots. Our experiments demonstrate that the proposed TransformerG2G model outperforms conventional multi-step methods and our prior work (DynG2G) in terms of both link prediction accuracy and computational efficiency, especially for high degree of novelty. Furthermore, the learned time-dependent attention weights across multiple graph snapshots reveal the development of an automatic adaptive time stepping enabled by the transformer. Importantly, by examining the attention weights, we can uncover temporal dependencies, identify influential elements, and gain insights into the complex interactions within the graph structure. For example, we identified a strong correlation between attention weights and node degree at the various stages of the graph topology evolution.
Heterogeneous graph neural networks (GNNs) have been successful in handling heterogeneous graphs. In existing heterogeneous GNNs, meta-path plays an essential role. However, recent work pointed out that simple homogeneous graph model without meta-path can also achieve comparable results, which calls into question the necessity of meta-path. In this paper, we first present the intrinsic difference about meta-path-based and meta-path-free models, i.e., how to select neighbors for node aggregation. Then, we propose a novel framework to utilize the rich type semantic information in heterogeneous graphs comprehensively, namely HAGNN (Hybrid Aggregation for Heterogeneous GNNs). The core of HAGNN is to leverage the meta-path neighbors and the directly connected neighbors simultaneously for node aggregations. HAGNN divides the overall aggregation process into two phases: meta-path-based intra-type aggregation and meta-path-free inter-type aggregation. During the intra-type aggregation phase, we propose a new data structure called fused meta-path graph and perform structural semantic aware aggregation on it. Finally, we combine the embeddings generated by each phase. Compared with existing heterogeneous GNN models, HAGNN can take full advantage of the heterogeneity in heterogeneous graphs. Extensive experimental results on node classification, node clustering, and link prediction tasks show that HAGNN outperforms the existing modes, demonstrating the effectiveness of HAGNN.
Traditional convolutional neural networks are limited to handling Euclidean space data, overlooking the vast realm of real-life scenarios represented as graph data, including transportation networks, social networks, and reference networks. The pivotal step in transferring convolutional neural networks to graph data analysis and processing lies in the construction of graph convolutional operators and graph pooling operators. This comprehensive review article delves into the world of graph convolutional neural networks. Firstly, it elaborates on the fundamentals of graph convolutional neural networks. Subsequently, it elucidates the graph neural network models based on attention mechanisms and autoencoders, summarizing their application in node classification, graph classification, and link prediction along with the associated datasets.