Graph distillation (GD) is an effective approach to extract useful information from large-scale network structures. However, existing methods, which operate in Euclidean space to generate condensed graphs, struggle to capture the inherent tree-like geometry of real-world networks, resulting in distilled graphs with limited task-specific information for downstream tasks. Furthermore, these methods often fail to extract dynamic properties from graphs, which are crucial for understanding information flow and facilitating graph continual learning. This paper presents the Hyperbolic Graph Distillation with Random Walks Optimization (HyDRO), a novel graph distillation approach that leverages hyperbolic embeddings to capture complex geometric patterns and optimize the spectral gap in hyperbolic space. Experiments show that HyDRO demonstrates strong task generalization, consistently outperforming state-of-the-art methods in both node classification and link prediction tasks. HyDRO also effectively preserves graph random walk properties, producing condensed graphs that achieve enhanced performance in continual graph learning. Additionally, HyDRO achieves competitive results on mainstream graph distillation benchmarks, while maintaining a strong balance between privacy and utility, and exhibiting robust resistance to noises.
The success of Large Language Models (LLMs) in various domains has led researchers to apply them to graph-related problems by converting graph data into natural language text. However, unlike graph data, natural language inherently has sequential order. We observe a counter-intuitive fact that when the order of nodes or edges in the natural language description of a graph is shuffled, despite describing the same graph, model performance fluctuates between high performance and random guessing. Additionally, due to LLMs' limited input context length, current methods typically randomly sample neighbors of target nodes as representatives of their neighborhood, which may not always be effective for accurate reasoning. To address these gaps, we introduce GraphSOS (Graph Sampling and Order Selection). This novel model framework features an Order Selector Module to ensure proper serialization order of the graph and a Subgraph Sampling Module to sample subgraphs with better structure for better reasoning. Furthermore, we propose Graph CoT obtained through distillation, and enhance LLM's reasoning and zero-shot learning capabilities for graph tasks through instruction tuning. Experiments on multiple datasets for node classification and graph question-answering demonstrate that GraphSOS improves LLMs' performance and generalization ability on graph tasks.
The updated recommendations on diagnostic procedures and treatment pathways for a medical condition are documented as graphical flows in Clinical Practice Guidelines (CPGs). For effective use of the CPGs in helping medical professionals in the treatment decision process, it is necessary to fully capture the guideline knowledge, particularly the contexts and their relationships in the graph. While several existing works have utilized these guidelines to create rule bases for Clinical Decision Support Systems, limited work has been done toward directly capturing the full medical knowledge contained in CPGs. This work proposes an approach to create a contextually enriched, faithful digital representation of National Comprehensive Cancer Network (NCCN) Cancer CPGs in the form of graphs using automated extraction and node & relationship classification. We also implement semantic enrichment of the model by using Large Language Models (LLMs) for node classification, achieving an accuracy of 80.86% and 88.47% with zero-shot learning and few-shot learning, respectively. Additionally, we introduce a methodology for answering natural language questions with constraints to guideline text by leveraging LLMs to extract the relevant subgraph from the guideline knowledge base. By generating natural language answers based on subgraph paths and semantic information, we mitigate the risk of incorrect answers and hallucination associated with LLMs, ensuring factual accuracy in medical domain Question Answering.
Blockchain technology, with implications in the financial domain, offers data in the form of large-scale transaction networks. Analyzing transaction networks facilitates fraud detection, market analysis, and supports government regulation. Despite many graph representation learning methods for transaction network analysis, we pinpoint two salient limitations that merit more investigation. Existing methods predominantly focus on the snapshots of transaction networks, sidelining the evolving nature of blockchain transaction networks. Existing methodologies may not sufficiently emphasize efficient, incremental learning capabilities, which are essential for addressing the scalability challenges in ever-expanding large-scale transaction networks. To address these challenges, we employed an incremental approach for random walk-based node representation learning in transaction networks. Further, we proposed a Metropolis-Hastings-based random walk mechanism for improved efficiency. The empirical evaluation conducted on blockchain transaction datasets reveals comparable performance in node classification tasks while reducing computational overhead. Potential applications include transaction network monitoring, the efficient classification of blockchain addresses for fraud detection or the identification of specialized address types within the network.
Representation learning on heterogeneous text-rich networks (HTRNs), which consist of multiple types of nodes and edges with each node associated with textual information, is essential for various real-world applications. Given the success of pretrained language models (PLMs) in processing text data, recent efforts have focused on integrating PLMs into HTRN representation learning. These methods typically handle textual and structural information separately, using both PLMs and heterogeneous graph neural networks (HGNNs). However, this separation fails to capture the critical interactions between these two types of information within HTRNs. Additionally, it necessitates an extra alignment step, which is challenging due to the fundamental differences between distinct embedding spaces generated by PLMs and HGNNs. To deal with it, we propose HierPromptLM, a novel pure PLM-based framework that seamlessly models both text data and graph structures without the need for separate processing. Firstly, we develop a Hierarchical Prompt module that employs prompt learning to integrate text data and heterogeneous graph structures at both the node and edge levels, within a unified textual space. Building upon this foundation, we further introduce two innovative HTRN-tailored pretraining tasks to fine-tune PLMs for representation learning by emphasizing the inherent heterogeneity and interactions between textual and structural information within HTRNs. Extensive experiments on two real-world HTRN datasets demonstrate HierPromptLM outperforms state-of-the-art methods, achieving significant improvements of up to 6.08% for node classification and 10.84% for link prediction.
Recent efforts leverage Large Language Models (LLMs) for modeling text-attributed graph structures in node classification tasks. These approaches describe graph structures for LLMs to understand or aggregate LLM-generated textual attribute embeddings through graph structure. However, these approaches face two main limitations in modeling graph structures with LLMs. (i) Graph descriptions become verbose in describing high-order graph structure. (ii) Textual attributes alone do not contain adequate graph structure information. It is challenging to model graph structure concisely and adequately with LLMs. LLMs lack built-in mechanisms to model graph structures directly. They also struggle with complex long-range dependencies between high-order nodes and target nodes. Inspired by the observation that LLMs pre-trained on one language can achieve exceptional performance on another with minimal additional training, we propose \textbf{G}raph-\textbf{D}efined \textbf{L}anguage for \textbf{L}arge \textbf{L}anguage \textbf{M}odel (GDL4LLM). This novel framework enables LLMs to transfer their powerful language understanding capabilities to graph-structured data. GDL4LLM translates graphs into a graph language corpus instead of graph descriptions and pre-trains LLMs on this corpus to adequately understand graph structures. During fine-tuning, this corpus describes the structural information of target nodes concisely with only a few tokens. By treating graphs as a new language, GDL4LLM enables LLMs to model graph structures adequately and concisely for node classification tasks. Extensive experiments on three real-world datasets demonstrate that GDL4LLM outperforms description-based and textual attribute embeddings-based baselines by efficiently modeling different orders of graph structure with LLMs.
Dynamic graph augmentation is used to improve the performance of dynamic GNNs. Most methods assume temporal locality, meaning that recent edges are more influential than earlier edges. However, for temporal changes in edges caused by random noise, overemphasizing recent edges while neglecting earlier ones may lead to the model capturing noise. To address this issue, we propose STAA (SpatioTemporal Activity-Aware Random Walk Diffusion). STAA identifies nodes likely to have noisy edges in spatiotemporal dimensions. Spatially, it analyzes critical topological positions through graph wavelet coefficients. Temporally, it analyzes edge evolution through graph wavelet coefficient change rates. Then, random walks are used to reduce the weights of noisy edges, deriving a diffusion matrix containing spatiotemporal information as an augmented adjacency matrix for dynamic GNN learning. Experiments on multiple datasets show that STAA outperforms other dynamic graph augmentation methods in node classification and link prediction tasks.
Representation learning on graphs is a fundamental problem that can be crucial in various tasks. Graph neural networks, the dominant approach for graph representation learning, are limited in their representation power. Therefore, it can be beneficial to explicitly extract and incorporate high-order topological and geometric information into these models. In this paper, we propose a principled approach to extract the rich connectivity information of graphs based on the theory of persistent homology. Our method utilizes the topological features to enhance the representation learning of graph neural networks and achieve state-of-the-art performance on various node classification and link prediction benchmarks. We also explore the option of end-to-end learning of the topological features, i.e., treating topological computation as a differentiable operator during learning. Our theoretical analysis and empirical study provide insights and potential guidelines for employing topological features in graph learning tasks.
Graph Neural Networks (GNNs) have demonstrated remarkable ability in semi-supervised node classification. However, most existing GNNs rely heavily on a large amount of labeled data for training, which is labor-intensive and requires extensive domain knowledge. In this paper, we first analyze the restrictions of GNNs generalization from the perspective of supervision signals in the context of few-shot semi-supervised node classification. To address these challenges, we propose a novel algorithm named NormProp, which utilizes the homophily assumption of unlabeled nodes to generate additional supervision signals, thereby enhancing the generalization against label scarcity. The key idea is to efficiently capture both the class information and the consistency of aggregation during message passing, via decoupling the direction and Euclidean norm of node representations. Moreover, we conduct a theoretical analysis to determine the upper bound of Euclidean norm, and then propose homophilous regularization to constraint the consistency of unlabeled nodes. Extensive experiments demonstrate that NormProp achieve state-of-the-art performance under low-label rate scenarios with low computational complexity.
Many real-world systems can be modeled as dynamic graphs, where nodes and edges evolve over time, requiring specialized models to capture their evolving dynamics in risk-sensitive applications effectively. Temporal graph neural networks (GNNs) are one such category of specialized models. For the first time, our approach integrates a reject option strategy within the framework of GNNs for continuous-time dynamic graphs. This allows the model to strategically abstain from making predictions when the uncertainty is high and confidence is low, thus minimizing the risk of critical misclassification and enhancing the results and reliability. We propose a coverage-based abstention prediction model to implement the reject option that maximizes prediction within a specified coverage. It improves the prediction score for link prediction and node classification tasks. Temporal GNNs deal with extremely skewed datasets for the next state prediction or node classification task. In the case of class imbalance, our method can be further tuned to provide a higher weightage to the minority class. Exhaustive experiments are presented on four datasets for dynamic link prediction and two datasets for dynamic node classification tasks. This demonstrates the effectiveness of our approach in improving the reliability and area under the curve (AUC)/ average precision (AP) scores for predictions in dynamic graph scenarios. The results highlight our model's ability to efficiently handle the trade-offs between prediction confidence and coverage, making it a dependable solution for applications requiring high precision in dynamic and uncertain environments.
Graph Neural Networks (GNNs) are popular deep learning models designed to process graph-structured data through recursive neighborhood aggregations in the message passing process. When applied to semi-supervised node classification, the message-passing enables GNNs to understand short-range spatial interactions, but also causes them to suffer from over-smoothing and over-squashing. These challenges hinder model expressiveness and prevent the use of deeper models to capture long-range node interactions (LRIs) within the graph. Popular solutions for LRIs detection are either too expensive to process large graphs due to high time complexity or fail to generalize across diverse graph structures. To address these limitations, we propose a mechanism called \emph{information flow control}, which leverages a novel connectivity measure, called \emph{information flow score}, to address over-smoothing and over-squashing with linear computational overhead, supported by theoretical evidence. Finally, to prove the efficacy of our methodology we design DeltaGNN, the first scalable and generalizable approach for detecting long-range and short-range interactions. We benchmark our model across 10 real-world datasets, including graphs with varying sizes, topologies, densities, and homophilic ratios, showing superior performance with limited computational complexity. The implementation of the proposed methods are publicly available at https://github.com/basiralab/DeltaGNN.
Graph-based fraud detection faces significant challenges, such as severe class imbalance, inconsistent connections due to the scarcity of fraudulent nodes, and the camouflage of these nodes appearing like benign nodes. Existing studies often adopt the approach of filtering similar nodes to strengthen the homophily assumption of graph neural networks. However, to effectively address these issues, it is important to distinguish and adaptively utilize the labels of neighboring nodes. In this study, we propose the Label-Exploring Graph Neural Network (LEX-GNN), designed to enhance fraud detection by actively leveraging labeled node information. The core idea is that the manner of message passing and reception should vary depending on the node types. Specifically, we first predict the labels of nodes based on their original or previous representations. Subsequently, each node transmits differently processed messages according to its probability of being fraudulent. Finally, target nodes also receive the messages differently depending on their pre-predicted probability. Extensive experimental results on real-world benchmarks demonstrate that LEX-GNN outperforms existing state-of-the-art baselines. Our code is available at https://github.com/wdhyun/LEX-GNN.
Egocentric videos capture scenes from a wearer's viewpoint, resulting in dynamic backgrounds, frequent motion, and occlusions, posing challenges to accurate keystep recognition. We propose a flexible graph-learning framework for fine-grained keystep recognition that is able to effectively leverage long-term dependencies in egocentric videos, and leverage alignment between egocentric and exocentric videos during training for improved inference on egocentric videos. Our approach consists of constructing a graph where each video clip of the egocentric video corresponds to a node. During training, we consider each clip of each exocentric video (if available) as additional nodes. We examine several strategies to define connections across these nodes and pose keystep recognition as a node classification task on the constructed graphs. We perform extensive experiments on the Ego-Exo4D dataset and show that our proposed flexible graph-based framework notably outperforms existing methods by more than 12 points in accuracy. Furthermore, the constructed graphs are sparse and compute efficient. We also present a study examining on harnessing several multimodal features, including narrations, depth, and object class labels, on a heterogeneous graph and discuss their corresponding contribution to the keystep recognition performance.
In many applications, both data samples and features have underlying hierarchical structures. However, existing methods for learning these latent structures typically focus on either samples or features, ignoring possible coupling between them. In this paper, we introduce a coupled hierarchical structure learning method using tree-Wasserstein distance (TWD). Our method jointly computes TWDs for samples and features, representing their latent hierarchies as trees. We propose an iterative, unsupervised procedure to build these sample and feature trees based on diffusion geometry, hyperbolic geometry, and wavelet filters. We show that this iterative procedure converges and empirically improves the quality of the constructed trees. The method is also computationally efficient and scales well in high-dimensional settings. Our method can be seamlessly integrated with hyperbolic graph convolutional networks (HGCN). We demonstrate that our method outperforms competing approaches in sparse approximation and unsupervised Wasserstein distance learning on several word-document and single-cell RNA-sequencing datasets. In addition, integrating our method into HGCN enhances performance in link prediction and node classification tasks.
Graph Neural Networks (GNNs) has been widely used in a variety of fields because of their great potential in representing graph-structured data. However, lacking of rigorous uncertainty estimations limits their application in high-stakes. Conformal Prediction (CP) can produce statistically guaranteed uncertainty estimates by using the classifier's probability estimates to obtain prediction sets, which contains the true class with a user-specified probability. In this paper, we propose a Rank-based CP during training framework to GNNs (RCP-GNN) for reliable uncertainty estimates to enhance the trustworthiness of GNNs in the node classification scenario. By exploiting rank information of the classifier's outcome, prediction sets with desired coverage rate can be efficiently constructed. The strategy of CP during training with differentiable rank-based conformity loss function is further explored to adapt prediction sets according to network topology information. In this way, the composition of prediction sets can be guided by the goal of jointly reducing inefficiency and probability estimation errors. Extensive experiments on several real-world datasets show that our model achieves any pre-defined target marginal coverage while significantly reducing the inefficiency compared with state-of-the-art methods.
Recent advances in Graph Neural Networks (GNNs) have revolutionized graph-structured data modeling, yet traditional GNNs struggle with complex heterogeneous structures prevalent in real-world scenarios. Despite progress in handling heterogeneous interactions, two fundamental challenges persist: noisy data significantly compromising embedding quality and learning performance, and existing methods' inability to capture intricate semantic transitions among heterogeneous relations, which impacts downstream predictions. To address these fundamental issues, we present the Heterogeneous Graph Diffusion Model (DiffGraph), a pioneering framework that introduces an innovative cross-view denoising strategy. This advanced approach transforms auxiliary heterogeneous data into target semantic spaces, enabling precise distillation of task-relevant information. At its core, DiffGraph features a sophisticated latent heterogeneous graph diffusion mechanism, implementing a novel forward and backward diffusion process for superior noise management. This methodology achieves simultaneous heterogeneous graph denoising and cross-type transition, while significantly simplifying graph generation through its latent-space diffusion capabilities. Through rigorous experimental validation on both public and industrial datasets, we demonstrate that DiffGraph consistently surpasses existing methods in link prediction and node classification tasks, establishing new benchmarks for robustness and efficiency in heterogeneous graph processing. The model implementation is publicly available at: https://github.com/HKUDS/DiffGraph.
In this work, we present a probabilistic model for directed graphs where nodes have attributes and labels. This model serves as a generative classifier capable of predicting the labels of unseen nodes using either maximum likelihood or maximum a posteriori estimations. The predictions made by this model are highly interpretable, contrasting with some common methods for node classification, such as graph neural networks. We applied the model to two datasets, demonstrating predictive performance that is competitive with, and even superior to, state-of-the-art methods. One of the datasets considered is adapted from the Math Genealogy Project, which has not previously been utilized for this purpose. Consequently, we evaluated several classification algorithms on this dataset to compare the performance of our model and provide benchmarks for this new resource.
One of the emerging techniques in node classification in heterogeneous graphs is to restrict message aggregation to pre-defined, semantically meaningful structures called metapaths. This work is the first attempt to incorporate attention into the process of encoding entire metapaths without dropping intermediate nodes. In particular, we construct two encoders: the first uses sequential attention to extend the multi-hop message passing algorithm designed in \citet{magna} to the metapath setting, and the second incorporates direct attention to extract semantic relations in the metapath. The model then employs the intra-metapath and inter-metapath aggregation mechanisms of \citet{han}. We furthermore use the powerful training scheduler specialized for heterogeneous graphs that was developed in \citet{lts}, ensuring the model slowly learns how to classify the most difficult nodes. The result is a resilient, general-purpose framework for capturing semantic structures in heterogeneous graphs. In particular, we demonstrate that our model is competitive with state-of-the-art models on performing node classification on the IMDB dataset, a popular benchmark introduced in \citet{benchmark}.
Node classification on static graphs has achieved significant success, but achieving accurate node classification on dynamic graphs where node topology, attributes, and labels change over time has not been well addressed. Existing methods based on RNNs and self-attention only aggregate features of the same node across different time slices, which cannot adequately address and capture the diverse dynamic changes in dynamic graphs. Therefore, we propose a novel model named Hypergraph-Based Multi-granularity Dynamic Graph Node Classification (HYDG). After obtaining basic node representations for each slice through a GNN backbone, HYDG models the representations of each node in the dynamic graph through two modules. The individual-level hypergraph captures the spatio-temporal node representations between individual nodes, while the group-level hypergraph captures the multi-granularity group temporal representations among nodes of the same class. Each hyperedge captures different temporal dependencies of varying lengths by connecting multiple nodes within specific time ranges. More accurate representations are obtained through weighted information propagation and aggregation by the hypergraph neural network. Extensive experiments on five real dynamic graph datasets using two GNN backbones demonstrate the superiority of our proposed framework.
Class imbalance is pervasive in real-world graph datasets, where the majority of annotated nodes belong to a small set of classes (majority classes), leaving many other classes (minority classes) with only a handful of labeled nodes. Graph Neural Networks (GNNs) suffer from significant performance degradation in the presence of class imbalance, exhibiting bias towards majority classes and struggling to generalize effectively on minority classes. This limitation stems, in part, from the message passing process, leading GNNs to overfit to the limited neighborhood of annotated nodes from minority classes and impeding the propagation of discriminative information throughout the entire graph. In this paper, we introduce a novel Unified Graph Neural Network Learning (Uni-GNN) framework to tackle class-imbalanced node classification. The proposed framework seamlessly integrates both structural and semantic connectivity representations through semantic and structural node encoders. By combining these connectivity types, Uni-GNN extends the propagation of node embeddings beyond immediate neighbors, encompassing non-adjacent structural nodes and semantically similar nodes, enabling efficient diffusion of discriminative information throughout the graph. Moreover, to harness the potential of unlabeled nodes within the graph, we employ a balanced pseudo-label generation mechanism that augments the pool of available labeled nodes from minority classes in the training set. Experimental results underscore the superior performance of our proposed Uni-GNN framework compared to state-of-the-art class-imbalanced graph learning baselines across multiple benchmark datasets.