Predicting drug-gene associations is crucial for drug development and disease treatment. While graph neural networks (GNN) have shown effectiveness in this task, they face challenges with data sparsity and efficient contrastive learning implementation. We introduce a graph diffusion network for drug-gene prediction (GDNDGP), a framework that addresses these limitations through two key innovations. First, it employs meta-path-based homogeneous graph learning to capture drug-drug and gene-gene relationships, ensuring similar entities share embedding spaces. Second, it incorporates a parallel diffusion network that generates hard negative samples during training, eliminating the need for exhaustive negative sample retrieval. Our model achieves superior performance on the DGIdb 4.0 dataset and demonstrates strong generalization capability on tripartite drug-gene-disease networks. Results show significant improvements over existing methods in drug-gene prediction tasks, particularly in handling complex heterogeneous relationships. The source code is publicly available at https://github.com/csjywu1/GDNDGP.
Deep neural networks have enabled researchers to create powerful generalized frameworks, such as transformers, that can be used to solve well-studied problems in various application domains, such as text and image. However, such generalized frameworks are not available for solving graph problems. Graph structures are ubiquitous in many applications around us and many graph problems have been widely studied over years. In recent times, there has been a surge in deep neural network based approaches to solve graph problems, with growing availability of graph structured datasets across diverse domains. Nevertheless, existing methods are mostly tailored to solve a specific task and lack the capability to create a generalized model leading to solutions for different downstream tasks. In this work, we propose a novel, resource-efficient framework named \emph{U}nified \emph{G}raph \emph{N}etwork (UGN) by leveraging the feature extraction capability of graph convolutional neural networks (GCN) and 2-dimensional convolutional neural networks (Conv2D). UGN unifies various graph learning tasks, such as link prediction, node classification, community detection, graph-to-graph translation, knowledge graph completion, and more, within a cohesive framework, while exercising minimal task-specific extensions (e.g., formation of supernodes for coarsening massive networks to increase scalability, use of \textit{mean target connectivity matrix} (MTCM) representation for achieving scalability in graph translation task, etc.) to enhance the generalization capability of graph learning and analysis. We test the novel UGN framework for six uncorrelated graph problems, using twelve different datasets. Experimental results show that UGN outperforms the state-of-the-art baselines by a significant margin on ten datasets, while producing comparable results on the remaining dataset.
Remote sensing pansharpening aims to reconstruct spatial-spectral properties during the fusion of panchromatic (PAN) images and low-resolution multi-spectral (LR-MS) images, finally generating the high-resolution multi-spectral (HR-MS) images. In the mainstream modeling strategies, i.e., CNN and Transformer, the input images are treated as the equal-sized grid of pixels in the Euclidean space. They have limitations in facing remote sensing images with irregular ground objects. Graph is the more flexible structure, however, there are two major challenges when modeling spatial-spectral properties with graph: \emph{1) constructing the customized graph structure for spatial-spectral relationship priors}; \emph{2) learning the unified spatial-spectral representation through the graph}. To address these challenges, we propose the spatial-spectral heterogeneous graph learning network, named \textbf{HetSSNet}. Specifically, HetSSNet initially constructs the heterogeneous graph structure for pansharpening, which explicitly describes pansharpening-specific relationships. Subsequently, the basic relationship pattern generation module is designed to extract the multiple relationship patterns from the heterogeneous graph. Finally, relationship pattern aggregation module is exploited to collaboratively learn unified spatial-spectral representation across different relationships among nodes with adaptive importance learning from local and global perspectives. Extensive experiments demonstrate the significant superiority and generalization of HetSSNet.
Adversarial evasion attacks pose significant threats to graph learning, with lines of studies that have improved the robustness of Graph Neural Networks (GNNs). However, existing works rely on priors about clean graphs or attacking strategies, which are often heuristic and inconsistent. To achieve robust graph learning over different types of evasion attacks and diverse datasets, we investigate this problem from a prior-free structure purification perspective. Specifically, we propose a novel Diffusion-based Structure Purification framework named DiffSP, which creatively incorporates the graph diffusion model to learn intrinsic distributions of clean graphs and purify the perturbed structures by removing adversaries under the direction of the captured predictive patterns without relying on priors. DiffSP is divided into the forward diffusion process and the reverse denoising process, during which structure purification is achieved. To avoid valuable information loss during the forward process, we propose an LID-driven nonisotropic diffusion mechanism to selectively inject noise anisotropically. To promote semantic alignment between the clean graph and the purified graph generated during the reverse process, we reduce the generation uncertainty by the proposed graph transfer entropy guided denoising mechanism. Extensive experiments demonstrate the superior robustness of DiffSP against evasion attacks.
Medical time series has been playing a vital role in real-world healthcare systems as valuable information in monitoring health conditions of patients. Accurate classification for medical time series, e.g., Electrocardiography (ECG) signals, can help for early detection and diagnosis. Traditional methods towards medical time series classification rely on handcrafted feature extraction and statistical methods; with the recent advancement of artificial intelligence, the machine learning and deep learning methods have become more popular. However, existing methods often fail to fully model the complex spatial dynamics under different scales, which ignore the dynamic multi-resolution spatial and temporal joint inter-dependencies. Moreover, they are less likely to consider the special baseline wander problem as well as the multi-view characteristics of medical time series, which largely hinders their prediction performance. To address these limitations, we propose a Multi-resolution Spatiotemporal Graph Learning framework, MedGNN, for medical time series classification. Specifically, we first propose to construct multi-resolution adaptive graph structures to learn dynamic multi-scale embeddings. Then, to address the baseline wander problem, we propose Difference Attention Networks to operate self-attention mechanisms on the finite difference for temporal modeling. Moreover, to learn the multi-view characteristics, we utilize the Frequency Convolution Networks to capture complementary information of medical time series from the frequency domain. In addition, we introduce the Multi-resolution Graph Transformer architecture to model the dynamic dependencies and fuse the information from different resolutions. Finally, we have conducted extensive experiments on multiple medical real-world datasets that demonstrate the superior performance of our method. Our Code is available.
Benchmark datasets have proved pivotal to the success of graph learning, and good benchmark datasets are crucial to guide the development of the field. Recent research has highlighted problems with graph-learning datasets and benchmarking practices -- revealing, for example, that methods which ignore the graph structure can outperform graph-based approaches on popular benchmark datasets. Such findings raise two questions: (1) What makes a good graph-learning dataset, and (2) how can we evaluate dataset quality in graph learning? Our work addresses these questions. As the classic evaluation setup uses datasets to evaluate models, it does not apply to dataset evaluation. Hence, we start from first principles. Observing that graph-learning datasets uniquely combine two modes -- the graph structure and the node features -- , we introduce RINGS, a flexible and extensible mode-perturbation framework to assess the quality of graph-learning datasets based on dataset ablations -- i.e., by quantifying differences between the original dataset and its perturbed representations. Within this framework, we propose two measures -- performance separability and mode complementarity -- as evaluation tools, each assessing, from a distinct angle, the capacity of a graph dataset to benchmark the power and efficacy of graph-learning methods. We demonstrate the utility of our framework for graph-learning dataset evaluation in an extensive set of experiments and derive actionable recommendations for improving the evaluation of graph-learning methods. Our work opens new research directions in data-centric graph learning, and it constitutes a first step toward the systematic evaluation of evaluations.
Graph learning on molecules makes use of information from both the molecular structure and the features attached to that structure. Much work has been conducted on biasing either towards structure or features, with the aim that bias bolsters performance. Identifying which information source a dataset favours, and therefore how to approach learning that dataset, is an open issue. Here we propose Noise-Noise Ratio Difference (NNRD), a quantitative metric for whether there is more useful information in structure or features. By employing iterative noising on features and structure independently, leaving the other intact, NNRD measures the degradation of information in each. We employ NNRD over a range of molecular tasks, and show that it corresponds well to a loss of information, with intuitive results that are more expressive than simple performance aggregates. Our future work will focus on expanding data domains, tasks and types, as well as refining our choice of baseline model.
Graph learning tasks often hinge on identifying key substructure patterns -- such as triadic closures in social networks or benzene rings in molecular graphs -- that underpin downstream performance. However, most existing graph neural networks (GNNs) rely on message passing, which aggregates local neighborhood information iteratively and struggles to explicitly capture such fundamental motifs, like triangles, k-cliques, and rings. This limitation hinders both expressiveness and long-range dependency modeling. In this paper, we introduce the Neural Graph Pattern Machine (GPM), a novel framework that bypasses message passing by learning directly from graph substructures. GPM efficiently extracts, encodes, and prioritizes task-relevant graph patterns, offering greater expressivity and improved ability to capture long-range dependencies. Empirical evaluations across four standard tasks -- node classification, link prediction, graph classification, and graph regression -- demonstrate that GPM outperforms state-of-the-art baselines. Further analysis reveals that GPM exhibits strong out-of-distribution generalization, desirable scalability, and enhanced interpretability. Code and datasets are available at: https://github.com/Zehong-Wang/GPM.
For rapidly spreading diseases where many cases show no symptoms, swift and effective contact tracing is essential. While exposure notification applications provide alerts on potential exposures, a fully automated system is needed to track the infectious transmission routes. To this end, our research leverages large-scale contact networks from real human mobility data to identify the path of transmission. More precisely, we introduce a new Infectious Path Centrality network metric that informs a graph learning edge classifier to identify important transmission events, achieving an F1-score of 94%. Additionally, we explore bidirectional contact tracing, which quarantines individuals both retroactively and proactively, and compare its effectiveness against traditional forward tracing, which only isolates individuals after testing positive. Our results indicate that when only 30% of symptomatic individuals are tested, bidirectional tracing can reduce infectious effective reproduction rate by 71%, thus significantly controlling the outbreak.
Existing literature lacks a graph domain adaptation technique for handling large distribution shifts, primarily due to the difficulty in simulating an evolving path from source to target graph. To make a breakthrough, we present a graph gradual domain adaptation (GGDA) framework with the construction of a compact domain sequence that minimizes information loss in adaptations. Our approach starts with an efficient generation of knowledge-preserving intermediate graphs over the Fused Gromov-Wasserstein (FGW) metric. With the bridging data pool, GGDA domains are then constructed via a novel vertex-based domain progression, which comprises "close" vertex selections and adaptive domain advancement to enhance inter-domain information transferability. Theoretically, our framework concretizes the intractable inter-domain distance $W_p(\mu_t,\mu_{t+1})$ via implementable upper and lower bounds, enabling flexible adjustments of this metric for optimizing domain formation. Extensive experiments under various transfer scenarios validate the superior performance of our GGDA framework.
Dynamic graphs (DGs), which capture time-evolving relationships between graph entities, have widespread real-world applications. To efficiently encode DGs for downstream tasks, most dynamic graph neural networks follow the traditional message-passing mechanism and extend it with time-based techniques. Despite their effectiveness, the growth of historical interactions introduces significant scalability issues, particularly in industry scenarios. To address this limitation, we propose ScaDyG, with the core idea of designing a time-aware scalable learning paradigm as follows: 1) Time-aware Topology Reformulation: ScaDyG first segments historical interactions into time steps (intra and inter) based on dynamic modeling, enabling weight-free and time-aware graph propagation within pre-processing. 2) Dynamic Temporal Encoding: To further achieve fine-grained graph propagation within time steps, ScaDyG integrates temporal encoding through a combination of exponential functions in a scalable manner. 3) Hypernetwork-driven Message Aggregation: After obtaining the propagated features (i.e., messages), ScaDyG utilizes hypernetwork to analyze historical dependencies, implementing node-wise representation by an adaptive temporal fusion. Extensive experiments on 12 datasets demonstrate that ScaDyG performs comparably well or even outperforms other SOTA methods in both node and link-level downstream tasks, with fewer learnable parameters and higher efficiency.
The growing importance of textual and relational systems has driven interest in enhancing large language models (LLMs) for graph-structured data, particularly Text-Attributed Graphs (TAGs), where samples are represented by textual descriptions interconnected by edges. While research has largely focused on developing specialized graph LLMs through task-specific instruction tuning, a comprehensive benchmark for evaluating LLMs solely through prompt design remains surprisingly absent. Without such a carefully crafted evaluation benchmark, most if not all, tailored graph LLMs are compared against general LLMs using simplistic queries (e.g., zero-shot reasoning with LLaMA), which can potentially camouflage many advantages as well as unexpected predicaments of them. To achieve more general evaluations and unveil the true potential of LLMs for graph tasks, we introduce Graph In-context Learning (GraphICL) Benchmark, a comprehensive benchmark comprising novel prompt templates designed to capture graph structure and handle limited label knowledge. Our systematic evaluation shows that general-purpose LLMs equipped with our GraphICL outperform state-of-the-art specialized graph LLMs and graph neural network models in resource-constrained settings and out-of-domain tasks. These findings highlight the significant potential of prompt engineering to enhance LLM performance on graph learning tasks without training and offer a strong baseline for advancing research in graph LLMs.
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.
Federated graph learning (FGL) has emerged as a promising paradigm for collaborative machine learning, enabling multiple parties to jointly train models while preserving the privacy of raw graph data. However, existing FGL methods often overlook the model-centric heterogeneous FGL (MHtFGL) problem, which arises in real-world applications, such as the aggregation of models from different companies with varying scales and architectures. MHtFGL presents an additional challenge: the diversity of client model architectures hampers common learning and integration of graph representations. To address this issue, we propose the Federated Graph Knowledge Collaboration (FedGKC) framework, comprising two key components: Client-side Self-Mutual Knowledge Distillation, which fosters effective knowledge sharing among clients through copilot models; and Server-side Knowledge-Aware Model Aggregation, which enhances model integration by accounting for the knowledge acquired by clients. Experiments on eight benchmark datasets demonstrate that FedGKC achieves an average accuracy improvement of 3.74% over baseline models in MHtFGL scenarios, while also maintaining excellent performance in homogeneous settings.
Invariant learning demonstrates substantial potential for enhancing the generalization of graph neural networks (GNNs) with out-of-distribution (OOD) data. It aims to recognize stable features in graph data for classification, based on the premise that these features causally determine the target label, and their influence is invariant to changes in distribution. Along this line, most studies have attempted to pinpoint these stable features by emphasizing explicit substructures in the graph, such as masked or attentive subgraphs, and primarily enforcing the invariance principle in the semantic space, i.e., graph representations. However, we argue that focusing only on the semantic space may not accurately identify these stable features. To address this, we introduce the Unified Invariant Learning (UIL) framework for graph classification. It provides a unified perspective on invariant graph learning, emphasizing both structural and semantic invariance principles to identify more robust stable features. In the graph space, UIL adheres to the structural invariance principle by reducing the distance between graphons over a set of stable features across different environments. Simultaneously, to confirm semantic invariance, UIL underscores that the acquired graph representations should demonstrate exemplary performance across diverse environments. We present both theoretical and empirical evidence to confirm our method's ability to recognize superior stable features. Moreover, through a series of comprehensive experiments complemented by in-depth analyses, we demonstrate that UIL considerably enhances OOD generalization, surpassing the performance of leading baseline methods. Our codes are available at https://github.com/yongduosui/UIL.
Temporal Knowledge Graph Forecasting (TKGF) aims to predict future events based on the observed events in history. Recently, Large Language Models (LLMs) have exhibited remarkable capabilities, generating significant research interest in their application for reasoning over temporal knowledge graphs (TKGs). Existing LLM-based methods have integrated retrieved historical facts or static graph representations into LLMs. Despite the notable performance of LLM-based methods, they are limited by the insufficient modeling of temporal patterns and ineffective cross-modal alignment between graph and language, hindering the ability of LLMs to fully grasp the temporal and structural information in TKGs. To tackle these issues, we propose a novel framework TGL-LLM to integrate temporal graph learning into LLM-based temporal knowledge graph model. Specifically, we introduce temporal graph learning to capture the temporal and relational patterns and obtain the historical graph embedding. Furthermore, we design a hybrid graph tokenization to sufficiently model the temporal patterns within LLMs. To achieve better alignment between graph and language, we employ a two-stage training paradigm to finetune LLMs on high-quality and diverse data, thereby resulting in better performance. Extensive experiments on three real-world datasets show that our approach outperforms a range of state-of-the-art (SOTA) methods.
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.
With the advancement of information technology, the Social Internet of Things (SIoT) has fostered the integration of physical devices and social networks, deepening the study of complex interaction patterns. Text Attribute Graphs (TAGs) capture both topological structures and semantic attributes, enhancing the analysis of complex interactions within the SIoT. However, existing graph learning methods are typically designed for complete attributed graphs, and the common issue of missing attributes in Attribute Missing Graphs (AMGs) increases the difficulty of analysis tasks. To address this, we propose the Topology-Driven Attribute Recovery (TDAR) framework, which leverages topological data for AMG learning. TDAR introduces an improved pre-filling method for initial attribute recovery using native graph topology. Additionally, it dynamically adjusts propagation weights and incorporates homogeneity strategies within the embedding space to suit AMGs' unique topological structures, effectively reducing noise during information propagation. Extensive experiments on public datasets demonstrate that TDAR significantly outperforms state-of-the-art methods in attribute reconstruction and downstream tasks, offering a robust solution to the challenges posed by AMGs. The code is available at https://github.com/limengran98/TDAR.
In the realm of multi-object tracking, the challenge of accurately capturing the spatial and temporal relationships between objects in video sequences remains a significant hurdle. This is further complicated by frequent occurrences of mutual occlusions among objects, which can lead to tracking errors and reduced performance in existing methods. Motivated by these challenges, we propose a novel adaptive key frame mining strategy that addresses the limitations of current tracking approaches. Specifically, we introduce a Key Frame Extraction (KFE) module that leverages reinforcement learning to adaptively segment videos, thereby guiding the tracker to exploit the intrinsic logic of the video content. This approach allows us to capture structured spatial relationships between different objects as well as the temporal relationships of objects across frames. To tackle the issue of object occlusions, we have developed an Intra-Frame Feature Fusion (IFF) module. Unlike traditional graph-based methods that primarily focus on inter-frame feature fusion, our IFF module uses a Graph Convolutional Network (GCN) to facilitate information exchange between the target and surrounding objects within a frame. This innovation significantly enhances target distinguishability and mitigates tracking loss and appearance similarity due to occlusions. By combining the strengths of both long and short trajectories and considering the spatial relationships between objects, our proposed tracker achieves impressive results on the MOT17 dataset, i.e., 68.6 HOTA, 81.0 IDF1, 66.6 AssA, and 893 IDS, proving its effectiveness and accuracy.