Graph Neural Networks (GNNs) are widely used and deployed for graph-based prediction tasks. However, as good as GNNs are for learning graph data, they also come with the risk of privacy leakage. For instance, an attacker can run carefully crafted queries on the GNNs and, from the responses, can infer the existence of an edge between a pair of nodes. This attack, dubbed as a "link-stealing" attack, can jeopardize the user's privacy by leaking potentially sensitive information. To protect against this attack, we propose an approach called "$(N)$ode $(A)$ugmentation for $(R)$estricting $(G)$raphs from $(I)$nsinuating their $(S)$tructure" ($NARGIS$) and study its feasibility. $NARGIS$ is focused on reshaping the graph embedding space so that the posterior from the GNN model will still provide utility for the prediction task but will introduce ambiguity for the link-stealing attackers. To this end, $NARGIS$ applies spectral clustering on the given graph to facilitate it being augmented with new nodes -- that have learned features instead of fixed ones. It utilizes tri-level optimization for learning parameters for the GNN model, surrogate attacker model, and our defense model (i.e. learnable node features). We extensively evaluate $NARGIS$ on three benchmark citation datasets over eight knowledge availability settings for the attackers. We also evaluate the model fidelity and defense performance on influence-based link inference attacks. Through our studies, we have figured out the best feature of $NARGIS$ -- its superior fidelity-privacy performance trade-off in a significant number of cases. We also have discovered in which cases the model needs to be improved, and proposed ways to integrate different schemes to make the model more robust against link stealing attacks.
Abstract— Recently, many data mining models based on heterogeneous graph (HG) have emerged. Among these, HG embedding is an important and indispensable process. However, the existing HG embedding models usually use graph neural network to learn embeddings separately on different meta-paths, ignoring the fact that different meta-paths contain not only their unique semantics but also related semantics. This may result in semantic overlap or irrelevance, which needs to be a feasible and effective tradeoff for high-quality HG embedding, yet studies thereof have rarely been reported. In this article, we propose semantic tradeoff HG embedding (STHGE) by first introducing the Hilbert–Schmidt independence criterion (HSIC) as restriction. The main idea of STHGE is to regard semantic tradeoff as independence tradeoff (or correlation) between different meta-path spaces. Specifically, we first transform the original features of nodes into different meta-path feature spaces with HSIC restriction between them. Then, we use graph attention network to learn the embeddings of nodes on different meta-paths with HSIC restrictions. Finally, we concatenate the embeddings on different meta-paths to perform prediction. Experimental results on three heterogeneous datasets not only demonstrate the effectiveness of STHGE but also demonstrate that STHGE can achieve a new semantic tradeoff between different meta-paths. Furthermore, we demonstrate the robustness of STHGE.
Zero-shot learning (ZL) is crucial for tasks involving unseen categories, such as natural language processing, image classification, and cross-lingual transfer. Current applications often fail to accurately infer and handle new relations or entities involving unseen categories, severely limiting their scalability and practicality in open-domain scenarios. ZL learning faces the challenge of effectively transferring semantic information of unseen categories in multi-modal knowledge graph (MMKG) embedding representation learning. In this paper, we propose ZSLLM, a framework for zero-shot embedding learning of MMKGs using large language models (LLMs). We leverage textual modality information of unseen categories as prompts to fully utilize the reasoning capabilities of LLMs, enabling semantic information transfer across different modalities for unseen categories. Through model-based learning, the embedding representation of unseen categories in MMKG is enhanced. Extensive experiments conducted on multiple real-world datasets demonstrate the superiority of our approach compared to state-of-the-art methods.
Graph clustering aims to divide the graph into different clusters. The recently emerging deep graph clustering approaches are largely built on graph neural networks (GNN). However, GNN is designed for general graph encoding and there is a common issue of representation collapse in existing GNN-based deep graph clustering algorithms. We attribute two main reasons for such issues: (i) the inductive bias of GNN models: GNNs tend to generate similar representations for proximal nodes. Since graphs often contain a non-negligible amount of inter-cluster links, the bias results in error message passing and leads to biased clustering; (ii) the clustering guided loss function: most traditional approaches strive to make all samples closer to pre-learned cluster centers, which causes a degenerate solution assigning all data points to a single label thus make all samples and less discriminative. To address these challenges, we investigate graph clustering from a graph cut perspective and propose an innovative and non-GNN-based Deep Cut-informed Graph embedding and Clustering framework, namely DCGC. This framework includes two modules: (i) cut-informed graph encoding; (ii) self-supervised graph clustering via optimal transport. For the encoding module, we derive a cut-informed graph embedding objective to fuse graph structure and attributes by minimizing their joint normalized cut. For the clustering module, we utilize the optimal transport theory to obtain the clustering assignments, which can balance the guidance of "proximity to the pre-learned cluster center". With the above two tailored designs, DCGC is more suitable for the graph clustering task, which can effectively alleviate the problem of representation collapse and achieve better performance. We conduct extensive experiments to demonstrate that our method is simple but effective compared with benchmarks.
Graph neural networks (GNNs) have emerged as the state of the art for a variety of graph-related tasks and have been widely used in Heterogeneous Graphs (HetGs), where meta-paths help encode specific semantics between various node types. Despite the revolutionary representation capabilities of existing heterogeneous GNNs (HGNNs) due to their focus on improving the effectiveness of heterogeneity capturing, the huge training costs hinder their practical deployment in real-world scenarios that frequently require handling ad-hoc queries with user-defined meta-paths. To address this, we propose FHGE, a Fast Heterogeneous Graph Embedding designed for efficient, retraining-free generation of meta-path-guided graph embeddings. The key design of the proposed framework is two-fold: segmentation and reconstruction modules. It employs Meta-Path Units (MPUs) to segment the graph into local and global components, enabling swift integration of node embeddings from relevant MPUs during reconstruction and allowing quick adaptation to specific meta-paths. In addition, a dual attention mechanism is applied to enhance semantics capturing. Extensive experiments across diverse datasets demonstrate the effectiveness and efficiency of FHGE in generating meta-path-guided graph embeddings and downstream tasks, such as link prediction and node classification, highlighting its significant advantages for real-time graph analysis in ad-hoc queries.
Time series clustering poses a significant challenge with diverse applications across domains. A prominent drawback of existing solutions lies in their limited interpretability, often confined to presenting users with centroids. In addressing this gap, our work presents $k$-Graph, an unsupervised method explicitly crafted to augment interpretability in time series clustering. Leveraging a graph representation of time series subsequences, $k$-Graph constructs multiple graph representations based on different subsequence lengths. This feature accommodates variable-length time series without requiring users to predetermine subsequence lengths. Our experimental results reveal that $k$-Graph outperforms current state-of-the-art time series clustering algorithms in accuracy, while providing users with meaningful explanations and interpretations of the clustering outcomes.
The rapid evolution of malware has necessitated the development of sophisticated detection methods that go beyond traditional signature-based approaches. Graph learning techniques have emerged as powerful tools for modeling and analyzing the complex relationships inherent in malware behavior, leveraging advancements in Graph Neural Networks (GNNs) and related methods. This survey provides a comprehensive exploration of recent advances in malware detection, focusing on the interplay between graph learning and explainability. It begins by reviewing malware analysis techniques and datasets, emphasizing their foundational role in understanding malware behavior and supporting detection strategies. The survey then discusses feature engineering, graph reduction, and graph embedding methods, highlighting their significance in transforming raw data into actionable insights, while ensuring scalability and efficiency. Furthermore, this survey focuses on explainability techniques and their applications in malware detection, ensuring transparency and trustworthiness. By integrating these components, this survey demonstrates how graph learning and explainability contribute to building robust, interpretable, and scalable malware detection systems. Future research directions are outlined to address existing challenges and unlock new opportunities in this critical area of cybersecurity.
Decoder-only transformers lead to a step-change in capability of large language models. However, opinions are mixed as to whether they are really planning or reasoning. A path to making progress in this direction is to study the model's behavior in a setting with carefully controlled data. Then interpret the learned representations and reverse-engineer the computation performed internally. We study decoder-only transformer language models trained from scratch to predict shortest paths on simple, connected and undirected graphs. In this setting, the representations and the dynamics learned by the model are interpretable. We present three major results: (1) Two-layer decoder-only language models can learn to predict shortest paths on simple, connected graphs containing up to 10 nodes. (2) Models learn a graph embedding that is correlated with the spectral decomposition of the line graph. (3) Following the insights, we discover a novel approximate path-finding algorithm Spectral Line Navigator (SLN) that finds shortest path by greedily selecting nodes in the space of spectral embedding of the line graph.
In this paper, we propose a novel loop closure detection algorithm that uses graph attention neural networks to encode semantic graphs to perform place recognition and then use semantic registration to estimate the 6 DoF relative pose constraint. Our place recognition algorithm has two key modules, namely, a semantic graph encoder module and a graph comparison module. The semantic graph encoder employs graph attention networks to efficiently encode spatial, semantic and geometric information from the semantic graph of the input point cloud. We then use self-attention mechanism in both node-embedding and graph-embedding steps to create distinctive graph vectors. The graph vectors of the current scan and a keyframe scan are then compared in the graph comparison module to identify a possible loop closure. Specifically, employing the difference of the two graph vectors showed a significant improvement in performance, as shown in ablation studies. Lastly, we implemented a semantic registration algorithm that takes in loop closure candidate scans and estimates the relative 6 DoF pose constraint for the LiDAR SLAM system. Extensive evaluation on public datasets shows that our model is more accurate and robust, achieving 13% improvement in maximum F1 score on the SemanticKITTI dataset, when compared to the baseline semantic graph algorithm. For the benefit of the community, we open-source the complete implementation of our proposed algorithm and custom implementation of semantic registration at https://github.com/crepuscularlight/SemanticLoopClosure
High-dimensional multiplex graphs are characterized by their high number of complementary and divergent dimensions. The existence of multiple hierarchical latent relations between the graph dimensions poses significant challenges to embedding methods. In particular, the geometric distortions that might occur in the representational space have been overlooked in the literature. This work studies the problem of high-dimensional multiplex graph embedding from a geometric perspective. We find that the node representations reside on highly curved manifolds, thus rendering their exploitation more challenging for downstream tasks. Moreover, our study reveals that increasing the number of graph dimensions can cause further distortions to the highly curved manifolds. To address this problem, we propose a novel multiplex graph embedding method that harnesses hierarchical dimension embedding and Hyperbolic Graph Neural Networks. The proposed approach hierarchically extracts hyperbolic node representations that reside on Riemannian manifolds while gradually learning fewer and more expressive latent dimensions of the multiplex graph. Experimental results on real-world high-dimensional multiplex graphs show that the synergy between hierarchical and hyperbolic embeddings incurs much fewer geometric distortions and brings notable improvements over state-of-the-art approaches on downstream tasks.
Multimodal knowledge graph completion (MMKGC) aims to predict missing links in multimodal knowledge graphs (MMKGs) by leveraging information from various modalities alongside structural data. Existing MMKGC approaches primarily extend traditional knowledge graph embedding (KGE) models, which often require creating an embedding for every entity. This results in large model sizes and inefficiencies in integrating multimodal information, particularly for real-world graphs. Meanwhile, Transformer-based models have demonstrated competitive performance in knowledge graph completion (KGC). However, their focus on single-modal knowledge limits their capacity to utilize cross-modal information. Recently, Large vision-language models (VLMs) have shown potential in cross-modal tasks but are constrained by the high cost of training. In this work, we propose a novel approach that integrates Transformer-based KGE models with cross-modal context generated by pre-trained VLMs, thereby extending their applicability to MMKGC. Specifically, we employ a pre-trained VLM to transform relevant visual information from entities and their neighbors into textual sequences. We then frame KGC as a sequence-to-sequence task, fine-tuning the model with the generated cross-modal context. This simple yet effective method significantly reduces model size compared to traditional KGE approaches while achieving competitive performance across multiple large-scale datasets with minimal hyperparameter tuning.
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.
Meshes are used to represent complex objects in high fidelity physics simulators across a variety of domains, such as radar sensing and aerodynamics. There is growing interest in using neural networks to accelerate physics simulations, and also a growing body of work on applying neural networks directly to irregular mesh data. Since multiple mesh topologies can represent the same object, mesh augmentation is typically required to handle topological variation when training neural networks. Due to the sensitivity of physics simulators to small changes in mesh shape, it is challenging to use these augmentations when training neural network-based physics simulators. In this work, we show that variations in mesh topology can significantly reduce the performance of neural network simulators. We evaluate whether pretraining can be used to address this issue, and find that employing an established autoencoder pretraining technique with graph embedding models reduces the sensitivity of neural network simulators to variations in mesh topology. Finally, we highlight future research directions that may further reduce neural simulator sensitivity to mesh topology.
Large Language Models (LLMs) have attracted a lot of attention in various fields due to their superior performance, aiming to train hundreds of millions or more parameters on large amounts of text data to understand and generate natural language. As the superior performance of LLMs becomes apparent, they are increasingly being applied to knowledge graph embedding (KGE) related tasks to improve the processing results. As a deep learning model in the field of Natural Language Processing (NLP), it learns a large amount of textual data to predict the next word or generate content related to a given text. However, LLMs have recently been invoked to varying degrees in different types of KGE related scenarios such as multi-modal KGE and open KGE according to their task characteristics. In this paper, we investigate a wide range of approaches for performing LLMs-related tasks in different types of KGE scenarios. To better compare the various approaches, we summarize each KGE scenario in a classification. In addition to the categorization methods, we provide a tabular overview of the methods and their source code links for a more direct comparison. In the article we also discuss the applications in which the methods are mainly used and suggest several forward-looking directions for the development of this new research area.
Efficiently solving Optimal Power Flow (OPF) problems in power systems is crucial for operational planning and grid management. There is a growing need for scalable algorithms capable of handling the increasing variability, constraints, and uncertainties in modern power networks while providing accurate and fast solutions. To address this, machine learning techniques, particularly Graph Neural Networks (GNNs) have emerged as promising approaches. This letter introduces SafePowerGraph-LLM, the first framework explicitly designed for solving OPF problems using Large Language Models (LLM)s. The proposed approach combines graph and tabular representations of power grids to effectively query LLMs, capturing the complex relationships and constraints in power systems. A new implementation of in-context learning and fine-tuning protocols for LLMs is introduced, tailored specifically for the OPF problem. SafePowerGraph-LLM demonstrates reliable performances using off-the-shelf LLM. Our study reveals the impact of LLM architecture, size, and fine-tuning and demonstrates our framework's ability to handle realistic grid components and constraints.
Graph embedding generation techniques aim to learn low-dimensional vectors for each node in a graph and have recently gained increasing research attention. Publishing low-dimensional node vectors enables various graph analysis tasks, such as structural equivalence and link prediction. Yet, improper publication opens a backdoor to malicious attackers, who can infer sensitive information of individuals from the low-dimensional node vectors. Existing methods tackle this issue by developing deep graph learning models with differential privacy (DP). However, they often suffer from large noise injections and cannot provide structural preferences consistent with mining objectives. Recently, skip-gram based graph embedding generation techniques are widely used due to their ability to extract customizable structures. Based on skip-gram, we present SE-PrivGEmb, a structure-preference enabled graph embedding generation under DP. For arbitrary structure preferences, we design a unified noise tolerance mechanism via perturbing non-zero vectors. This mechanism mitigates utility degradation caused by high sensitivity. By carefully designing negative sampling probabilities in skip-gram, we theoretically demonstrate that skip-gram can preserve arbitrary proximities, which quantify structural features in graphs. Extensive experiments show that our method outperforms existing state-of-the-art methods under structural equivalence and link prediction tasks.
Biomedical Knowledge Graphs (BKGs) integrate diverse datasets to elucidate complex relationships within the biomedical field. Effective link prediction on these graphs can uncover valuable connections, such as potential novel drug-disease relations. We introduce a novel multimodal approach that unifies embeddings from specialized Language Models (LMs) with Graph Contrastive Learning (GCL) to enhance intra-entity relationships while employing a Knowledge Graph Embedding (KGE) model to capture inter-entity relationships for effective link prediction. To address limitations in existing BKGs, we present PrimeKG++, an enriched knowledge graph incorporating multimodal data, including biological sequences and textual descriptions for each entity type. By combining semantic and relational information in a unified representation, our approach demonstrates strong generalizability, enabling accurate link predictions even for unseen nodes. Experimental results on PrimeKG++ and the DrugBank drug-target interaction dataset demonstrate the effectiveness and robustness of our method across diverse biomedical datasets. Our source code, pre-trained models, and data are publicly available at https://github.com/HySonLab/BioMedKG
Hyperspectral image (HSI) clustering has been a fundamental but challenging task with zero training labels. Currently, some deep graph clustering methods have been successfully explored for HSI due to their outstanding performance in effective spatial structural information encoding. Nevertheless, insufficient structural information utilization, poor feature presentation ability, and weak graph update capability limit their performance. Thus, in this paper, a homophily structure graph learning with an adaptive filter clustering method (AHSGC) for HSI is proposed. Specifically, homogeneous region generation is first developed for HSI processing and constructing the original graph. Afterward, an adaptive filter graph encoder is designed to adaptively capture the high and low frequency features on the graph for subsequence processing. Then, a graph embedding clustering self-training decoder is developed with KL Divergence, with which the pseudo-label is generated for network training. Meanwhile, homophily-enhanced structure learning is introduced to update the graph according to the clustering task, in which the orient correlation estimation is adopted to estimate the node connection, and graph edge sparsification is designed to adjust the edges in the graph dynamically. Finally, a joint network optimization is introduced to achieve network self-training and update the graph. The K-means is adopted to express the latent features. Extensive experiments and repeated comparative analysis have verified that our AHSGC contains high clustering accuracy, low computational complexity, and strong robustness. The code source will be available at https://github.com/DY-HYX.
Identifying druggable genes is essential for developing effective pharmaceuticals. With the availability of extensive, high-quality data, computational methods have become a significant asset. Protein Interaction Network (PIN) is valuable but challenging to implement due to its high dimensionality and sparsity. Previous methods relied on indirect integration, leading to resolution loss. This study proposes GAN-TAT, a framework utilizing an advanced graph embedding technology, ImGAGN, to directly integrate PIN for druggable gene inference work. Tested on three Pharos datasets, GAN-TAT achieved the highest AUC-ROC score of 0.951 on Tclin. Further evaluation shows that GAN-TAT's predictions are supported by clinical evidence, highlighting its potential practical applications in pharmacogenomics. This research represents a methodological attempt with the direct utilization of PIN, expanding potential new solutions for developing drug targets. The source code of GAN-TAT is available at (https://github.com/george-yuanji-wang/GAN-TAT).
Knowledge Graphs (KGs) provide a structured representation of knowledge but often suffer from challenges of incompleteness. To address this, link prediction or knowledge graph completion (KGC) aims to infer missing new facts based on existing facts in KGs. Previous knowledge graph embedding models are limited in their ability to capture expressive features, especially when compared to deeper, multi-layer models. These approaches also assign a single static embedding to each entity and relation, disregarding the fact that entities and relations can exhibit different behaviors in varying graph contexts. Due to complex context over a fact triple of a KG, existing methods have to leverage complex non-linear context encoder, like transformer, to project entity and relation into low dimensional representations, resulting in high computation cost. To overcome these limitations, we propose Triple Receptance Perception (TRP) architecture to model sequential information, enabling the learning of dynamic context of entities and relations. Then we use tensor decomposition to calculate triple scores, providing robust relational decoding capabilities. This integration allows for more expressive representations. Experiments on benchmark datasets such as YAGO3-10, UMLS, FB15k, and FB13 in link prediction and triple classification tasks demonstrate that our method performs better than several state-of-the-art models, proving the effectiveness of the integration.