arXiv subjects

Shirui Pan

Publications and source records attributed to Shirui Pan.

At least 109 records · Page 6Linked to original sources

arXiv2025

Test-time GNN Model Evaluation on Dynamic Graphs

Dynamic graph neural networks (DGNNs) have emerged as a leading paradigm for learning from dynamic graphs, which are commonly used to model real-world systems and applications. However, due to the evolving nature of dynamic graph data distributions over time, well-trained DGNNs often face significant performance uncertainty when inferring on unseen and unlabeled test graphs in practical deployment. In this case, evaluating the performance of deployed DGNNs at test time is crucial to determine whether a well-trained DGNN is suited for inference on an unseen dynamic test graph. In this work, we introduce a new research problem: DGNN model evaluation, which aims to assess the performance of a specific DGNN model trained on observed dynamic graphs by estimating its performance on unseen dynamic graphs during test time. Specifically, we propose a Dynamic Graph neural network Evaluator, dubbed DyGEval, to address this new problem. The proposed DyGEval involves a two-stage framework: (1) test-time dynamic graph simulation, which captures the training-test distributional differences as supervision signals and trains an evaluator; and (2) DyGEval development and training, which accurately estimates the performance of the well-trained DGNN model on the test-time dynamic graphs. Extensive experiments demonstrate that the proposed DyGEval serves as an effective evaluator for assessing various DGNN backbones across different dynamic graphs under distribution shifts.

cs.LG↗

arXiv2025

Character-Level Perturbations Disrupt LLM Watermarks

Large Language Model (LLM) watermarking embeds detectable signals into generated text for copyright protection, misuse prevention, and content detection. While prior studies evaluate robustness using watermark removal attacks, these methods are often suboptimal, creating the misconception that effective removal requires large perturbations or powerful adversaries. To bridge the gap, we first formalize the system model for LLM watermark, and characterize two realistic threat models constrained on limited access to the watermark detector. We then analyze how different types of perturbation vary in their attack range, i.e., the number of tokens they can affect with a single edit. We observe that character-level perturbations (e.g., typos, swaps, deletions, homoglyphs) can influence multiple tokens simultaneously by disrupting the tokenization process. We demonstrate that character-level perturbations are significantly more effective for watermark removal under the most restrictive threat model. We further propose guided removal attacks based on the Genetic Algorithm (GA) that uses a reference detector for optimization. Under a practical threat model with limited black-box queries to the watermark detector, our method demonstrates strong removal performance. Experiments confirm the superiority of character-level perturbations and the effectiveness of the GA in removing watermarks under realistic constraints. Additionally, we argue there is an adversarial dilemma when considering potential defenses: any fixed defense can be bypassed by a suitable perturbation strategy. Motivated by this principle, we propose an adaptive compound character-level attack. Experimental results show that this approach can effectively defeat the defenses. Our findings highlight significant vulnerabilities in existing LLM watermark schemes and underline the urgency for the development of new robust mechanisms.

cs.CR↗

arXiv2025

DACAD: Domain Adaptation Contrastive Learning for Anomaly Detection in Multivariate Time Series

In time series anomaly detection (TSAD), the scarcity of labeled data poses a challenge to the development of accurate models. Unsupervised domain adaptation (UDA) offers a solution by leveraging labeled data from a related domain to detect anomalies in an unlabeled target domain. However, existing UDA methods assume consistent anomalous classes across domains. To address this limitation, we propose a novel Domain Adaptation Contrastive learning model for Anomaly Detection in multivariate time series (DACAD), combining UDA with contrastive learning. DACAD utilizes an anomaly injection mechanism that enhances generalization across unseen anomalous classes, improving adaptability and robustness. Additionally, our model employs supervised contrastive loss for the source domain and self-supervised contrastive triplet loss for the target domain, ensuring comprehensive feature representation learning and domain-invariant feature extraction. Finally, an effective Center-based Entropy Classifier (CEC) accurately learns normal boundaries in the source domain. Extensive evaluations on multiple real-world datasets and a synthetic dataset highlight DACAD's superior performance in transferring knowledge across domains and mitigating the challenge of limited labeled data in TSAD.

cs.LG↗

arXiv2025

Enhancing Large Language Model for Knowledge Graph Completion via Structure-Aware Alignment-Tuning

Knowledge graph completion (KGC) aims to infer new knowledge and make predictions from knowledge graphs. Recently, large language models (LLMs) have exhibited remarkable reasoning capabilities. LLM-enhanced KGC methods primarily focus on designing task-specific instructions, achieving promising advancements. However, there are still two critical challenges. First, existing methods often ignore the inconsistent representation spaces between natural language and graph structures. Second, most approaches design separate instructions for different KGC tasks, leading to duplicate works and time-consuming processes. To address these challenges, we propose SAT, a novel framework that enhances LLMs for KGC via structure-aware alignment-tuning. Specifically, we first introduce hierarchical knowledge alignment to align graph embeddings with the natural language space through multi-task contrastive learning. Then, we propose structural instruction tuning to guide LLMs in performing structure-aware reasoning over KGs, using a unified graph instruction combined with a lightweight knowledge adapter. Experimental results on two KGC tasks across four benchmark datasets demonstrate that SAT significantly outperforms state-of-the-art methods, especially in the link prediction task with improvements ranging from 8.7% to 29.8%.

cs.CL↗

arXiv2025

Graph-Augmented Large Language Model Agents: Current Progress and Future Prospects

Autonomous agents based on large language models (LLMs) have demonstrated impressive capabilities in a wide range of applications, including web navigation, software development, and embodied control. While most LLMs are limited in several key agentic procedures, such as reliable planning, long-term memory, tool management, and multi-agent coordination, graphs can serve as a powerful auxiliary structure to enhance structure, continuity, and coordination in complex agent workflows. Given the rapid growth and fragmentation of research on Graph-augmented LLM Agents (GLA), this paper offers a timely and comprehensive overview of recent advances and also highlights key directions for future work. Specifically, we categorize existing GLA methods by their primary functions in LLM agent systems, including planning, memory, and tool usage, and then analyze how graphs and graph learning algorithms contribute to each. For multi-agent systems, we further discuss how GLA solutions facilitate the orchestration, efficiency optimization, and trustworthiness of MAS. Finally, we highlight key future directions to advance this field, from improving structural adaptability to enabling unified, scalable, and multimodal GLA systems. We hope this paper can serve as a roadmap for future research on GLA and foster a deeper understanding of the role of graphs in LLM agent systems.

cs.AI↗

arXiv2025

OASIS: Harnessing Diffusion Adversarial Network for Ocean Salinity Imputation using Sparse Drifter Trajectories

Ocean salinity plays a vital role in circulation, climate, and marine ecosystems, yet its measurement is often sparse, irregular, and noisy, especially in drifter-based datasets. Traditional approaches, such as remote sensing and optimal interpolation, rely on linearity and stationarity, and are limited by cloud cover, sensor drift, and low satellite revisit rates. While machine learning models offer flexibility, they often fail under severe sparsity and lack principled ways to incorporate physical covariates without specialized sensors. In this paper, we introduce the OceAn Salinity Imputation System (OASIS), a novel diffusion adversarial framework designed to address these challenges.

cs.LG↗

arXiv2025

Intellectual Property in Graph-Based Machine Learning as a Service: Attacks and Defenses

Graph-structured data, which captures non-Euclidean relationships and interactions between entities, is growing in scale and complexity. As a result, training state-of-the-art graph machine learning (GML) models have become increasingly resource-intensive, turning these models and data into invaluable Intellectual Property (IP). To address the resource-intensive nature of model training, graph-based Machine-Learning-as-a-Service (GMLaaS) has emerged as an efficient solution by leveraging third-party cloud services for model development and management. However, deploying such models in GMLaaS also exposes them to potential threats from attackers. Specifically, while the APIs within a GMLaaS system provide interfaces for users to query the model and receive outputs, they also allow attackers to exploit and steal model functionalities or sensitive training data, posing severe threats to the safety of these GML models and the underlying graph data. To address these challenges, this survey systematically introduces the first taxonomy of threats and defenses at the level of both GML model and graph-structured data. Such a tailored taxonomy facilitates an in-depth understanding of GML IP protection. Furthermore, we present a systematic evaluation framework to assess the effectiveness of IP protection methods, introduce a curated set of benchmark datasets across various domains, and discuss their application scopes and future challenges. Finally, we establish an open-sourced versatile library named PyGIP, which evaluates various attack and defense techniques in GMLaaS scenarios and facilitates the implementation of existing benchmark methods. The library resource can be accessed at: https://labrai.github.io/PyGIP. We believe this survey will play a fundamental role in intellectual property protection for GML and provide practical recipes for the GML community.

cs.CR↗

arXiv2025

BiMark: Unbiased Multilayer Watermarking for Large Language Models

Recent advances in Large Language Models (LLMs) have raised urgent concerns about LLM-generated text authenticity, prompting regulatory demands for reliable identification mechanisms. Although watermarking offers a promising solution, existing approaches struggle to simultaneously achieve three critical requirements: text quality preservation, model-agnostic detection, and message embedding capacity, which are crucial for practical implementation. To achieve these goals, the key challenge lies in balancing the trade-off between text quality preservation and message embedding capacity. To address this challenge, we propose BiMark, a novel watermarking framework that achieves these requirements through three key innovations: (1) a bit-flip unbiased reweighting mechanism enabling model-agnostic detection, (2) a multilayer architecture enhancing detectability without compromising generation quality, and (3) an information encoding approach supporting multi-bit watermarking. Through theoretical analysis and extensive experiments, we validate that, compared to state-of-the-art multi-bit watermarking methods, BiMark achieves up to 30% higher extraction rates for short texts while maintaining text quality indicated by lower perplexity, and performs comparably to non-watermarked text on downstream tasks such as summarization and translation.

cs.CL↗

arXiv2025

FreeGAD: A Training-Free yet Effective Approach for Graph Anomaly Detection

Graph Anomaly Detection (GAD) aims to identify nodes that deviate from the majority within a graph, playing a crucial role in applications such as social networks and e-commerce. Despite the current advancements in deep learning-based GAD, existing approaches often suffer from high deployment costs and poor scalability due to their complex and resource-intensive training processes. Surprisingly, our empirical findings suggest that the training phase of deep GAD methods, commonly perceived as crucial, may actually contribute less to anomaly detection performance than expected. Inspired by this, we propose FreeGAD, a novel training-free yet effective GAD method. Specifically, it leverages an affinity-gated residual encoder to generate anomaly-aware representations. Meanwhile, FreeGAD identifies anchor nodes as pseudo-normal and anomalous guides, followed by calculating anomaly scores through anchor-guided statistical deviations. Extensive experiments demonstrate that FreeGAD achieves superior anomaly detection performance, efficiency, and scalability on multiple benchmark datasets from diverse domains, without any training or iterative optimization.

cs.LG↗

arXiv2025

$\text{M}^{2}$LLM: Multi-view Molecular Representation Learning with Large Language Models

Accurate molecular property prediction is a critical challenge with wide-ranging applications in chemistry, materials science, and drug discovery. Molecular representation methods, including fingerprints and graph neural networks (GNNs), achieve state-of-the-art results by effectively deriving features from molecular structures. However, these methods often overlook decades of accumulated semantic and contextual knowledge. Recent advancements in large language models (LLMs) demonstrate remarkable reasoning abilities and prior knowledge across scientific domains, leading us to hypothesize that LLMs can generate rich molecular representations when guided to reason in multiple perspectives. To address these gaps, we propose $\text{M}^{2}$LLM, a multi-view framework that integrates three perspectives: the molecular structure view, the molecular task view, and the molecular rules view. These views are fused dynamically to adapt to task requirements, and experiments demonstrate that $\text{M}^{2}$LLM achieves state-of-the-art performance on multiple benchmarks across classification and regression tasks. Moreover, we demonstrate that representation derived from LLM achieves exceptional performance by leveraging two core functionalities: the generation of molecular embeddings through their encoding capabilities and the curation of molecular features through advanced reasoning processes.

cs.LG↗

arXiv2025

GraphRAG-Induced Dual Knowledge Structure Graphs for Personalized Learning Path Recommendation

Learning path recommendation seeks to provide learners with a structured sequence of learning items (\eg, knowledge concepts or exercises) to optimize their learning efficiency. Despite significant efforts in this area, most existing methods primarily rely on prerequisite relationships, which present two major limitations: 1) Requiring prerequisite relationships between knowledge concepts, which are difficult to obtain due to the cost of expert annotation, hindering the application of current learning path recommendation methods. 2) Relying on a single, sequentially dependent knowledge structure based on prerequisite relationships implies that difficulties at any stage can cause learning blockages, which in turn disrupt subsequent learning processes. To address these challenges, we propose a novel approach, GraphRAG-Induced Dual Knowledge Structure Graphs for Personalized Learning Path Recommendation (KnowLP), which enhances learning path recommendations by incorporating both prerequisite and similarity relationships between knowledge concepts. Specifically, we introduce a knowledge concept structure graph generation module EDU-GraphRAG that adaptively constructs knowledge concept structure graphs for different educational datasets, significantly improving the generalizability of learning path recommendation methods. We then propose a Discrimination Learning-driven Reinforcement Learning (DLRL) module, which mitigates the issue of blocked learning paths, further enhancing the efficacy of learning path recommendations. Finally, we conduct extensive experiments on three benchmark datasets, demonstrating that our method not only achieves state-of-the-art performance but also provides interpretable reasoning for the recommended learning paths.

cs.IR↗

arXiv2025

Raising the Bar in Graph OOD Generalization: Invariant Learning Beyond Explicit Environment Modeling

Out-of-distribution (OOD) generalization has emerged as a critical challenge in graph learning, as real-world graph data often exhibit diverse and shifting environments that traditional models fail to generalize across. A promising solution to address this issue is graph invariant learning (GIL), which aims to learn invariant representations by disentangling label-correlated invariant subgraphs from environment-specific subgraphs. However, existing GIL methods face two major challenges: (1) the difficulty of capturing and modeling diverse environments in graph data, and (2) the semantic cliff, where invariant subgraphs from different classes are difficult to distinguish, leading to poor class separability and increased misclassifications. To tackle these challenges, we propose a novel method termed Multi-Prototype Hyperspherical Invariant Learning (MPHIL), which introduces two key innovations: (1) hyperspherical invariant representation extraction, enabling robust and highly discriminative hyperspherical invariant feature extraction, and (2) multi-prototype hyperspherical classification, which employs class prototypes as intermediate variables to eliminate the need for explicit environment modeling in GIL and mitigate the semantic cliff issue. Derived from the theoretical framework of GIL, we introduce two novel objective functions: the invariant prototype matching loss to ensure samples are matched to the correct class prototypes, and the prototype separation loss to increase the distinction between prototypes of different classes in the hyperspherical space. Extensive experiments on 11 OOD generalization benchmark datasets demonstrate that MPHIL achieves state-of-the-art performance, significantly outperforming existing methods across graph data from various domains and with different distribution shifts.

cs.LG↗

arXiv2025

INSPIRE-GNN: Intelligent Sensor Placement to Improve Sparse Bicycling Network Prediction via Reinforcement Learning Boosted Graph Neural Networks

Accurate link-level bicycling volume estimation is essential for sustainable urban transportation planning. However, many cities face significant challenges of high data sparsity due to limited bicycling count sensor coverage. To address this issue, we propose INSPIRE-GNN, a novel Reinforcement Learning (RL)-boosted hybrid Graph Neural Network (GNN) framework designed to optimize sensor placement and improve link-level bicycling volume estimation in data-sparse environments. INSPIRE-GNN integrates Graph Convolutional Networks (GCN) and Graph Attention Networks (GAT) with a Deep Q-Network (DQN)-based RL agent, enabling a data-driven strategic selection of sensor locations to maximize estimation performance. Applied to Melbourne's bicycling network, comprising 15,933 road segments with sensor coverage on only 141 road segments (99% sparsity) - INSPIRE-GNN demonstrates significant improvements in volume estimation by strategically selecting additional sensor locations in deployments of 50, 100, 200 and 500 sensors. Our framework outperforms traditional heuristic methods for sensor placement such as betweenness centrality, closeness centrality, observed bicycling activity and random placement, across key metrics such as Mean Squared Error (MSE), Root Mean Squared Error (RMSE) and Mean Absolute Error (MAE). Furthermore, our experiments benchmark INSPIRE-GNN against standard machine learning and deep learning models in the bicycle volume estimation performance, underscoring its effectiveness. Our proposed framework provides transport planners actionable insights to effectively expand sensor networks, optimize sensor placement and maximize volume estimation accuracy and reliability of bicycling data for informed transportation planning decisions.

cs.LG↗

arXiv2025

DrugPilot: LLM-based Parameterized Reasoning Agent for Drug Discovery

Large language models (LLMs) integrated with autonomous agents hold significant potential for advancing scientific discovery through automated reasoning and task execution. However, applying LLM agents to drug discovery is still constrained by challenges such as large-scale multimodal data processing, limited task automation, and poor support for domain-specific tools. To overcome these limitations, we introduce DrugPilot, a LLM-based agent system with a parameterized reasoning architecture designed for end-to-end scientific workflows in drug discovery. DrugPilot enables multi-stage research processes by integrating structured tool use with a novel parameterized memory pool. The memory pool converts heterogeneous data from both public sources and user-defined inputs into standardized representations. This design supports efficient multi-turn dialogue, reduces information loss during data exchange, and enhances complex scientific decision-making. To support training and benchmarking, we construct a drug instruction dataset covering eight core drug discovery tasks. Under the Berkeley function-calling benchmark, DrugPilot significantly outperforms state-of-the-art agents such as ReAct and LoT, achieving task completion rates of 98.0%, 93.5%, and 64.0% for simple, multi-tool, and multi-turn scenarios, respectively. These results highlight DrugPilot's potential as a versatile agent framework for computational science domains requiring automated, interactive, and data-integrated reasoning.

cs.AI↗

arXiv2025

Graphs Meet AI Agents: Taxonomy, Progress, and Future Opportunities

AI agents have experienced a paradigm shift, from early dominance by reinforcement learning (RL) to the rise of agents powered by large language models (LLMs), and now further advancing towards a synergistic fusion of RL and LLM capabilities. This progression has endowed AI agents with increasingly strong abilities. Despite these advances, to accomplish complex real-world tasks, agents are required to plan and execute effectively, maintain reliable memory, and coordinate smoothly with other agents. Achieving these capabilities involves contending with ever-present intricate information, operations, and interactions. In light of this challenge, data structurization can play a promising role by transforming intricate and disorganized data into well-structured forms that agents can more effectively understand and process. In this context, graphs, with their natural advantage in organizing, managing, and harnessing intricate data relationships, present a powerful data paradigm for structurization to support the capabilities demanded by advanced AI agents. To this end, this survey presents a first systematic review of how graphs can empower AI agents. Specifically, we explore the integration of graph techniques with core agent functionalities, highlight notable applications, and identify prospective avenues for future research. By comprehensively surveying this burgeoning intersection, we hope to inspire the development of next-generation AI agents equipped to tackle increasingly sophisticated challenges with graphs. Related resources are collected and continuously updated for the community in the Github link.

cs.AI↗

arXiv2025

Mitigating Over-Squashing in Graph Neural Networks by Spectrum-Preserving Sparsification

The message-passing paradigm of Graph Neural Networks often struggles with exchanging information across distant nodes typically due to structural bottlenecks in certain graph regions, a limitation known as \textit{over-squashing}. To reduce such bottlenecks, \textit{graph rewiring}, which modifies graph topology, has been widely used. However, existing graph rewiring techniques often overlook the need to preserve critical properties of the original graph, e.g., \textit{spectral properties}. Moreover, many approaches rely on increasing edge count to improve connectivity, which introduces significant computational overhead and exacerbates the risk of over-smoothing. In this paper, we propose a novel graph rewiring method that leverages \textit{spectrum-preserving} graph \textit{sparsification}, for mitigating over-squashing. Our method generates graphs with enhanced connectivity while maintaining sparsity and largely preserving the original graph spectrum, effectively balancing structural bottleneck reduction and graph property preservation. Experimental results validate the effectiveness of our approach, demonstrating its superiority over strong baseline methods in classification accuracy and retention of the Laplacian spectrum.

cs.LG↗

arXiv2025

Uncertainty-Aware Graph Neural Networks: A Multi-Hop Evidence Fusion Approach

Graph neural networks (GNNs) excel in graph representation learning by integrating graph structure and node features. Existing GNNs, unfortunately, fail to account for the uncertainty of class probabilities that vary with the depth of the model, leading to unreliable and risky predictions in real-world scenarios. To bridge the gap, in this paper, we propose a novel Evidence Fusing Graph Neural Network (EFGNN for short) to achieve trustworthy prediction, enhance node classification accuracy, and make explicit the risk of wrong predictions. In particular, we integrate the evidence theory with multi-hop propagation-based GNN architecture to quantify the prediction uncertainty of each node with the consideration of multiple receptive fields. Moreover, a parameter-free cumulative belief fusion (CBF) mechanism is developed to leverage the changes in prediction uncertainty and fuse the evidence to improve the trustworthiness of the final prediction. To effectively optimize the EFGNN model, we carefully design a joint learning objective composed of evidence cross-entropy, dissonance coefficient, and false confident penalty. The experimental results on various datasets and theoretical analyses demonstrate the effectiveness of the proposed model in terms of accuracy and trustworthiness, as well as its robustness to potential attacks. The source code of EFGNN is available at https://github.com/Shiy-Li/EFGNN.

cs.LG↗

arXiv2025

A Comprehensive Survey in LLM(-Agent) Full Stack Safety: Data, Training and Deployment

The remarkable success of Large Language Models (LLMs) has illuminated a promising pathway toward achieving Artificial General Intelligence for both academic and industrial communities, owing to their unprecedented performance across various applications. As LLMs continue to gain prominence in both research and commercial domains, their security and safety implications have become a growing concern, not only for researchers and corporations but also for every nation. Currently, existing surveys on LLM safety primarily focus on specific stages of the LLM lifecycle, e.g., deployment phase or fine-tuning phase, lacking a comprehensive understanding of the entire "lifechain" of LLMs. To address this gap, this paper introduces, for the first time, the concept of "full-stack" safety to systematically consider safety issues throughout the entire process of LLM training, deployment, and eventual commercialization. Compared to the off-the-shelf LLM safety surveys, our work demonstrates several distinctive advantages: (I) Comprehensive Perspective. We define the complete LLM lifecycle as encompassing data preparation, pre-training, post-training, deployment and final commercialization. To our knowledge, this represents the first safety survey to encompass the entire lifecycle of LLMs. (II) Extensive Literature Support. Our research is grounded in an exhaustive review of over 800+ papers, ensuring comprehensive coverage and systematic organization of security issues within a more holistic understanding. (III) Unique Insights. Through systematic literature analysis, we have developed reliable roadmaps and perspectives for each chapter. Our work identifies promising research directions, including safety in data generation, alignment techniques, model editing, and LLM-based agent systems. These insights provide valuable guidance for researchers pursuing future work in this field.

cs.CR↗