Searcharxiv⌕ Search

arXiv subjects

Shirui Pan

Publications and source records attributed to Shirui Pan.

At least 91 records · Page 5Linked to original sources
arXiv2025

DyG-Mamba: Continuous State Space Modeling on Dynamic Graphs

Dynamic graph modeling aims to uncover evolutionary patterns in real-world systems, enabling accurate social recommendation and early detection of cancer cells. Inspired by the success of recent state space models in efficiently capturing long-term dependencies, we propose DyG-Mamba by translating dynamic graph modeling into a long-term sequence modeling problem. Specifically, inspired by Ebbinghaus' forgetting curve, we treat the irregular timespans between events as control signals, allowing DyG-Mamba to dynamically adjust the forgetting of historical information. This mechanism ensures effective usage of irregular timespans, thereby improving both model effectiveness and inductive capability. In addition, inspired by Ebbinghaus' review cycle, we redefine core parameters to ensure that DyG-Mamba selectively reviews historical information and filters out noisy inputs, further enhancing the model's robustness. Through exhaustive experiments on 12 datasets covering dynamic link prediction and node classification tasks, we show that DyG-Mamba achieves state-of-the-art performance on most datasets, while demonstrating significantly improved computational and memory efficiency. Code is available at https://github.com/Clearloveyuan/DyG-Mamba.

cs.LG↗
arXiv2025

GFM-RAG: Graph Foundation Model for Retrieval Augmented Generation

Retrieval-augmented generation (RAG) has proven effective in integrating knowledge into large language models (LLMs). However, conventional RAGs struggle to capture complex relationships between pieces of knowledge, limiting their performance in intricate reasoning that requires integrating knowledge from multiple sources. Recently, graph-enhanced retrieval augmented generation (GraphRAG) builds graph structure to explicitly model these relationships, enabling more effective and efficient retrievers. Nevertheless, its performance is still hindered by the noise and incompleteness within the graph structure. To address this, we introduce GFM-RAG, a novel graph foundation model (GFM) for retrieval augmented generation. GFM-RAG is powered by an innovative graph neural network that reasons over graph structure to capture complex query-knowledge relationships. The GFM with 8M parameters undergoes a two-stage training process on large-scale datasets, comprising 60 knowledge graphs with over 14M triples and 700k documents. This results in impressive performance and generalizability for GFM-RAG, making it the first graph foundation model applicable to unseen datasets for retrieval without any fine-tuning required. Extensive experiments on three multi-hop QA datasets and seven domain-specific RAG datasets demonstrate that GFM-RAG achieves state-of-the-art performance while maintaining efficiency and alignment with neural scaling laws, highlighting its potential for further improvement.

cs.IR↗
arXiv2025

A Survey on Diffusion Models for Time Series and Spatio-Temporal Data

Diffusion models have been widely used in time series and spatio-temporal data, enhancing generative, inferential, and downstream capabilities. These models are applied across diverse fields such as healthcare, recommendation, climate, energy, audio, and traffic. By separating applications for time series and spatio-temporal data, we offer a structured perspective on model category, task type, data modality, and practical application domain. This study aims to provide a solid foundation for researchers and practitioners, inspiring future innovations that tackle traditional challenges and foster novel solutions in diffusion model-based data mining tasks and applications. For more detailed information, we have open-sourced a repository at https://github.com/yyysjz1997/Awesome-TimeSeries-SpatioTemporal-Diffusion-Model.

cs.LG↗
arXiv2025

Assemble Your Crew: Automatic Multi-agent Communication Topology Design via Autoregressive Graph Generation

Multi-agent systems (MAS) based on large language models (LLMs) have emerged as a powerful solution for dealing with complex problems across diverse domains. The effectiveness of MAS is critically dependent on its collaboration topology, which has become a focal point for automated design research. However, existing approaches are fundamentally constrained by their reliance on a template graph modification paradigm with a predefined set of agents and hard-coded interaction structures, significantly limiting their adaptability to task-specific requirements. To address these limitations, we reframe MAS design as a conditional autoregressive graph generation task, where both the system composition and structure are designed jointly. We propose ARG-Designer, a novel autoregressive model that operationalizes this paradigm by constructing the collaboration graph from scratch. Conditioned on a natural language task query, ARG-Designer sequentially and dynamically determines the required number of agents, selects their appropriate roles from an extensible pool, and establishes the optimal communication links between them. This generative approach creates a customized topology in a flexible and extensible manner, precisely tailored to the unique demands of different tasks. Extensive experiments across six diverse benchmarks demonstrate that ARG-Designer not only achieves state-of-the-art performance but also enjoys significantly greater token efficiency and enhanced extensibility. The source code of ARG-Designer is available at https://github.com/Shiy-Li/ARG-Designer.

cs.MA↗
arXiv2025

LLM-based Agents Suffer from Hallucinations: A Survey of Taxonomy, Methods, and Directions

Driven by the rapid advancements of Large Language Models (LLMs), LLM-based agents have emerged as powerful intelligent systems capable of human-like cognition, reasoning, and interaction. These agents are increasingly being deployed across diverse real-world applications, including student education, scientific research, and financial analysis. However, despite their remarkable potential, LLM-based agents remain vulnerable to hallucination issues, which can result in erroneous task execution and undermine the reliability of the overall system design. Addressing this critical challenge requires a deep understanding and a systematic consolidation of recent advances on LLM-based agents. To this end, we present the first comprehensive survey of hallucinations in LLM-based agents. By carefully analyzing the complete workflow of agents, we propose a new taxonomy that identifies different types of agent hallucinations occurring at different stages. Furthermore, we conduct an in-depth examination of eighteen triggering causes underlying the emergence of agent hallucinations. Through a detailed review of a large number of existing studies, we summarize approaches for hallucination mitigation and detection, and highlight promising directions for future research. We hope this survey will inspire further efforts toward addressing hallucinations in LLM-based agents, ultimately contributing to the development of more robust and reliable agent systems.

cs.AI↗
arXiv2025

Correcting False Alarms from Unseen: Adapting Graph Anomaly Detectors at Test Time

Graph anomaly detection (GAD), which aims to detect outliers in graph-structured data, has received increasing research attention recently. However, existing GAD methods assume identical training and testing distributions, which is rarely valid in practice. In real-world scenarios, unseen but normal samples may emerge during deployment, leading to a normality shift that degrades the performance of GAD models trained on the original data. Through empirical analysis, we reveal that the degradation arises from (1) semantic confusion, where unseen normal samples are misinterpreted as anomalies due to their novel patterns, and (2) aggregation contamination, where the representations of seen normal nodes are distorted by unseen normals through message aggregation. While retraining or fine-tuning GAD models could be a potential solution to the above challenges, the high cost of model retraining and the difficulty of obtaining labeled data often render this approach impractical in real-world applications. To bridge the gap, we proposed a lightweight and plug-and-play Test-time adaptation framework for correcting Unseen Normal pattErns (TUNE) in GAD. To address semantic confusion, a graph aligner is employed to align the shifted data to the original one at the graph attribute level. Moreover, we utilize the minimization of representation-level shift as a supervision signal to train the aligner, which leverages the estimated aggregation contamination as a key indicator of normality shift. Extensive experiments on 10 real-world datasets demonstrate that TUNE significantly enhances the generalizability of pre-trained GAD models to both synthetic and real unseen normal patterns.

cs.LG↗
arXiv2025

Diagnosing and Addressing Pitfalls in KG-RAG Datasets: Toward More Reliable Benchmarking

Knowledge Graph Question Answering (KGQA) systems rely on high-quality benchmarks to evaluate complex multi-hop reasoning. However, despite their widespread use, popular datasets such as WebQSP and CWQ suffer from critical quality issues, including inaccurate or incomplete ground-truth annotations, poorly constructed questions that are ambiguous, trivial, or unanswerable, and outdated or inconsistent knowledge. Through a manual audit of 16 popular KGQA datasets, including WebQSP and CWQ, we find that the average factual correctness rate is only 57 %. To address these issues, we introduce KGQAGen, an LLM-in-the-loop framework that systematically resolves these pitfalls. KGQAGen combines structured knowledge grounding, LLM-guided generation, and symbolic verification to produce challenging and verifiable QA instances. Using KGQAGen, we construct KGQAGen-10k, a ten-thousand scale benchmark grounded in Wikidata, and evaluate a diverse set of KG-RAG models. Experimental results demonstrate that even state-of-the-art systems struggle on this benchmark, highlighting its ability to expose limitations of existing models. Our findings advocate for more rigorous benchmark construction and position KGQAGen as a scalable framework for advancing KGQA evaluation.

cs.CL↗
arXiv2025

ShapeX: Shapelet-Driven Post Hoc Explanations for Time Series Classification Models

Explaining time series classification models is crucial, particularly in high-stakes applications such as healthcare and finance, where transparency and trust play a critical role. Although numerous time series classification methods have identified key subsequences, known as shapelets, as core features for achieving state-of-the-art performance and validating their pivotal role in classification outcomes, existing post-hoc time series explanation (PHTSE) methods primarily focus on timestep-level feature attribution. These explanation methods overlook the fundamental prior that classification outcomes are predominantly driven by key shapelets. To bridge this gap, we present ShapeX, an innovative framework that segments time series into meaningful shapelet-driven segments and employs Shapley values to assess their saliency. At the core of ShapeX lies the Shapelet Describe-and-Detect (SDD) framework, which effectively learns a diverse set of shapelets essential for classification. We further demonstrate that ShapeX produces explanations which reveal causal relationships instead of just correlations, owing to the atomicity properties of shapelets. Experimental results on both synthetic and real-world datasets demonstrate that ShapeX outperforms existing methods in identifying the most relevant subsequences, enhancing both the precision and causal fidelity of time series explanations.

cs.LG↗
arXiv2025

TED++: Submanifold-Aware Backdoor Detection via Layerwise Tubular-Neighbourhood Screening

As deep neural networks power increasingly critical applications, stealthy backdoor attacks, where poisoned training inputs trigger malicious model behaviour while appearing benign, pose a severe security risk. Many existing defences are vulnerable when attackers exploit subtle distance-based anomalies or when clean examples are scarce. To meet this challenge, we introduce TED++, a submanifold-aware framework that effectively detects subtle backdoors that evade existing defences. TED++ begins by constructing a tubular neighbourhood around each class's hidden-feature manifold, estimating its local ``thickness'' from a handful of clean activations. It then applies Locally Adaptive Ranking (LAR) to detect any activation that drifts outside the admissible tube. By aggregating these LAR-adjusted ranks across all layers, TED++ captures how faithfully an input remains on the evolving class submanifolds. Based on such characteristic ``tube-constrained'' behaviour, TED++ flags inputs whose LAR-based ranking sequences deviate significantly. Extensive experiments are conducted on benchmark datasets and tasks, demonstrating that TED++ achieves state-of-the-art detection performance under both adaptive-attack and limited-data scenarios. Remarkably, even with only five held-out examples per class, TED++ still delivers near-perfect detection, achieving gains of up to 14\% in AUROC over the next-best method. The code is publicly available at https://github.com/namle-w/TEDpp.

cs.LG↗
arXiv2025

Few-shot Molecular Property Prediction: A Survey

AI-assisted molecular property prediction has become a promising technique in early-stage drug discovery and materials design in recent years. However, due to high-cost and complex wet-lab experiments, real-world molecules usually experience the issue of scarce annotations, leading to limited labeled data for effective supervised AI model learning. In light of this, few-shot molecular property prediction (FSMPP) has emerged as an expressive paradigm that enables learning from only a few labeled examples. Despite rapidly growing attention, existing FSMPP studies remain fragmented, without a coherent framework to capture methodological advances and domain-specific challenges. In this work, we present the first comprehensive and systematic survey of few-shot molecular property prediction. We begin by analyzing the few-shot phenomenon in molecular datasets and highlighting two core challenges: (1) cross-property generalization under distribution shifts, where each task corresponding to each property, may follow a different data distribution or even be inherently weakly related to others from a biochemical perspective, requiring the model to transfer knowledge across heterogeneous prediction tasks, and (2) cross-molecule generalization under structural heterogeneity, where molecules involved in different or same properties may exhibit significant structural diversity, making model difficult to achieve generalization. Then, we introduce a unified taxonomy that organizes existing methods into data, model, and learning paradigm levels, reflecting their strategies for extracting knowledge from scarce supervision in few-shot molecular property prediction. Next, we compare representative methods, summarize benchmark datasets and evaluation protocols. In the end, we identify key trends and future directions for advancing the continued research on FSMPP.

cs.CE↗
arXiv2025

Reasoning over User Preferences: Knowledge Graph-Augmented LLMs for Explainable Conversational Recommendations

Conversational Recommender Systems (CRSs) aim to provide personalized recommendations by capturing user preferences through interactive dialogues. Explainability in CRSs is crucial as it enables users to understand the reasoning behind recommendations, increasing system transparency and trustworthiness. However, current CRSs often leverage knowledge graphs (KGs) or language models to extract and represent user preferences as latent vectors, which limits their explainability. Large language models (LLMs) offer powerful reasoning capabilities that can bridge this gap by generating human-understandable preference summaries. However, effectively reasoning over user preferences in CRSs remains challenging as LLMs pre-trained on large-scale corpora may not be well-suited for analyzing user preferences. While KGs provide rich domain knowledge, integrating them with LLMs encounters a significant modality gap between structured KG information and unstructured conversations. In this paper, we propose COMPASS, a plug-and-play framework that synergizes LLMs and KGs to reason over user preferences, enhancing the performance and explainability of existing CRSs. COMPASS employs a two-stage training approach: first, it bridges the gap between the structured KG and natural language through novel graph entity captioning pre-training. Next, COMPASS optimizes user preference reasoning via knowledge-aware instruction fine-tuning, where the LLM learns to reason and summarize user preferences from dialogue histories and KG-augmented context. This enables COMPASS to perform knowledge-aware reasoning and generate interpretable user preferences that can seamlessly integrate with existing CRS models for improving recommendation performance and explainability. Our experiments on benchmark datasets demonstrate the effectiveness of COMPASS in improving various CRS models.

cs.CL↗
arXiv2025

Estimating Time Series Foundation Model Transferability via In-Context Learning

Time series foundation models (TSFMs) offer strong zero-shot forecasting via large-scale pre-training, yet fine-tuning remains critical for boosting performance in domains with limited public data. With the growing number of TSFMs, efficiently identifying the best model for downstream fine-tuning becomes increasingly challenging. In this work, we introduce TimeTic, a transferability estimation framework that recasts model selection as an in-context-learning problem: given observations on known (source) datasets, it predicts how a TSFM will perform after fine-tuning on a downstream (target) dataset. TimeTic flexibly organizes the observed model-data relationships as contextual information, allowing it to adapt seamlessly to various test-time scenarios. Leveraging the natural tabular structure formed by dataset meta-features, model characteristics, and fine-tuned performance, we employ tabular foundation models to serve as in-context learners. We further introduce a novel model characterization based on entropy evolution across model layers, capturing embedding-space distinctions and enabling TimeTic to generalize across arbitrary model sets. We establish a comprehensive benchmark for transferability estimation including 10 datasets, 10 foundation models, and 3 forecasting tasks. On this benchmark, TimeTic's estimation demonstrates strong alignment with actual fine-tuned performance for previously unseen datasets, achieving a mean rank correlation of approximately 0.6 and a 30% improvement compared to using zero-shot performance as the transferability score.

cs.LG↗
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↗