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Shirui Pan

Publications and source records attributed to Shirui Pan.

At least 109 records · Page 6Linked to original sources
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↗
arXiv2025

Understanding the Information Propagation Effects of Communication Topologies in LLM-based Multi-Agent Systems

The communication topology in large language model-based multi-agent systems fundamentally governs inter-agent collaboration patterns, critically shaping both the efficiency and effectiveness of collective decision-making. While recent studies for communication topology automated design tend to construct sparse structures for efficiency, they often overlook why and when sparse and dense topologies help or hinder collaboration. In this paper, we present a causal framework to analyze how agent outputs, whether correct or erroneous, propagate under topologies with varying sparsity. Our empirical studies reveal that moderately sparse topologies, which effectively suppress error propagation while preserving beneficial information diffusion, typically achieve optimal task performance. Guided by this insight, we propose a novel topology design approach, EIB-leanrner, that balances error suppression and beneficial information propagation by fusing connectivity patterns from both dense and sparse graphs. Extensive experiments show the superior effectiveness, communication cost, and robustness of EIB-leanrner.

cs.MA↗
arXiv2025

Graph-constrained Reasoning: Faithful Reasoning on Knowledge Graphs with Large Language Models

Large language models (LLMs) have demonstrated impressive reasoning abilities, but they still struggle with faithful reasoning due to knowledge gaps and hallucinations. To address these issues, knowledge graphs (KGs) have been utilized to enhance LLM reasoning through their structured knowledge. However, existing KG-enhanced methods, either retrieval-based or agent-based, encounter difficulties in accurately retrieving knowledge and efficiently traversing KGs at scale. In this work, we introduce graph-constrained reasoning (GCR), a novel framework that bridges structured knowledge in KGs with unstructured reasoning in LLMs. To eliminate hallucinations, GCR ensures faithful KG-grounded reasoning by integrating KG structure into the LLM decoding process through KG-Trie, a trie-based index that encodes KG reasoning paths. KG-Trie constrains the decoding process, allowing LLMs to directly reason on graphs and generate faithful reasoning paths grounded in KGs. Additionally, GCR leverages a lightweight KG-specialized LLM for graph-constrained reasoning alongside a powerful general LLM for inductive reasoning over multiple reasoning paths, resulting in accurate reasoning with zero reasoning hallucination. Extensive experiments on several KGQA benchmarks demonstrate that GCR achieves state-of-the-art performance and exhibits strong zero-shot generalizability to unseen KGs without additional training.

cs.CL↗
arXiv2025

TimeFilter: Patch-Specific Spatial-Temporal Graph Filtration for Time Series Forecasting

Time series forecasting methods generally fall into two main categories: Channel Independent (CI) and Channel Dependent (CD) strategies. While CI overlooks important covariate relationships, CD captures all dependencies without distinction, introducing noise and reducing generalization. Recent advances in Channel Clustering (CC) aim to refine dependency modeling by grouping channels with similar characteristics and applying tailored modeling techniques. However, coarse-grained clustering struggles to capture complex, time-varying interactions effectively. To address these challenges, we propose TimeFilter, a GNN-based framework for adaptive and fine-grained dependency modeling. After constructing the graph from the input sequence, TimeFilter refines the learned spatial-temporal dependencies by filtering out irrelevant correlations while preserving the most critical ones in a patch-specific manner. Extensive experiments on 13 real-world datasets from diverse application domains demonstrate the state-of-the-art performance of TimeFilter. The code is available at https://github.com/TROUBADOUR000/TimeFilter.

cs.LG↗
arXiv2025

Adaptive Tokenization: On the Hop-Overpriority Problem in Tokenized Graph Learning Models

Graph Transformers, leveraging the global attention to capture long-range dependencies in graph structures, have significantly advanced graph machine learning, but face prohibitive computational complexity. Tokenized Graph Learning Models (TGLMs) address this issue by converting graphs into ordered token lists for scalable processing. Besides, TGLMs also empower Large Language Models (LLMs) to handle text-attributed graphs more effectively and thus are also employed in Graph LLMs. However, existing TGLMs rely on hand-designed token lists and their adaptability to diverse graph learning scenarios remains unexplored. In this paper, we first conduct extensive empirical and theoretical preliminary studies for hand-designed token lists. Surprisingly, we identify an unexplored hop-overpriority problem: the common pre-defined token lists overemphasize nearby nodes and overwhelm the ability of TGLMs to balance local and global signals. This phenomenon is especially harmful for heterophilic graphs. To address this problem, we propose the Learnable Graph Token List (LGTL), a plug-and-play module to replace hand-designed token lists in TGLMs. Specifically, LGTL adaptively adjusts the weights across hops and prioritizes informative nodes within hops through a graph attention gate module and a selection module, respectively. In this way, contextually informative nodes can be adaptively emphasized for both homophilic and heterophilic graphs. Besides, we theoretically show that LGTL can address the hop-overpriority problem. Extensive experiments on benchmarks validate the efficacy of LGTL across both Graph Transformers and Graph LLM backbones.

cs.LG↗
arXiv2025

Fragment-Masked Diffusion for Molecular Optimization

Molecular optimization is a crucial aspect of drug discovery, aimed at refining molecular structures to enhance drug efficacy and minimize side effects, ultimately accelerating the overall drug development process. Many molecular optimization methods have been proposed, significantly advancing drug discovery. These methods primarily on understanding the specific drug target structures or their hypothesized roles in combating diseases. However, challenges such as a limited number of available targets and a difficulty capturing clear structures hinder innovative drug development. In contrast, phenotypic drug discovery (PDD) does not depend on clear target structures and can identify hits with novel and unbiased polypharmacology signatures. As a result, PDD-based molecular optimization can reduce potential safety risks while optimizing phenotypic activity, thereby increasing the likelihood of clinical success. Therefore, we propose a fragment-masked molecular optimization method based on PDD (FMOP). FMOP employs a regression-free diffusion model to conditionally optimize the molecular masked regions, effectively generating new molecules with similar scaffolds. On the large-scale drug response dataset GDSCv2, we optimize the potential molecules across all 985 cell lines. The overall experiments demonstrate that the in-silico optimization success rate reaches 95.4\%, with an average efficacy increase of 7.5\%. Additionally, we conduct extensive ablation and visualization experiments, confirming that FMOP is an effective and robust molecular optimization method. The code is available at: https://anonymous.4open.science/r/FMOP-98C2.

q-bio.BM↗