Zhenjun Li

Daohan Su, Xunkai Li, Zhenjun Li et al.

Recently, graph neural network (GNN) has emerged as a powerful representation learning tool for graph-structured data. However, most approaches are tailored for undirected graphs, neglecting the abundant information in the edges of directed graphs (digraphs). In fact, digraphs are widely applied in the real world and confirmed to address heterophily challenges. Despite recent advancements, existing spatial- and spectral-based DiGNNs have limitations due to their complex learning mechanisms and reliance on high-quality topology, resulting in low efficiency and unstable performance. To address these issues, we propose Directed Random Walk (DiRW), a plug-and-play strategy for most spatial-based DiGNNs and also an innovative model which offers a new digraph learning paradigm. Specifically, it utilizes a direction-aware path sampler optimized from the perspectives of walk probability, length, and number in a weight-free manner by considering node profiles and topologies. Building upon this, DiRW incorporates a node-wise learnable path aggregator for generalized node representations. Extensive experiments on 9 datasets demonstrate that DiRW: (1) enhances most spatial-based methods as a plug-and-play strategy; (2) achieves SOTA performance as a new digraph learning paradigm. The source code and data are available at https://github.com/dhsiuu/DiRW.

Bowen Fan, Zhilin Guo, Xunkai Li et al.

Graph Neural Networks (GNNs) have become a pivotal framework for modeling graph-structured data, enabling a wide range of applications from social network analysis to molecular chemistry. By integrating large language models (LLMs), text-attributed graphs (TAGs) enhance node representations with rich textual semantics, significantly boosting the expressive power of graph-based learning. However, this sophisticated synergy introduces critical vulnerabilities, as Graph-LLMs are susceptible to adversarial attacks on both their structural topology and textual attributes. Although specialized attack methods have been designed for each of these aspects, no work has yet unified them into a comprehensive approach. In this work, we propose the Interpretable Multi-Dimensional Graph Attack (IMDGA), a novel human-centric adversarial attack framework designed to orchestrate multi-level perturbations across both graph structure and textual features. IMDGA utilizes three tightly integrated modules to craft attacks that balance interpretability and impact, enabling a deeper understanding of Graph-LLM vulnerabilities. Through rigorous theoretical analysis and comprehensive empirical evaluations on diverse datasets and architectures, IMDGA demonstrates superior interpretability, attack effectiveness, stealthiness, and robustness compared to existing methods. By exposing critical weaknesses in TAG representation learning, this work uncovers a previously underexplored semantic dimension of vulnerability in Graph-LLMs, offering valuable insights for improving their resilience. Our code and resources are publicly available at https://anonymous.4open.science/r/IMDGA-7289.

Zihao Zhang, Xunkai Li, Rong-Hua Li et al.

Recent advancements in Large Language Models (LLMs) and the proliferation of Text-Attributed Graphs (TAGs) across various domains have positioned LLM-enhanced TAG learning as a critical research area. By utilizing rich graph descriptions, this paradigm leverages LLMs to generate high-quality embeddings, thereby enhancing the representational capacity of Graph Neural Networks (GNNs). However, the field faces significant challenges: (1) the absence of a unified framework to systematize the diverse optimization perspectives arising from the complex interactions between LLMs and GNNs, and (2) the lack of a robust method capable of handling real-world TAGs, which often suffer from texts and edge sparsity, leading to suboptimal performance. To address these challenges, we propose UltraTAG, a unified pipeline for LLM-enhanced TAG learning. UltraTAG provides a unified comprehensive and domain-adaptive framework that not only organizes existing methodologies but also paves the way for future advancements in the field. Building on this framework, we propose UltraTAG-S, a robust instantiation of UltraTAG designed to tackle the inherent sparsity issues in real-world TAGs. UltraTAG-S employs LLM-based text propagation and text augmentation to mitigate text sparsity, while leveraging LLM-augmented node selection techniques based on PageRank and edge reconfiguration strategies to address edge sparsity. Our extensive experiments demonstrate that UltraTAG-S significantly outperforms existing baselines, achieving improvements of 2.12\% and 17.47\% in ideal and sparse settings, respectively. Moreover, as the data sparsity ratio increases, the performance improvement of UltraTAG-S also rises, which underscores the effectiveness and robustness of UltraTAG-S.

Zekai Chen, Xunkai Li, Sirui Zhang et al.

De novo ligand design is a fundamental task that seeks to generate protein or molecule candidates that can effectively dock with protein receptors and achieve strong binding affinity entirely from scratch. It holds paramount significance for a wide spectrum of biomedical applications. However, most existing studies are constrained by the \textbf{Pseudo De Novo}, \textbf{Limited Docking Modeling}, and \textbf{Inflexible Ligand Type}. To address these issues, we propose MagicDock, a forward-looking framework grounded in the progressive pipeline and differentiable surface modeling. (1) We adopt a well-designed gradient inversion framework. To begin with, general docking knowledge of receptors and ligands is incorporated into the backbone model. Subsequently, the docking knowledge is instantiated as reverse gradient flows by binding prediction, which iteratively guide the de novo generation of ligands. (2) We emphasize differentiable surface modeling in the docking process, leveraging learnable 3D point-cloud representations to precisely capture binding details, thereby ensuring that the generated ligands preserve docking validity through direct and interpretable spatial fingerprints. (3) We introduce customized designs for different ligand types and integrate them into a unified gradient inversion framework with flexible triggers, thereby ensuring broad applicability. Moreover, we provide rigorous theoretical guarantees for each component of MagicDock. Extensive experiments across 9 scenarios demonstrate that MagicDock achieves average improvements of 27.1\% and 11.7\% over SOTA baselines specialized for protein or molecule ligand design, respectively.

Zhihan Zhang, Xunkai Li, Yilong Zuo et al.

Text-attributed graphs (TAGs) have become a key form of graph-structured data in modern data management and analytics, combining structural relationships with rich textual semantics for diverse applications. However, the effectiveness of analytical models, particularly graph neural networks (GNNs), is highly sensitive to data quality. Our empirical analysis shows that both conventional and LLM-enhanced GNNs degrade notably under textual, structural, and label imperfections, underscoring TAG quality as a key bottleneck for reliable analytics. Existing studies have explored data-level optimization for TAGs, but most focus on specific degradation types and target a single aspect like structure or label, lacking a systematic and comprehensive perspective on data quality improvement. To address this gap, we propose LAGA (Large Language and Graph Agent), a unified multi-agent framework for comprehensive TAG quality optimization. LAGA formulates graph quality control as a data-centric process, integrating detection, planning, action, and evaluation agents into an automated loop. It holistically enhances textual, structural, and label aspects through coordinated multi-modal optimization. Extensive experiments on 5 datasets and 16 baselines across 9 scenarios demonstrate the effectiveness, robustness and scalability of LAGA, confirming the importance of data-centric quality optimization for reliable TAG analytics.

Xunkai Li, Daohan Su, Sicheng Liu et al.

Inspired by the success of LLMs, GFMs are designed to learn the optimal embedding functions from multi-domain text-attributed graphs for the downstream cross-task generalization capability. Among the diverse architectures, graph VQ-MAE stands out among the increasingly diverse landscape of GFM. This is attributed to its ability to jointly encode topology and textual attributes from multiple domains into discrete embedding spaces with clear semantic boundaries. Despite its potential, domain generalization conflicts cause imperceptible pitfalls. In this paper, we instantiate two of them, and they are just like two sides of the same GFM optimization coin - Side 1 Model Degradation: The encoder and codebook fail to capture the diversity of inputs; Side 2 Representation Collapse: The hidden embedding and codebook vector fail to preserve semantic separability due to constraints from narrow representation subspaces. These two pitfalls (sides) collectively impair the decoder and generate the low-quality reconstructed supervision, causing the GFM optimization dilemma during pre-training (coin). Through empirical investigation, we attribute the above challenges to Information Bottleneck and Regularization Deficit. To address them, we propose MoT - (1) Information Tinker for Two Pitfalls, which utilizes an edge-wise semantic fusion strategy and a mixture-of-codebooks with domain-aware routing to improve information capacity. (2) Regularization Tinker for Optimization Coin, which utilizes two additional regularizations to further improve gradient supervision in our proposed Information Tinker. Notably, as a flexible architecture, MoT adheres to the scaling laws of GFM, offering a controllable model scale. Compared to SOTA baselines, experiments on 22 datasets across 6 domains demonstrate that MoT achieves significant improvements in supervised, few-shot, and zero-shot scenarios.

Yanheng Hou, Xunkai Li, Zhenjun Li et al.

In recent years, Hypergraph Neural Networks (HNNs) have demonstrated immense potential in handling complex systems with high-order interactions. However, acquiring large-scale, high-quality labeled data for these models is costly, making Active Learning (AL) a critical technique. Existing Graph Active Learning (GAL) methods, when applied to hypergraphs, often rely on techniques like "clique expansion," which destroys the high-order structural information crucial to a hypergraph's success, thereby leading to suboptimal performance. To address this challenge, we introduce HIAL (Hypergraph Active Learning), a native active learning framework designed specifically for hypergraphs. We innovatively reformulate the Hypergraph Active Learning (HAL) problem as an Influence Maximization task. The core of HIAL is a dual-perspective influence function that, based on our novel "High-Order Interaction-Aware (HOI-Aware)" propagation mechanism, synergistically evaluates a node's feature-space coverage (via Magnitude of Influence, MoI) and its topological influence (via Expected Diffusion Value, EDV). We prove that this objective function is monotone and submodular, thus enabling the use of an efficient greedy algorithm with a formal (1-1/e) approximation guarantee. Extensive experiments on seven public datasets demonstrate that HIAL significantly outperforms state-of-the-art baselines in terms of performance, efficiency, generality, and robustness, establishing an efficient and powerful new paradigm for active learning on hypergraphs.