Hongchao Qin

Chenxi Wan, Xunkai Li, Yilong Zuo et al.

Multimodal-Attributed Graph (MAG) learning has achieved remarkable success in modeling complex real-world systems by integrating graph topology with rich attributes from multiple modalities. With the rapid proliferation of novel MAG models capable of handling intricate cross-modal semantics and structural dependencies, establishing a rigorous and unified evaluation standard has become imperative. Although existing benchmarks have facilitated initial progress, they exhibit critical limitations in domain coverage, encoder flexibility, model diversity, and task scope, presenting significant challenges to fair evaluation. To bridge this gap, we present OpenMAG, a comprehensive benchmark that integrates 19 datasets across 6 domains and incorporates 16 encoders to support both static and trainable feature encoding. OpenMAG further implements a standardized library of 24 state-of-the-art models and supports 8 downstream tasks, enabling fair comparisons within a unified framework. Through systematic assessment of necessity, data quality, effectiveness, robustness, and efficiency, we derive 14 fundamental insights into MAG learning to guide future advancements. Our code is available at https://github.com/YUKI-N810/OpenMAG.

Ru Zhang, Xunkai Li, Yaxin Deng et al.

Recently, data-centric AI methodology has been a dominant paradigm in single-cell transcriptomics analysis, which treats data representation rather than model complexity as the fundamental bottleneck. In the review of current studies, earlier sequence methods treat cells as independent entities and adapt prevalent ML models to analyze their directly inherited sequence data. Despite their simplicity and intuition, these methods overlook the latent intercellular relationships driven by the functional mechanisms of biological systems and the inherent quality issues of the raw sequence data. Therefore, a series of structured methods has emerged. Although they employ various heuristic rules to capture intricate intercellular relationships and enhance the raw sequencing data, these methods often neglect biological prior knowledge. This omission incurs substantial overhead and yields suboptimal graph representations, thereby hindering the utility of ML models. To address them, we propose DOGMA, a holistic data-centric framework designed for the structural reshaping and semantic enhancement of raw data through multi-level biological prior knowledge. Transcending reliance on stochastic heuristics, DOGMA redefines graph construction by integrating Statistical Anchors with Cell Ontology and Phylogenetic Trees to enable deterministic structure discovery and robust cross-species alignment. Furthermore, Gene Ontology is utilized to bridge the feature-level semantic gap by incorporating functional priors. In complex multi-species and multi-organ benchmarks, DOGMA achieves SOTA performance, exhibiting superior zero-shot robustness and sample efficiency while operating with significantly lower computational cost.

Xunkai Li, Zhengyu Wu, Zekai Chen et al.

Recently, the rapid advancement of multimodal domains has driven a data-centric paradigm shift in graph ML, transitioning from text-attributed to multimodal-attributed graphs. This advancement significantly enhances data representation and expands the scope of graph downstream tasks, such as modality-oriented tasks, thereby improving the practical utility of graph ML. Despite its promise, limitations exist in the current neural paradigms: (1) Neglect Context in Modality Alignment: Most existing methods adopt topology-constrained or modality-specific operators as tokenizers. These aligners inevitably neglect graph context and inhibit modality interaction, resulting in suboptimal alignment. (2) Lack of Adaptation in Modality Fusion: Most existing methods are simple adaptations for 2-modality graphs and fail to adequately exploit aligned tokens equipped with topology priors during fusion, leading to poor generalizability and performance degradation. To address the above issues, we propose LION (c\underline{LI}ff\underline{O}rd \underline{N}eural paradigm) based on the Clifford algebra and decoupled graph neural paradigm (i.e., propagation-then-aggregation) to implement alignment-then-fusion in multimodal-attributed graphs. Specifically, we first construct a modality-aware geometric manifold grounded in Clifford algebra. This geometric-induced high-order graph propagation efficiently achieves modality interaction, facilitating modality alignment. Then, based on the geometric grade properties of aligned tokens, we propose adaptive holographic aggregation. This module integrates the energy and scale of geometric grades with learnable parameters to improve modality fusion. Extensive experiments on 9 datasets demonstrate that LION significantly outperforms SOTA baselines across 3 graph and 3 modality downstream tasks.

Zekai Chen, Haodong Lu, Xunkai Li et al.

Federated graph learning (FGL) enables collaborative training on graph data across multiple clients. With the rise of large language models (LLMs), textual attributes in FGL graphs are gaining attention. Text-attributed graph federated learning (TAG-FGL) improves FGL by explicitly leveraging LLMs to process and integrate these textual features. However, current TAG-FGL methods face three main challenges: \textbf{(1) Overhead.} LLMs for processing long texts incur high token and computation costs. To make TAG-FGL practical, we introduce graph condensation (GC) to reduce computation load, but this choice also brings new issues. \textbf{(2) Suboptimal.} To reduce LLM overhead, we introduce GC into TAG-FGL by compressing multi-hop texts/neighborhoods into a condensed core with fixed LLM surrogates. However, this one-shot condensation is often not client-adaptive, leading to suboptimal performance. \textbf{(3) Interpretability.} LLM-based condensation further introduces a black-box bottleneck: summaries lack faithful attribution and clear grounding to specific source spans, making local inspection and auditing difficult. To address the above issues, we propose \textbf{DANCE}, a new TAG-FGL paradigm with GC. To improve \textbf{suboptimal} performance, DANCE performs round-wise, model-in-the-loop condensation refresh using the latest global model. To enhance \textbf{interpretability}, DANCE preserves provenance by storing locally inspectable evidence packs that trace predictions to selected neighbors and source text spans. Across 8 TAG datasets, DANCE improves accuracy by \textbf{2.33\%} at an \textbf{8\%} condensation ratio, with \textbf{33.42\%} fewer tokens than baselines.

Sicheng Liu, Xunkai Li, Daohan Su et al.

Graph Foundation Models (GFMs) have achieved remarkable success in generalizing across diverse domains. However, they mainly focus on Text-Attributed Graphs (TAGs), leaving Multimodal-Attributed Graphs (MAGs) largely untapped. Developing Multimodal Graph Foundation Models (MGFMs) allows for leveraging the rich multimodal information in MAGs, and extends applicability to broader types of downstream tasks. While recent MGFMs integrate diverse modality information, our empirical investigation reveals two fundamental limitations of existing MGFMs: (1)they fail to explicitly model modality interaction, essential for capturing intricate cross-modal semantics beyond simple aggregation, and (2)they exhibit sub-optimal modality alignment, which is critical for bridging the significant semantic disparity between distinct modal spaces. To address these challenges, we propose PLANET (graPh topoLogy-aware modAlity iNteraction and alignmEnT), a novel framework employing a Divide-and-Conquer strategy to decouple modality interaction and alignment across distinct granularities. At the embedding granularity, (1)Embedding-wise Domain Gating (EDG) performs local semantic enrichment by adaptively infusing topology-aware cross-modal context, achieving modality interaction. At the node granularity, (2)Node-wise Discretization Retrieval (NDR) ensures global modality alignment by constructing a Discretized Semantic Representation Space (DSRS) to bridge modality gaps. Extensive experiments demonstrate that PLANET significantly outperforms state-of-the-art baselines across diverse graph-centric and multimodal generative tasks.

Xiang Wu, Rong-Hua Li, Xunkai Li et al.

Graph coarsening reduces the size of a graph while preserving certain properties. Most existing methods preserve either spectral or spatial characteristics. Recent research has shown that preserving topological features helps maintain the predictive performance of graph neural networks (GNNs) trained on the coarsened graph but suffers from exponential time complexity. To address these problems, we propose Scalable Topology-Preserving Graph Coarsening (STPGC) by introducing the concepts of graph strong collapse and graph edge collapse extended from algebraic topology. STPGC comprises three new algorithms, GStrongCollapse, GEdgeCollapse, and NeighborhoodConing based on these two concepts, which eliminate dominated nodes and edges while rigorously preserving topological features. We further prove that STPGC preserves the GNN receptive field and develop approximate algorithms to accelerate GNN training. Experiments on node classification with GNNs demonstrate the efficiency and effectiveness of STPGC.

Daohan Su, Hao Liu, Xunkai Li et al.

Multimodal Graph Neural Networks (MGNNs) have shown strong potential for learning from multimodal attributed graphs, yet most existing approaches rely on tightly coupled architectures that suffer from prohibitive computational overhead. In this paper, we present a systematic empirical analysis showing that decoupled MGNNs are substantially more efficient and scalable for large-scale graph learning. However, we identify a critical bottleneck in existing decoupled pipelines, namely modal conflict, which arises in both the propagation and aggregation stages. Specifically, independent multi-hop diffusion causes cross-modal semantic divergence during propagation, while naive fusion fails to align multi-hop feature trajectories during aggregation, jointly limiting effective representation learning. To address this challenge, we propose CAMPA, a Cross-modal Aligned Multimodal Propagation & Aggregation framework for decoupled multimodal graph learning. Concretely, CAMPA introduces a two-stage alignment mechanism: (1) cross-modal aligned propagation, which injects cross-modal similarity priors into message passing to preserve semantic consistency without additional parameter overhead; (2) trajectory aligned aggregation, which leverages trajectory-level self-attention and cross-attention to capture and align long-range dependencies across modalities and hops. Extensive experiments on diverse benchmark datasets and tasks demonstrate that CAMPA consistently outperforms strong coupled and decoupled baselines while preserving the efficiency advantages of the decoupled paradigm.

Sirui Zhang, Haonan Wang, Xunkai Li et al.

Recently, multimodal graph learning (MGL) has garnered significant attention for integrating diverse modality information and structured context to support various network applications. However, real-world graphs are often isolated due to data-sharing limitations across multiple parties, and their modalities are frequently incomplete. This highlights an urgent need to develop a robust federated approach. However, we find that existing methods remain insufficient. On the one hand, centralized MGL methods that handle missing modalities overlook the knowledge sharing and generalization in federated scenarios. On the other hand, while federated MGL methods have become increasingly mature, they primarily target non-graph data. Based on these technologies, we identify a two-stage pipeline wherein client-side completion reconstructs missing modalities, and server-side aggregation integrates the client-updated parameters of both the modality generator and the backbone models. Although this serves as a general solution, we identify two primary challenges in achieving greater robustness: (1) Topology-Isolated Local Completion: Client-side modality generation struggles to effectively leverage global semantics. (2) Reliability-Imbalanced Global Aggregation: Server-side multi-party collaboration is hindered by client updates with varying modality availability and recovery reliability. To address these challenges, we propose \textsc{FedMPO}, which utilizes topology-aware cross-modal generation to recover missing features using comprehensive graph context, missing-aware expert routing to locally filter out noisy recovered signals, and reliability-aware aggregation to appropriately down-weight unreliable updates. Extensive experiments on 3 tasks across 6 datasets demonstrate that FedMPO outperforms baselines, achieving performance gains of up to 4.10% and 5.65% in high-missing and non-IID settings.

Xiaoyu Leng, Hongchao Qin, Rong-Hua Li

Decomposing hypergraphs is a key task in hypergraph analysis with broad applications in community detection, pattern discovery, and task scheduling. Existing approaches such as $k$-core and neighbor-$k$-core rely on vertex degree constraints, which often fail to capture true density variations induced by multi-way interactions and may lead to sparse or uneven decomposition layers. To address these issues, we propose a novel \((k,δ)\)-dense subhypergraph model for decomposing hypergraphs based on integer density values. Here, $k$ represents the density level of a subhypergraph, while \(δ\) sets the upper limit for each hyperedge's contribution to density, allowing fine-grained control over density distribution across layers. Computing such dense subhypergraphs is algorithmically challenging, as it requires identifying an egalitarian orientation under bounded hyperedge contributions, which may incur an intuitive worst-case complexity of up to $O(2^{mδ})$. To enable efficient computation, we develop a fair-stable-based algorithm that reduces the complexity of mining a single $(k,δ)$-dense subhypergraph from $O(m^{2}δ^{2})$ to $O(nmδ)$. Building on this result, we further design a divide-and-conquer decomposition framework that improves the overall complexity of full density decomposition from $O(nmδ\cdot d^E_{\max} \cdot k_{\max})$ to $O(nmδ\cdot d^E_{\max} \cdot \log k_{\max})$. Experiments on nine real-world hypergraph datasets demonstrate that our approach produces more continuous and less redundant decomposition hierarchies than existing baselines, while maintaining strong computational efficiency. Case studies further illustrate the practical utility of our model by uncovering cohesive and interpretable community structures.

Xunkai Li, Zhengyu Wu, Kaichi Yu et al.

The directed graph (digraph), as a generalization of undirected graphs, exhibits superior representation capability in modeling complex topology systems and has garnered considerable attention in recent years. Despite the notable efforts made by existing DiGraph Neural Networks (DiGNNs) to leverage directed edges, they still fail to comprehensively delve into the abundant data knowledge concealed in the digraphs. This data-level limitation results in model-level sub-optimal predictive performance and underscores the necessity of further exploring the potential correlations between the directed edges (topology) and node profiles (feature and labels) from a data-centric perspective, thereby empowering model-centric neural networks with stronger encoding capabilities. In this paper, we propose \textbf{E}ntropy-driven \textbf{D}igraph knowl\textbf{E}dge distillatio\textbf{N} (EDEN), which can serve as a data-centric digraph learning paradigm or a model-agnostic hot-and-plug data-centric Knowledge Distillation (KD) module. The core idea is to achieve data-centric ML, guided by our proposed hierarchical encoding theory for structured data. Specifically, EDEN first utilizes directed structural measurements from a topology perspective to construct a coarse-grained Hierarchical Knowledge Tree (HKT). Subsequently, EDEN quantifies the mutual information of node profiles to refine knowledge flow in the HKT, enabling data-centric KD supervision within model training. As a general framework, EDEN can also naturally extend to undirected scenarios and demonstrate satisfactory performance. In our experiments, EDEN has been widely evaluated on 14 (di)graph datasets (homophily and heterophily) and across 4 downstream tasks. The results demonstrate that EDEN attains SOTA performance and exhibits strong improvement for prevalent (Di)GNNs.

Xunkai Li, Daohan Su, Zhengyu Wu et al.

The $q$-parameterized magnetic Laplacian serves as the foundation of directed graph (digraph) convolution, enabling this kind of digraph neural network (MagDG) to encode node features and structural insights by complex-domain message passing. As a generalization of undirected methods, MagDG shows superior capability in modeling intricate web-scale topology. Despite the great success achieved by existing MagDGs, limitations still exist: (1) Hand-crafted $q$: The performance of MagDGs depends on selecting an appropriate $q$-parameter to construct suitable graph propagation equations in the complex domain. This parameter tuning, driven by downstream tasks, limits model flexibility and significantly increases manual effort. (2) Coarse Message Passing: Most approaches treat all nodes with the same complex-domain propagation and aggregation rules, neglecting their unique digraph contexts. This oversight results in sub-optimal performance. To address the above issues, we propose two key techniques: (1) MAP is crafted to be a plug-and-play complex-domain propagation optimization strategy in the context of digraph learning, enabling seamless integration into any MagDG to improve predictions while enjoying high running efficiency. (2) MAP++ is a new digraph learning framework, further incorporating a learnable mechanism to achieve adaptively edge-wise propagation and node-wise aggregation in the complex domain for better performance. Extensive experiments on 12 datasets demonstrate that MAP enjoys flexibility for it can be incorporated with any MagDG, and scalability as it can deal with web-scale digraphs. MAP++ achieves SOTA predictive performance on 4 different downstream tasks.

Zhiqiu Zou, Ziqi Yin, Rong-Hua Li et al.

Range-filtered approximate nearest neighbor (RFANN) search is a fundamental operation in modern data systems. Given a set of objects, each with a vector and a numerical attribute, an RFANN query retrieves the nearest neighbors to a query vector among those objects whose numerical attributes fall within the range specified by the query. Existing state-of-the-art methods for RFANN search often require constructing multiple range-specific graph indexes to achieve high query performance, which incurs significant indexing overhead. To address this, we first establish a novel graph indexing theory, the range-aware relative neighborhood graph (RRNG), which jointly considers spatial and attribute proximity. We prove that the RRNG satisfies two crucial properties: (1) monotonic search-ability, which ensures correct nearest neighbor retrieval via beam search; and (2) structural heredity, which guarantees that any range-induced subgraph remains a valid RRNG, thus enabling efficient search with a single graph index. Based on this theoretical foundation, we propose a new graph index called RNSG as a practical solution that efficiently approximates RRNG. We develop fast algorithms for both constructing the RNSG index and processing RFANN queries with it. Extensive experiments on five real-world datasets show that RNSG achieves significantly higher query performance with a more compact index and lower construction cost than existing state-of-the-art methods.