Xuanting Xie

Haolu Liu, Xiyue Wang, Xuanting Xie et al.

Standard IMVC evaluation retrains separate models for different missing-data configurations. We show that this paradigm obscures a fundamental vulnerability: missing rate alone is insufficient to characterize data incompleteness. Specifically, we show that protocols with identical nominal missing rates can differ by up to $50\times$ in their proportion of fully observed samples, inducing drastically different learning regimes. We formalize this phenomenon as incompleteness divergence, providing measures that capture structural disparities across missing-data protocols. We further prove that for a broad class of reconstruction-based objectives, learning becomes structurally ill-posed when the proportion of complete samples falls below a critical threshold, leading to near-random performance. To bypass this theoretical bound, we propose CRAFT (Complete-data Robust Attention-masked Fusion Transformer). CRAFT shifts the burden of robustness from the loss function to the architecture via two key properties: (i) per-sample independence, which removes reliance on complete-sample co-occurrence, and (ii) mask-aware variable-length fusion, which aggregates only observed views through attention masking. This design allows a single model, trained once on complete data, to generalize to diverse missing patterns at inference time without retraining. Extensive experiments on seven benchmarks show that CRAFT matches or outperforms per-configuration baselines while reducing training overhead by $8.8\times$, demonstrating that robustness to missing data can be achieved as an inherent architectural property. Code (CRAFT) and our imvc-audit toolkit are available at https://anonymous.4open.science/r/CRAFT-BF80/ and https://anonymous.4open.science/r/imvc-audit-8263/.

Xuanting Xie, Zhaochen Guo, Bingheng Li et al.

Chain-of-Thought (CoT) prompting has shown promise in enhancing the reasoning capabilities of large language models (LLMs) on text-attributed graphs (TAGs). This work reframes CoT-based graph learning through the principle of clustering as reasoning, offering a $k$-means interpretation of how iterative reasoning operates over graph-structured data. We observe that existing graph CoT methods rely on disjoint architectures and fixed graph representations, limiting step-by-step semantic-topological interaction and interpretability. To overcome this limitation, we propose a unified framework named KCoT that integrates CoT reasoning with graph representation learning. Our key theoretical result reveals a formal mathematical correspondence between a Transformer block and the $k$-means algorithm, allowing reasoning to be interpreted as iterative assignment and update steps. Based on this insight, we introduce a Semantic Discriminating Prompt that explicitly formulates these steps as structured CoT reasoning, together with a structure-grounded alignment strategy to fuse topological priors with evolving thought-conditioned representations. Experiments on standard benchmarks demonstrate consistent improvements over state-of-the-art methods, validating clustering as a principled mechanism for CoT-based graph learning.

Zhibin Wang, Zhixing Zhang, Shuqi Wang et al.

Graph Neural Networks (GNNs) have demonstrated impressive performance on task-specific benchmarks, yet their ability to generalize across diverse domains and tasks remains limited. Existing approaches often struggle with negative transfer, scalability issues, and high adaptation costs. To address these challenges, we propose GMoPE (Graph Mixture of Prompt-Experts), a novel framework that seamlessly integrates the Mixture-of-Experts (MoE) architecture with prompt-based learning for graphs. GMoPE leverages expert-specific prompt vectors and structure-aware MoE routing to enable each expert to specialize in distinct subdomains and dynamically contribute to predictions. To promote diversity and prevent expert collapse, we introduce a soft orthogonality constraint across prompt vectors, encouraging expert specialization and facilitating a more balanced expert utilization. Additionally, we adopt a prompt-only fine-tuning strategy that significantly reduces spatiotemporal complexity during transfer. We validate GMoPE through extensive experiments under various pretraining strategies and multiple downstream tasks. Results show that GMoPE consistently outperforms state-of-the-art baselines and achieves performance comparable to full parameter fine-tuning-while requiring only a fraction of the adaptation overhead. Our work provides a principled and scalable framework for advancing generalizable and efficient graph foundation models.

Zhaochen Guo, Zhixiang Shen, Xuanting Xie et al.

Multimodal graphs, which integrate unstructured heterogeneous data with structured interconnections, offer substantial real-world utility but remain insufficiently explored in unsupervised learning. In this work, we initiate the study of multimodal graph clustering, aiming to bridge this critical gap. Through empirical analysis, we observe that real-world multimodal graphs often exhibit hybrid neighborhood patterns, combining both homophilic and heterophilic relationships. To address this challenge, we propose a novel framework -- \textsc{Disentangled Multimodal Graph Clustering (DMGC)} -- which decomposes the original hybrid graph into two complementary views: (1) a homophily-enhanced graph that captures cross-modal class consistency, and (2) heterophily-aware graphs that preserve modality-specific inter-class distinctions. We introduce a \emph{Multimodal Dual-frequency Fusion} mechanism that jointly filters these disentangled graphs through a dual-pass strategy, enabling effective multimodal integration while mitigating category confusion. Our self-supervised alignment objectives further guide the learning process without requiring labels. Extensive experiments on both multimodal and multi-relational graph datasets demonstrate that DMGC achieves state-of-the-art performance, highlighting its effectiveness and generalizability across diverse settings. Our code is available at https://github.com/Uncnbb/DMGC.

Xingtong Yu, Zhongwei Kuai, Chang Zhou et al.

Reasoning-acting frameworks enhance large language models (LLMs) by interleaving reasoning with actions for dynamic information acquisition. However, extending this paradigm to graph learning remains underexplored. Graph data is inherently structured, with information distributed across nodes and edges and encoded through both topology and latent representations. As a result, effective reasoning over graphs requires not only retrieving informative evidence from the graph, but also progressively refining the accumulated context during multi-step inference. In this work, we propose GraphReAct, a graph reasoning-acting framework that enables step-by-step inference over graph-structured data. Specifically, we design a graph-based action space with two complementary retrieval actions: topological retrieval, which captures local structural dependencies, and semantic retrieval, which accesses non-local but relevant evidence in the representation space. These actions dynamically expand the reasoning context. To further support multi-step reasoning, we introduce another type of action, context refinement, which distills and reorganizes accumulated information into a compact representation. By interleaving reasoning with both retrieval and refinement actions, our framework enables a progressive transition from context expansion to compression. Extensive experiments on six benchmark datasets demonstrate that GraphReAct consistently outperforms state-of-the-art methods, validating the effectiveness of reasoning-acting for graph learning.

Zhao Kang, Xuanting Xie, Bingheng Li et al.

In today's data-driven digital era, the amount as well as complexity, such as multi-view, non-Euclidean, and multi-relational, of the collected data are growing exponentially or even faster. Clustering, which unsupervisely extracts valid knowledge from data, is extremely useful in practice. However, existing methods are independently developed to handle one particular challenge at the expense of the others. In this work, we propose a simple but effective framework for complex data clustering (CDC) that can efficiently process different types of data with linear complexity. We first utilize graph filtering to fuse geometry structure and attribute information. We then reduce the complexity with high-quality anchors that are adaptively learned via a novel similarity-preserving regularizer. We illustrate the cluster-ability of our proposed method theoretically and experimentally. In particular, we deploy CDC to graph data of size 111M.

Bingheng Li, Xuanting Xie, Haoxiang Lei et al.

Graph Neural Networks (GNNs) have garnered significant attention for their success in learning the representation of homophilic or heterophilic graphs. However, they cannot generalize well to real-world graphs with different levels of homophily. In response, the Possion-Charlier Network (PCNet) \cite{li2024pc}, the previous work, allows graph representation to be learned from heterophily to homophily. Although PCNet alleviates the heterophily issue, there remain some challenges in further improving the efficacy and efficiency. In this paper, we simplify PCNet and enhance its robustness. We first extend the filter order to continuous values and reduce its parameters. Two variants with adaptive neighborhood sizes are implemented. Theoretical analysis shows our model's robustness to graph structure perturbations or adversarial attacks. We validate our approach through semi-supervised learning tasks on various datasets representing both homophilic and heterophilic graphs.

Xuanting Xie, Zhao Kang, Wenyu Chen

Graph is a fundamental mathematical structure in characterizing relations between different objects and has been widely used on various learning tasks. Most methods implicitly assume a given graph to be accurate and complete. However, real data is inevitably noisy and sparse, which will lead to inferior results. Despite the remarkable success of recent graph representation learning methods, they inherently presume that the graph is homophilic, and largely overlook heterophily, where most connected nodes are from different classes. In this regard, we propose a novel robust graph structure learning method to achieve a high-quality graph from heterophilic data for downstream tasks. We first apply a high-pass filter to make each node more distinctive from its neighbors by encoding structure information into the node features. Then, we learn a robust graph with an adaptive norm characterizing different levels of noise. Afterwards, we propose a novel regularizer to further refine the graph structure. Clustering and semi-supervised classification experiments on heterophilic graphs verify the effectiveness of our method.

Xuanting Xie, Bingheng Li, Erlin Pan et al.

Most existing graph clustering methods primarily focus on exploiting topological structure, often neglecting the ``missing-half" node feature information, especially how these features can enhance clustering performance. This issue is further compounded by the challenges associated with high-dimensional features. Feature selection in graph clustering is particularly difficult because it requires simultaneously discovering clusters and identifying the relevant features for these clusters. To address this gap, we introduce a novel paradigm called ``one node one model", which builds an exclusive model for each node and defines the node label as a combination of predictions for node groups. Specifically, the proposed ``Feature Personalized Graph Clustering (FPGC)" method identifies cluster-relevant features for each node using a squeeze-and-excitation block, integrating these features into each model to form the final representations. Additionally, the concept of feature cross is developed as a data augmentation technique to learn low-order feature interactions. Extensive experimental results demonstrate that FPGC outperforms state-of-the-art clustering methods. Moreover, the plug-and-play nature of our method provides a versatile solution to enhance GNN-based models from a feature perspective.

Xuanting Xie, Erlin Pan, Zhao Kang et al.

Graph clustering, an important unsupervised problem, has been shown to be more resistant to advances in Graph Neural Networks (GNNs). In addition, almost all clustering methods focus on homophilic graphs and ignore heterophily. This significantly limits their applicability in practice, since real-world graphs exhibit a structural disparity and cannot simply be classified as homophily and heterophily. Thus, a principled way to handle practical graphs is urgently needed. To fill this gap, we provide a novel solution with theoretical support. Interestingly, we find that most homophilic and heterophilic edges can be correctly identified on the basis of neighbor information. Motivated by this finding, we construct two graphs that are highly homophilic and heterophilic, respectively. They are used to build low-pass and high-pass filters to capture holistic information. Important features are further enhanced by the squeeze-and-excitation block. We validate our approach through extensive experiments on both homophilic and heterophilic graphs. Empirical results demonstrate the superiority of our method compared to state-of-the-art clustering methods.

Xuanting Xie, Bingheng Li, Erlin Pan et al.

Attention mechanisms have become a cornerstone in modern neural networks, driving breakthroughs across diverse domains. However, their application to graph structured data, where capturing topological connections is essential, remains underexplored and underperforming compared to Graph Neural Networks (GNNs), particularly in the graph clustering task. GNN tends to overemphasize neighborhood aggregation, leading to a homogenization of node representations. Conversely, Transformer tends to over globalize, highlighting distant nodes at the expense of meaningful local patterns. This dichotomy raises a key question: Is attention inherently redundant for unsupervised graph learning? To address this, we conduct a comprehensive empirical analysis, uncovering the complementary weaknesses of GNN and Transformer in graph clustering. Motivated by these insights, we propose the Attentive Graph Clustering Network (AGCN) a novel architecture that reinterprets the notion that graph is attention. AGCN directly embeds the attention mechanism into the graph structure, enabling effective global information extraction while maintaining sensitivity to local topological cues. Our framework incorporates theoretical analysis to contrast AGCN behavior with GNN and Transformer and introduces two innovations: (1) a KV cache mechanism to improve computational efficiency, and (2) a pairwise margin contrastive loss to boost the discriminative capacity of the attention space. Extensive experimental results demonstrate that AGCN outperforms state-of-the-art methods.

Xuanting Xie, Bingheng Li, Erlin Pan et al.

Graph Neural Networks (GNNs) have become a dominant approach to learning graph representations, primarily because of their message-passing mechanisms. However, GNNs typically adopt a fixed aggregator function such as Mean, Max, or Sum without principled reasoning behind the selection. This rigidity, especially in the presence of heterophily, often leads to poor, problem dependent performance. Although some attempts address this by designing more sophisticated aggregation functions, these methods tend to rely heavily on labeled data, which is often scarce in real-world tasks. In this work, we propose a novel unsupervised framework, "Aggregation-aware Multilayer Perceptron" (AMLP), which shifts the paradigm from directly crafting aggregation functions to making MLP adaptive to aggregation. Our lightweight approach consists of two key steps: First, we utilize a graph reconstruction method that facilitates high-order grouping effects, and second, we employ a single-layer network to encode varying degrees of heterophily, thereby improving the capacity and applicability of the model. Extensive experiments on node clustering and classification demonstrate the superior performance of AMLP, highlighting its potential for diverse graph learning scenarios.