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Chuan Shi

Publications and source records attributed to Chuan Shi.

At least 37 records · Page 2Linked to original sources
arXiv2026

RelPrism: A Multi-Faceted Pre-training Framework with Self-Generated Tasks for Relational Databases

Relational databases (RDBs) remain the cornerstone of modern data systems and support diverse predictive tasks. Recent relational deep learning (RDL) methods enable end-to-end prediction by converting RDBs into graphs, where rows are represented as nodes and inter-table interactions are represented as edges, and then applying graph-based models for representation learning. Despite the strong capability of RDL, effective self-supervised pre-training for RDBs remains non-trivial. RDB tasks often require multi-faceted information across different perspectives and granularities. For example, user churn classification may rely more on interaction patterns, whereas consumption value prediction requires both user-item behaviors and intrinsic user attributes for fine-grained regression. Such heterogeneous needs challenge RDB representation learning, as pre-training objectives should cover comprehensive information for downstream adaptation. However, existing SSL methods typically derive supervision from a single facet, such as node-level intrinsic attributes or subgraph-level relational structures, providing limited adaptability. To this end, we propose RelPrism, a multi-faceted self-supervised learning framework for RDBs. RelPrism constructs intrinsic, relational, and hybrid attributes from distinct perspectives, and applies multi-granularity clustering to each perspective to form corresponding pseudo-task pools. Pre-training over these pools exposes representations to broader perspectives and granularity levels, yielding a stronger basis for downstream adaptation. Experiments on 14 tasks across 5 real-world datasets show that RelPrism improves ROC-AUC by 4.15% for classification and reduces MAE by 10.75% for regression over state-of-the-art baselines. Our code is available at https://anonymous.4open.science/r/RelPrism.

cs.LG↗
arXiv2026

MASFactory: A Graph-centric Framework for Orchestrating LLM-Based Multi-Agent Systems with Vibe Graphing

Large language model-based (LLM-based) multi-agent systems (MAS) are increasingly used to extend agentic problem solving via role specialization and collaboration. MAS workflows can be naturally modeled as directed computation graphs, where nodes execute agents or sub-workflows and edges encode dependencies and message passing. However, implementing complex graph workflows in current frameworks still requires substantial manual effort, offers limited reuse, and makes it difficult to integrate heterogeneous external context sources. To overcome these limitations, we present MASFactory, a graph-centric framework for orchestrating LLM-based MAS. It introduces Vibe Graphing, a human-in-the-loop approach that compiles natural-language intent into an editable workflow specification and then into an executable graph. In addition, the framework provides reusable components, skill support, multimodal message handling, and pluggable context integration, as well as a visualizer for topology preview, runtime tracing, and human-in-the-loop interaction. We evaluate MASFactory on seven public benchmarks, validating both reproduction consistency for representative MAS methods and the effectiveness of Vibe Graphing. Our code (https://github.com/BUPT-GAMMA/MASFactory, licensed under Apache-2.0) and video demonstration (https://youtu.be/ANynzVfY32k) are publicly available.

cs.CL↗
arXiv2026

Revisiting Graph-Tokenizing Large Language Models: A Systematic Evaluation of Graph Token Understanding

The remarkable success of large language models (LLMs) has motivated researchers to adapt them as universal predictors for various graph tasks. As a widely recognized paradigm, Graph-Tokenizing LLMs (GTokenLLMs) compress complex graph data into graph tokens and treat them as prefix tokens for querying LLMs, leading many to believe that LLMs can understand graphs more effectively and efficiently. In this paper, we challenge this belief: \textit{Do GTokenLLMs fully understand graph tokens in the natural-language embedding space?} Motivated by this question, we formalize a unified framework for GTokenLLMs and propose an evaluation pipeline, \textbf{GTEval}, to assess graph-token understanding via instruction transformations at the format and content levels. We conduct extensive experiments on 6 representative GTokenLLMs with GTEval. The primary findings are as follows: (1) Existing GTokenLLMs do not fully understand graph tokens. They exhibit over-sensitivity or over-insensitivity to instruction changes, and rely heavily on text for reasoning; (2) Although graph tokens preserve task-relevant graph information and receive attention across LLM layers, their utilization varies across models and instruction variants; (3) Additional instruction tuning can improve performance on the original and seen instructions, but it does not fully address the challenge of graph-token understanding, calling for further improvement.

cs.CL↗
arXiv2026

Position: How can Graphs Help Large Language Models?

With the rapid advancement of large language models (LLMs), classic graph learning tasks have greatly benefited from LLMs, including improved encoding of textual features, more efficient construction of graphs from text, and enhanced reasoning over knowledge graphs. In this paper, we ask a complementary question: How can graphs help LLMs? We address this question from three perspectives: 1) graphs provide an up-to-date knowledge source that helps reduce LLM hallucinations, 2) graph-based prompting techniques-such as Chain-of-Thought (CoT), Tree-of-Thought (ToT), and Graph-of-Thought (GoT)-enhance LLM reasoning capabilities, and 3) integrating graphs into LLMs improves their understanding of structured data, expanding their applicability to domains such as e-commerce, code, and relational databases (RDBs). We further outlook some future directions including designing sparse LLM architectures based on graphs and brain-inspired memory systems.

cs.AI↗
arXiv2026

Detecting Hallucinations for Large Language Model-based Knowledge Graph Reasoning

Knowledge graph (KG) reasoning infers new knowledge from existing facts and is widely applied in question answering, recommendation, and decision support. With the rapid development of large language models (LLMs), LLM-based KG reasoning frameworks have become increasingly popular by leveraging retrieved KG information. However, hallucinations in LLMs remain a critical issue. Even when relevant KG knowledge is incorporated, models may still generate incorrect outputs, leading to misinformation and unreliable decisions. Existing hallucination detection methods either focus on LLM internal states or verify consistency with retrieved contexts, but both overlook the structural information in KGs, resulting in suboptimal performance. To address this gap, we propose LUCID, the first halLUcination deteCtIon method for LLM-based knowleDge graph reasoning frameworks. LUCID jointly leverages LLM attention scores, KG semantics, and structural information. Specifically, it extracts node and edge features from attention scores and semantic similarities, and integrates them with KG structure using a graph neural network. We also construct manually annotated benchmark datasets for evaluation. Experiments on nine datasets show that LUCID achieves state of the art performance compared to 15 baselines.

cs.CL↗
arXiv2026

Disentangled Graph Prompting for Out-Of-Distribution Detection

When testing data and training data come from different distributions, deep neural networks (DNNs) will face significant safety risks in practical applications. Therefore, out-of-distribution (OOD) detection techniques, which can identify OOD samples at test time and alert the system, are urgently needed. Existing graph OOD detection methods usually characterize fine-grained in-distribution (ID) patterns from multiple perspectives, and train end-to-end graph neural networks (GNNs) for prediction. However, due to the unavailability of OOD data during training, the absence of explicit supervision signals could lead to sub-optimal performance of end-to-end encoders. To address this issue, we follow the pre-training+prompting paradigm to utilize pre-trained GNN encoders, and propose Disentangled Graph Prompting (DGP), to capture fine-grained ID patterns with the help of ID graph labels. Specifically, we design two prompt generators that respectively generate class-specific and class-agnostic prompt graphs by modifying the edge weights of an input graph. We also design several effective losses to train the prompt generators and prevent trivial solutions. We conduct extensive experiments on ten datasets to demonstrate the superiority of our proposed DGP, which achieves a relative AUC improvement of 3.63% over the best graph OOD detection baseline. Ablation studies and hyper-parameter experiments further show the effectiveness of DGP. Code is available at https://github.com/BUPT-GAMMA/DGP.

cs.LG↗
arXiv2026

C$^2$-Cite: Contextual-Aware Citation Generation for Attributed Large Language Models

The attribution technique enhances the credibility of LLMs by adding citations to the generated sentences, enabling users to trace back to the original sources and verify the reliability of the output. However, existing instruction-tuned attributed LLMs often fail to properly interpret the contextual semantics of citation symbols (e.g., [i]) during text generation. This shortcoming arises from their insufficient awareness of the context information surrounding citation markers, which in turn leads to disjointed references and poor integration of retrieved knowledge into the generated content. To address this issue, we propose a novel \textbf{C}ontextual-aware \textbf{C}itation generation framework (\textbf{C$^2$}-\textbf{Cite}) that explicitly integrates the semantic relationships between citation markers and their referenced content. Specifically, a contextual citation alignment mechanism is adopted: it first encodes the retrieved document contexts into the symbol representation of citations, then aligns the marker numbers by decoding information from a citation router function. This mechanism enables the transformation of citation markers from generic placeholders into active knowledge pointers that link to the referenced source information. Experimental results on the ALCE benchmark across three datasets validate our framework C$^2$-Cite++: it outperforms the SOTA baseline by an average of 5.8\% in citation quality and 17.4\% in response correctness. The implementation is publicly available at https://github.com/BAI-LAB/c2cite

cs.IR↗
arXiv2026

GNNVerifier: Graph-based Verifier for LLM Task Planning

Large language models (LLMs) facilitate the development of autonomous agents. As a core component of such agents, task planning aims to decompose complex natural language requests into concrete, solvable sub-tasks. Since LLM-generated plans are frequently prone to hallucinations and sensitive to long-context prom-pts, recent research has introduced plan verifiers to identify and correct potential flaws. However, most existing approaches still rely on an LLM as the verifier via additional prompting for plan review or self-reflection. LLM-based verifiers can be misled by plausible narration and struggle to detect failures caused by structural relations across steps, such as type mismatches, missing intermediates, or broken dependencies. To address these limitations, we propose a graph-based verifier for LLM task planning. Specifically, the proposed method has four major components: Firstly, we represent a plan as a directed graph with enriched attributes, where nodes denote sub-tasks and edges encode execution order and dependency constraints. Secondly, a graph neural network (GNN) then performs structural evaluation and diagnosis, producing a graph-level plausibility score for plan acceptance as well as node/edge-level risk scores to localize erroneous regions. Thirdly, we construct controllable perturbations from ground truth plan graphs, and automatically generate training data with fine-grained annotations. Finally, guided by the feedback from our GNN verifier, we enable an LLM to conduct local edits (e.g., tool replacement or insertion) to correct the plan when the graph-level score is insufficient. Extensive experiments across diverse datasets, backbone LLMs, and planners demonstrate that our GNNVerifier achieves significant gains in improving plan quality. Our data and code is available at https://github.com/BUPT-GAMMA/GNNVerifier.

cs.LG↗
arXiv2026

Graph Tokenization for Bridging Graphs and Transformers

The success of large pretrained Transformers is closely tied to tokenizers, which convert raw input into discrete symbols. Extending these models to graph-structured data remains a significant challenge. In this work, we introduce a graph tokenization framework that generates sequential representations of graphs by combining reversible graph serialization, which preserves graph information, with Byte Pair Encoding (BPE), a widely adopted tokenizer in large language models (LLMs). To better capture structural information, the graph serialization process is guided by global statistics of graph substructures, ensuring that frequently occurring substructures appear more often in the sequence and can be merged by BPE into meaningful tokens. Empirical results demonstrate that the proposed tokenizer enables Transformers such as BERT to be directly applied to graph benchmarks without architectural modifications. The proposed approach achieves state-of-the-art results on 14 benchmark datasets and frequently outperforms both graph neural networks and specialized graph transformers. This work bridges the gap between graph-structured data and the ecosystem of sequence models. Our code is available at \href{https://github.com/BUPT-GAMMA/Graph-Tokenization-for-Bridging-Graphs-and-Transformers}{\color{blue}here}.

cs.LG↗
arXiv2026

Toward Graph-Tokenizing Large Language Models with Reconstructive Graph Instruction Tuning

The remarkable success of large language models (LLMs) has motivated researchers to adapt them as universal predictors for various graph-related tasks, with the ultimate goal of developing a graph foundation model that generalizes diverse scenarios. The key challenge is to align graph data with language spaces so that LLMs can better comprehend graphs. As a popular paradigm, Graph-Tokenizing LLMs (GTokenLLMs) encode complex structures and lengthy texts into a graph token sequence, and then align them with text tokens via language instructions tuning. Despite their initial success, our information-theoretic analysis reveals that existing GTokenLLMs rely solely on text supervision from language instructions, which achieve only implicit graph-text alignment, resulting in a text-dominant bias that underutilizes graph context. To overcome this limitation, we first prove that the alignment objective is upper-bounded by the mutual information between the input graphs and their hidden representations in the LLM, which motivates us to improve this upper bound to achieve better alignment. To this end, we further propose a reconstructive graph instruction tuning pipeline, RGLM. Our key idea is to reconstruct the graph information from the LLM's graph token outputs, explicitly incorporating graph supervision to constrain the alignment process. Technically, we embody RGLM by exploring three distinct variants from two complementary perspectives: RGLM-Decoder from the input space; RGLM-Similarizer and RGLM-Denoiser from the latent space. Additionally, we theoretically analyze the alignment effectiveness of each variant. Extensive experiments on various benchmarks and task scenarios validate the effectiveness of the proposed RGLM, paving the way for new directions in GTokenLLMs' alignment research.

cs.CL↗
arXiv2026

Multimodal Generative Retrieval Model with Staged Pretraining for Food Delivery on Meituan

Multimodal retrieval models are becoming increasingly important in scenarios such as food delivery, where rich multimodal features can meet diverse user needs and enable precise retrieval. Mainstream approaches typically employ a dual-tower architecture between queries and items, and perform joint optimization of intra-tower and inter-tower tasks. However, we observe that joint optimization often leads to certain modalities dominating the training process, while other modalities are neglected. In addition, inconsistent training speeds across modalities can easily result in the one-epoch problem. To address these challenges, we propose a staged pretraining strategy, which guides the model to focus on specialized tasks at each stage, enabling it to effectively attend to and utilize multimodal features, and allowing flexible control over the training process at each stage to avoid the one-epoch problem. Furthermore, to better utilize the semantic IDs that compress high-dimensional multimodal embeddings, we design both generative and discriminative tasks to help the model understand the associations between SIDs, queries, and item features, thereby improving overall performance. Extensive experiments on large-scale real-world Meituan data demonstrate that our method achieves improvements of 3.80%, 2.64%, and 2.17% on R@5, R@10, and R@20, and 5.10%, 4.22%, and 2.09% on N@5, N@10, and N@20 compared to mainstream baselines. Online A/B testing on the Meituan platform shows that our approach achieves a 1.12% increase in revenue and a 1.02% increase in click-through rate, validating the effectiveness and superiority of our method in practical applications.

cs.IR↗
arXiv2026

Spattack: Subgroup Poisoning Attacks on Federated Recommender Systems

Federated recommender systems (FedRec) have emerged as a promising approach to provide personalized recommendations while protecting user privacy. However, recent studies have shown their vulnerability to poisoning attacks, where malicious clients inject crafted gradients to promote target items to benign users. Existing attacks typically target the full user group, which compromises stealth and increases detection risk. In contrast, real-world adversaries may prefer to target specific user subgroups, such as promoting health supplements to older individuals, to maximize effectiveness while preserving stealth. Motivated by this gap, we introduce Spattack, the first poisoning attack designed to manipulate recommendations for specific user subgroups in federated settings. Spattack adopts an approximate-and-promote paradigm, which approximates user embeddings of target and non-target subgroups and then promotes target items to the target subgroup. We further reveal a trade-off between strong attack performance on the target subgroup and limited impact on the non-target subgroup. To achieve a better trade-off, we propose enhanced approximation and promotion strategies. For approximation, we push embeddings of different subgroups apart via contrastive learning and augment the target subgroup's relevant item set through clustering. For promotion, we align embeddings of target items and relevant items to strengthen their semantic connections, together with an adaptive weighting strategy to balance effects across subgroups. Experiments on three real-world datasets demonstrate that Spattack achieves strong attack performance on the target subgroup with minimal impact on non-target users, even when only 0.1% of users are malicious. Moreover, Spattack maintains competitive recommendation performance and shows strong resilience against mainstream defenses.

cs.CR↗
arXiv2026

Data-centric Prompt Tuning for Dynamic Graphs

Dynamic graphs have attracted increasing attention due to their ability to model complex and evolving relationships in real-world scenarios. Traditional approaches typically pre-train models using dynamic link prediction and directly apply the resulting node temporal embeddings to specific downstream tasks. However, the significant differences among downstream tasks often lead to performance degradation, especially under few-shot settings. Prompt tuning has emerged as an effective solution to this problem. Existing prompting methods are often strongly coupled with specific model architectures or pretraining tasks, which makes it difficult to adapt to recent or future model designs. Moreover, their exclusive focus on modifying node or temporal features while neglecting spatial structural information leads to limited expressiveness and degraded performance. To address these limitations, we propose DDGPrompt, a data-centric prompting framework designed to effectively refine pre-trained node embeddings at the input data level, enabling better adaptability to diverse downstream tasks. We first define a unified node expression feature matrix that aggregates all relevant temporal and structural information of each node, ensuring compatibility with a wide range of dynamic graph models. Then, we introduce three prompt matrices (temporal bias, edge weight, and feature mask) to adjust the feature matrix completely, achieving task-specific adaptation of node embeddings. We evaluate DDGPrompt under a strict few-shot setting on four public dynamic graph datasets. Experimental results demonstrate that our method significantly outperforms traditional methods and prompting approaches in scenarios with limited labels and cold-start conditions.

cs.LG↗
arXiv2025

Restoring Network Evolution from Static Structure

The dynamical evolution of complex networks underpins the structure-function relationships in natural and artificial systems. Yet, restoring a network's formation from a single static snapshot remains challenging. Here, we present a transferable machine learning framework that infers network evolutionary trajectories solely from present topology. By integrating graph neural networks with transformers, our approach unlocks a latent temporal dimension directly from the static topology. Evaluated across diverse domains, the framework achieves high transfer accuracy of up to 95.3%, demonstrating its robustness and transferability. Applied to the Drosophila brain connectome, it restores the formation times of over 2.6 million neural connections, revealing that early-forming links support essential behaviors such as mating and foraging, whereas later-forming connections underpin complex sensory and social functions. These results demonstrate that a substantial fraction of evolutionary information is encoded within static network architecture, offering a powerful, general tool for elucidating the hidden temporal dynamics of complex systems.

physics.soc-ph↗
arXiv2025

Bridging Code Graphs and Large Language Models for Better Code Understanding

Large Language Models (LLMs) have demonstrated remarkable performance in code intelligence tasks such as code generation, summarization, and translation. However, their reliance on linearized token sequences limits their ability to understand the structural semantics of programs. While prior studies have explored graphaugmented prompting and structure-aware pretraining, they either suffer from prompt length constraints or require task-specific architectural changes that are incompatible with large-scale instructionfollowing LLMs. To address these limitations, this paper proposes CGBridge, a novel plug-and-play method that enhances LLMs with Code Graph information through an external, trainable Bridge module. CGBridge first pre-trains a code graph encoder via selfsupervised learning on a large-scale dataset of 270K code graphs to learn structural code semantics. It then trains an external module to bridge the modality gap among code, graph, and text by aligning their semantics through cross-modal attention mechanisms. Finally, the bridge module generates structure-informed prompts, which are injected into a frozen LLM, and is fine-tuned for downstream code intelligence tasks. Experiments show that CGBridge achieves notable improvements over both the original model and the graphaugmented prompting method. Specifically, it yields a 16.19% and 9.12% relative gain in LLM-as-a-Judge on code summarization, and a 9.84% and 38.87% relative gain in Execution Accuracy on code translation. Moreover, CGBridge achieves over 4x faster inference than LoRA-tuned models, demonstrating both effectiveness and efficiency in structure-aware code understanding.

cs.CL↗
arXiv2025

GMoE: Empowering LLMs Fine-Tuning via MoE Graph Collaboration

The sparse Mixture-of-Experts (MoE) architecture of large language models (LLMs) confronts an inherent issue of load imbalance arising from the simplistic linear router strategy, which ultimately causes the instability and inefficient learning of LLMs. To address this challenge, we introduce a novel MoE graph-based framework $\textbf{GMoE}$, aimed at enhancing the collaboration among multiple experts. In GMoE, a graph router function is designed to capture the collaboration signals among experts. This enables all experts to dynamically allocate information derived from input data by sharing information with their neighboring experts. Moreover, we put forward two coordination strategies in GMoE: the $\textit{Poisson distribution-based distinction strategy}$ and the $\textit{Normal distribution-based balance strategy}$, to further release the capacity of each expert and increase the model stability in the fine-tuning of LLMs. Specifically, we leverage a parameter-efficient fine-tuning technique, i.e., Low-Rank Adaptation (LoRA), to implement the graph MoE architecture. Extensive experiments on four real-world benchmark datasets demonstrate the effectiveness of GMoE, showing the benefits of facilitating collaborations of multiple experts in LLM fine-tuning. The code of experimental implementation is available at https://github.com/BAI-LAB/GMoE

cs.LG↗
arXiv2025

Large Language Model Enhanced Graph Invariant Contrastive Learning for Out-of-Distribution Recommendation

Out-of-distribution (OOD) generalization has emerged as a significant challenge in graph recommender systems. Traditional graph neural network algorithms often fail because they learn spurious environmental correlations instead of stable causal relationships, leading to substantial performance degradation under distribution shifts. While recent advancements in Large Language Models (LLMs) offer a promising avenue due to their vast world knowledge and reasoning capabilities, effectively integrating this knowledge with the fine-grained topology of specific graphs to solve the OOD problem remains a significant challenge. To address these issues, we propose {$\textbf{Inv}$ariant $\textbf{G}$raph $\textbf{C}$ontrastive Learning with $\textbf{LLM}$s for Out-of-Distribution Recommendation (InvGCLLM)}, an innovative causal learning framework that synergistically integrates the strengths of data-driven models and knowledge-driven LLMs. Our framework first employs a data-driven invariant learning model to generate causal confidence scores for each user-item interaction. These scores then guide an LLM to perform targeted graph refinement, leveraging its world knowledge to prune spurious connections and augment missing causal links. Finally, the structurally purified graphs provide robust supervision for a causality-guided contrastive learning objective, enabling the model to learn representations that are resilient to spurious correlations. Experiments conducted on four public datasets demonstrate that InvGCLLM achieves significant improvements in out-of-distribution recommendation, consistently outperforming state-of-the-art baselines.

cs.IR↗
arXiv2025

PathRAG: Pruning Graph-based Retrieval Augmented Generation with Relational Paths

Retrieval-augmented generation (RAG) improves the response quality of large language models (LLMs) by retrieving knowledge from external databases. Typical RAG approaches split the text database into chunks, organizing them in a flat structure for efficient searches. To better capture the inherent dependencies and structured relationships across the text database, researchers propose to organize textual information into an indexing graph, known asgraph-based RAG. However, we argue that the limitation of current graph-based RAG methods lies in the redundancy of the retrieved information, rather than its insufficiency. Moreover, previous methods use a flat structure to organize retrieved information within the prompts, leading to suboptimal performance. To overcome these limitations, we propose PathRAG, which retrieves key relational paths from the indexing graph, and converts these paths into textual form for prompting LLMs. Specifically, PathRAG effectively reduces redundant information with flow-based pruning, while guiding LLMs to generate more logical and coherent responses with path-based prompting. Experimental results show that PathRAG consistently outperforms state-of-the-art baselines across six datasets and five evaluation dimensions. The code is available at the following link: https://github.com/BUPT-GAMMA/PathRAG

cs.CL↗