arXiv subjects

Di Jin

Publications and source records attributed to Di Jin.

At least 19 recordsLinked to original sources

arXiv2026

Query Entity-Oriented Graph Neural Networks for Knowledge Graph Completion

Knowledge Graph Completion (KGC) aims at predicting missing triplets from incomplete knowledge graphs, which is crucial for downstream applications. Recently, Graph Neural Network (GNN)-based methods have achieved remarkable success by performing message passing over a local subgraph centered on the query entity. In these methods, the query relation conditions message computation and aggregation, whereas the query entity serves only as a structural anchor for subgraph extraction. The query relation thus constitutes the sole explicit signal for evidence selection, even though the relevant evidence for the same relation can differ substantially across query entities. We propose Q-GNN, which incorporates the query entity as an explicit conditioning signal. Q-GNN characterizes the query entity by its local structural context and semantic type, and thus remains applicable in the inductive setting. The structural context, encoded by a dedicated encoder, modulates each message through feature-wise linear modulation, while the semantic type guides neighborhood attention and candidate scoring. Experiments in both transductive and inductive settings demonstrate the effectiveness of the proposed method.

cs.LG↗

arXiv2026

Federated Graph Retrieval-Augmented Generation

Graph Retrieval-Augmented Generation (GraphRAG) leverages centralized knowledge graphs to enhance large language models with structured knowledge retrieval. However, real-world knowledge is inherently distributed across multiple organizations rather than being centrally accessible. Privacy constraints further prohibit sharing entire local knowledge graphs, preventing GraphRAG from effectively retrieving and utilizing distributed knowledge. To this end, we propose Federated GraphRAG (FedGRAG), a unified framework for distributed graph retrieval and knowledge-enhanced generation over multiple clients with knowledge graphs. Specifically, we address two fundamental challenges in federated GraphRAG. First, the absence of a global knowledge graph makes unified retrieval impossible. To address this, we develop a Federated Knowledge Routing mechanism that efficiently identifies relevant clients through lightweight knowledge indices without exposing local graph structures. Second, local graph memory cannot be shared directly because it contains sensitive entities and knowledge information. We therefore propose a controlled-disclosure evidence construction method. It extracts retrieved evidence subgraphs and converts them into an evidence abstract, enabling evidence conversion and reconstruction on the server. Extensive experiments demonstrate that Federated GraphRAG consistently outperforms existing baselines in both retrieval and downstream generation tasks, establishing a new paradigm for deploying GraphRAG in federated environments.

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arXiv2026

Eigen-Agent: Adaptive Multi-Agent Scientific Reasoning with Monitor-Based RAG

Large language models (LLMs) have recently shown strong progress on scientific reasoning, yet two major bottlenecks remain. First, explicit retrieval fragments reasoning, imposing a hidden "tool tax" of extra tokens and steps. Second, multi-agent pipelines often dilute strong solutions by averaging across all candidates. We address these challenges with a unified framework that combines implicit retrieval and structured collaboration. At its foundation, a Monitor-based retrieval module operates at the token level, integrating external knowledge with minimal disruption to reasoning. On top of this substrate, Hierarchical Solution Refinement (HSR) iteratively designates each candidate as an anchor to be repaired by its peers, while Quality-Aware Iterative Reasoning (QAIR) adapts refinement to solution quality. On Humanity's Last Exam (HLE) Bio/Chem Gold, our framework achieves 48.3% accuracy - the highest reported to date, surpassing the strongest agent baseline by 13.4 points and leading frontier LLMs by up to 18.1 points, while simultaneously reducing token usage by 53.5% and agent steps by 43.7%. Results on SuperGPQA and TRQA confirm robustness across domains. Error analysis shows that reasoning failures and knowledge gaps co-occur in over 85% of cases, while diversity analysis reveals a clear dichotomy: retrieval tasks benefit from solution variety, whereas reasoning tasks favor consensus. Together, these findings demonstrate how implicit augmentation and structured refinement overcome the inefficiencies of explicit tool use and uniform aggregation. The code is available at https://github.com/tangxiangru/Eigen-1.

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arXiv2026

DeKoR: Decomposed Knowledge Routing for Efficient GNN--LLM Fusion

Large Language Models (LLMs) have shown strong potential for text-attributed graph learning by leveraging rich pre-trained knowledge and language understanding capabilities. Combining LLMs with Graph Neural Networks (GNNs) offers a promising paradigm for expanding the modeling capabilities of graph learning. However, LLMs and GNNs follow distinct learning paradigms, leading to a pronounced mismatch between their knowledge spaces. Such discrepancies make effective knowledge fusion nontrivial. Moreover, existing methods often incur substantial additional computation for only limited performance gains. To address these challenges, we propose DeKoR, an efficient framework for GNN and LLM knowledge fusion. To enable efficient knowledge transfer, DeKoR decomposes LLM knowledge into complementary local and global views and uses the LLM as an offline teacher to distill them into lightweight experts. To enable selective knowledge fusion, an adaptive router learns how much each node should rely on each expert. Extensive experiments on multiple benchmarks demonstrate that DeKoR outperforms existing baselines on both node and subgraph classification, achieving superior effectiveness and efficiency.

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arXiv2026

More Domains, No Gains? FLO: Fast-Slow Reciprocal Learning for Multi-Domain Graph Pre-training

Inspired by the great success of foundation models in the development of artificial general intelligence, Graph Foundation Models (GFMs) have recently attracted significant attention and have the potential to advance graph intelligence. Exhibiting such intelligence requires effectively learning knowledge from large-scale, multi-domain graph data during pre-training. Increasing domain diversity during pre-training is expected to yield richer and more generalizable knowledge. Most existing methods pursue this goal by designing domain alignment strategies that help a single graph model learn from multiple domains. However, we observe that existing methods struggle to benefit from increasing domain diversity. Through empirical and theoretical analysis, we reveal two key limitations. Firstly, pre-training in most GFMs is confined to a single message-passing paradigm. Since propagation flattens relations among neighboring nodes, the graph model can hardly perceive the knowledge beyond propagation, namely the attribute-predictable component of these relations. Secondly, domain alignment strategies often rely on randomly initialized parameters that are jointly updated with the graph model using immediate loss feedback, leaving early knowledge acquisition vulnerable to cross-domain interference. To address these issues, we propose FLO, a Fast--sLow reciprOcal approach for multi-domain graph pre-training. Specifically, a propagation-free attribute branch predicts the graph model's relations without message passing and returns these predictions to refine the model. We further stabilize knowledge acquisition by pairing a fast process that adapts to the current domain with a slow process that integrates knowledge across domains. On 12 datasets, FLO benefits from increasing domain diversity and achieves the best average performance in cross-domain and cross-task transfer.

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arXiv2026

SPR: Toward a Graph Foundation Model for Transferable Graph Cognition via Spectral Patterns and Relational Geometry

Recently, Graph Foundation Models (GFMs) have attracted increasing attention for their potential to learn unified and generalizable knowledge across diverse graphs, thereby supporting a wide range of graph scenarios. However, unlike natural language and images, graphs lack an intuitive and unified form for perceiving and organizing transferable knowledge. Therefore, despite many initial explorations, a key problem remains unresolved: the transferable cognitive mechanism for graphs. Existing GFMs usually rely on intuitively defined mechanisms to encode transferable graph patterns, such as handcrafted structural templates (e.g., cycles and trees), fixed propagation mechanisms, and predefined random-walk patterns. These mechanisms are often prescriptive and rigid, limiting their ability to flexibly characterize diverse graph patterns across domains. This motivates the exploration of a more flexible, graph-native, and transferable cognitive mechanism. To this end, we analyze graphs from the spectral perspective and propose SPR. SPR decomposes graph information into Chebyshev polynomial bases and learns shared spectral responses, enabling unified yet adaptive cognition of continuously varying spectral patterns across graphs. We further model cross-graph relational geometry to distill recurring pairwise organization from multiple graphs, providing a shared relational reference for transferring such graph cognition across domains. Extensive experiments across diverse graphs and downstream scenarios demonstrate that SPR enables effective and transferable graph cognition.

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arXiv2026

EnterpriseRAG: Benchmarking LLM Instruction Adherence and Robustness under Non-Ideal Enterprise Retrieval

Enterprise RAG deployments face a critical reliability gap: while LLMs satisfy 80% of individual constraints, only 26.8% of responses meet all requirements simultaneously, revealing a 57-point orchestration gap. Existing benchmarks assume clean retrieval with simple queries, failing to capture production conditions where noisy documents and multi-dimensional constraints coexist. We introduce EnterpriseRAG, a benchmark of 983 expert-validated samples across six domains that systematically simulates three failure modes absent from prior work: retrieval noise, knowledge gaps, and factual conflicts, coupled with complex instructions. Evaluation of 13 state-of-the-art LLMs reveals a severe instruction adherence collapse, where high per-constraint satisfaction masks low holistic compliance. Critical findings expose deep barriers under knowledge gaps and factual conflicts, even with reasoning-enhanced inference, indicating production RAG requires explicit context-aware protocols and calibrated judgment. EnterpriseRAG provides a reproducible foundation for measuring and closing these gaps, directly informing deployment decisions for enterprise-scale RAG systems. We will release the benchmark and evaluation framework upon publication.

cs.AI↗

arXiv2026

Beyond Feature and Structure Alignment: Learning Transferable Propagation Knowledge for Graph Foundation Models

Graph Foundation Models (GFMs) have recently emerged as a promising paradigm for enabling knowledge transfer across diverse domains. Unlike traditional graph learning methods that are typically designed for in-domain settings, GFMs aim to learn transferable knowledge that can generalize to unseen graph domains. However, unlike language or visual data, graphs lack intrinsic and unified representation units, such as tokens in language and patches in vision, making it challenging to identify transferable knowledge units for building graph foundation models. Existing graph foundation models mainly focus on mitigating domain discrepancies through feature alignment and structure alignment, while overlooking the exploration of transferable knowledge units underlying graph data. Moreover, these methods generally rely on fixed propagation mechanisms during message passing, overlooking the heterogeneity in propagation patterns, as different edges may exhibit distinct propagation patterns for different feature dimensions. To address these limitations, we propose a Propagation-aware Graph Foundation Model (ProGFM), which regards the propagation relationships between edges and feature dimensions as transferable knowledge units. Through a propagation relationship prototype bank, ProGFM learns cross-domain transferable propagation knowledge, enabling adaptive information aggregation in unseen graph domains. Extensive experiments across various cross-domain transfer scenarios demonstrate that ProGFM possesses strong cross-domain knowledge transfer capability and exhibits superior generalization performance compared with existing methods.

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arXiv2026

Towards Multi-Label Graph Foundation Models: from Single-Vector Representation Learning to Multi-Semantic Basis Learning

Multi-label node classification is an important yet challenging task in graph learning, where nodes exhibit multiple semantics simultaneously. Existing methods for multi-label node classification can effectively model multiple labels, while only considering in-domain scenarios where the model needs to be trained and tested within the same graph domain, resulting in limited cross-domain generalization. Recently, Graph Foundation Models (GFMs) have emerged as a promising paradigm for learning transferable graph representations across diverse graph domains and downstream tasks. However, existing GFMs are built upon single-label assumption, where all nodes are arbitrarily regarded as containing only one class of semantic and embedded into a single representation. For multi-label nodes, such a representation essentially approximates multiple semantics with a single point in the representation space, inevitably leading to semantic entanglement and making simultaneous discrimination of multiple labels difficult. To address these limitations, we propose a Multi-Semantic Basis Graph Foundation Model (MSB-GFM), a framework for cross-domain multi-label node classification. Specifically, we introduce a multi-semantic basis representation learning paradigm that models each multi-label node as an adaptive composition of semantic bases, thereby enabling flexible representational capacity for modeling multiple semantics. Furthermore, we develop a semantic-structure dual-channel architecture with domain adversarial training for effective cross-domain knowledge transfer. Extensive experiments demonstrate the effectiveness of our model.

cs.AI↗

arXiv2026

What Makes Graph Unified? Principles and Generative Sliding-Window Transformer for Graph Foundation Models

Graph Foundation Models (GFMs) have recently emerged as a promising paradigm for general-purpose graph learning, aiming to learn reusable knowledge that generalizes across diverse graph domains and downstream tasks, reducing the need for specific model development. Achieving this goal requires reconciling the substantial heterogeneity in node features, graph structures, and semantic information across domains. Among them, heterogeneous node features constitute a fundamental input-level barrier, as their dimensionality and semantics vary substantially across datasets. Existing studies typically project or map heterogeneous node features into a fixed-dimensional space, often implicitly equating dimensional uniformity with effective feature unification. Yet dimensional consistency alone does not ensure that the unified features preserve informative semantics and capture transferable patterns that can support cross-domain knowledge transfer. To bridge this conceptual gap, we distill four desiderata for cross-domain graph feature unification: formal uniformity, cross-domain transferability, information preservation, and backbone compatibility. Guided by these principles, we propose SliGFM, a graph foundation model built upon topology-aware sliding-window feature encoding and generative reconstruction. SliGFM orders feature dimensions by topological smoothness and scans the reordered features with a shared sliding-window feature encoder, transforming heterogeneous features into a common space of ordered fixed-dimensional feature tokens. This formulation enables a smoothness-aware transformer to capture transferable relational patterns among feature tokens within each node, while the generative reconstruction objective encourages preservation of the original feature information.

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arXiv2026

AgentGFM: A Graph Foundation Model with Node-Agent Information-Flow Control

Graph Foundation Models (GFMs) aim to learn transferable knowledge from multi-domain graphs and adapt to unseen scenarios. As a fundamental source of relational semantics in graphs, the transferability of topological patterns has long been central to GFM research. However, local structural patterns may vary across graphs and even among nodes within the same graph. Despite such structural variation, most existing GFMs rely on manually designed propagation schemes and apply them to new graphs largely unchanged. Such fixed schemes may not suit the diverse structural patterns of different nodes. This raises a key question: can each node autonomously determine how information should be propagated through the graph? We refer to this capability as information-flow control. Inspired by recent advances in agent technology, we formulate this problem as agent-based decision making and treat each node as an agent. Accordingly, we propose AgentGFM, in which all node agents follow a shared end-to-end trainable policy rather than using independent models. For adaptive information-flow control, each node interacts with the graph through a predict-act-observe-correct process. During the act stage, the node makes three decisions: source reception, signal-channel selection and gain-aware node-wise halting. The resulting observation is compared with the prediction and their discrepancy is used to correct the node state and guide subsequent interactions. Extensive experiments across node-level, graph-level and large-scale transfer scenarios demonstrate the effectiveness of AgentGFM across diverse graph topologies.

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arXiv2026

CHARM: A Multimodal Graph Foundation Model with Hierarchical Context Modeling for Zero-Shot Transfer

Graph foundation models (GFMs) have emerged as a promising paradigm for transferring knowledge across graph domains and tasks. Real-world graphs associate nodes with text, images, and other modalities, making multimodal graphs essential for representing complex entities and relations. Moreover, collecting labels and adapting models for every new graph domain is costly and often infeasible, motivating zero-shot transfer. Unfortunately, zero-shot transfer on multimodal graphs remains underexplored. Existing GNN-based graph foundation models typically require downstream adaptation, whereas LLM-based graph methods mainly address unimodal graphs or tasks within a single domain. This setting presents two key challenges. First, models must generalize knowledge from individual modalities while capturing transferable cross-modal relations. Second, without target-domain fine-tuning, node representations remain entangled with domain-specific structures and modality-specific characteristics, obscuring shared concepts in unseen domains. To address these challenges, we propose CHARM, a multimodal graph foundation model with hierarchical context modeling for zero-shot transfer. CHARM replaces isolated raw nodes with hierarchical graph contexts that capture multimodal semantics and cross-modal relations. These contexts map domain-specific node patterns to shared high-level concepts, reducing reliance on target-domain supervision or adaptation. A modality-aware graph context encoder integrates multimodal information with graph structure and converts the resulting representations into graph tokens for a large language model . Experiments show consistent improvements on zero-shot multimodal graph tasks.

cs.AI↗

arXiv2026

Revisiting Positive Samples in Graph Contrastive Learning: From the Perspective of Message Passing

Graph Contrastive Learning (GCL), which trains graph encoders by maximizing similarity between positive samples and minimizing it between negative ones, has emerged as a mainstream graph pre-training paradigm. It is widely recognized that positive samples are essential in GCLs. Ideally, maximizing the similarity of positive samples enables graph encoders to capture intrinsic semantic and patterns of graph data. However, we discover an interesting phenomenon: GCLs can achieve competitive performance even without positive samples. This motivates us to revisit the fundamental mechanism of positive samples in GCLs. From the perspective of Dirichlet energy, we theoretically finds that message passing, a key mechanism in graph encoders, trivializes the maximization of positive samples, preventing GCLs from effectively learning from positive samples. To address this, we propose SPGCL to mitigate the trivialization caused by message passing and restore the learning efficacy of positive samples. Specifically, we find that high Dirichlet energy features help positive samples provide effective learning signals while low Dirichlet energy features contribute little to positive learning signal but is useful for positive sampling. Based on this, SPGCL propagates only high Dirichlet energy features and uses low energy features to construct a probability matrix for reliable positive sampling. Extensive experiments demonstrate the effectiveness of SPGCL.

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arXiv2026

CHoE: Cross-Domain Heterogeneous Graph Prompt Learning via Structure-Conditioned Experts

Heterogeneous Graph Prompt Learning (HGPL)has emerged as a promising paradigm for bridging the gap between the objectives of pre-training foundation models and their downstream applications in heterogeneous graph settings. However, existing HGPL methods are primarily designed for in-domain scenarios, whereas real-world deployments often span multiple domains, and the data used for pre-training and downstream tasks may originate from different distributions. Consequently, the applicability of current HGPL approaches is limited to in-domain settings, and their performance typically degrades when application domains shift. To address this serious limitation, we develop CHoE, a cross-domain HGPL method built upon an expert network. During pre-training, we introduce and train structure-conditioned experts, and during prompt tuning, we adopt a structure-aware expert routing and load balancing mechanism to select structurally compatible experts for each meta-path view. In addition, we design a prompt-based semantic fusion module to integrate representations across multiple views for downstream prediction. Extensive experiments show that CHoE consistently improves performance in few-shot cross-domain applications, outperforming all baseline approaches.

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arXiv2026

Unified Multi-Domain Graph Pre-training for Homogeneous and Heterogeneous Graphs via Domain-Specific Expert Encoding

Graph pre-training has achieved remarkable success in recent years, delivering transferable representations for downstream adaptation. However, most existing methods are designed for either homogeneous or heterogeneous graphs, thereby hindering unified graph modeling across diverse graph types. This separation contradicts real-world applications, where mixed homogeneous and heterogeneous graphs are ubiquitous, and distribution shifts between upstream pre-training and downstream deployment are common. In this paper, we empirically demonstrate that a balanced mixture of homogeneous and heterogeneous graph pre-training benefits downstream tasks and propose a unified multi-domain \textbf{G}raph \textbf{P}re-training method across \textbf{H}omogeneous and \textbf{H}eterogeneous graphs ($\mathbf{GPH^{2}}$). To address the lack of a unified encoder for homogeneous and heterogeneous graphs, we propose a Unified Multi-View Graph Construction that simultaneously encodes both without explicit graph-type-specific designs. To cope with the increased cross-domain distribution discrepancies arising from mixed graphs, we introduce domain-specific expert encoding. Each expert is independently pre-trained on a single graph to capture domain-specific knowledge, thereby shielding the pre-training encoder from the adverse effects of cross-domain discrepancies. For downstream tasks, we further design a Task-oriented Expert Fusion Strategy that adaptively integrates multiple experts based on their discriminative strengths. Extensive experiments on mixed graphs demonstrate that $\text{GPH}^{2}$ enables stable transfer across graph types and domains, significantly outperforming existing graph pre-training methods.

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arXiv2026

TGFormer: Towards Temporal Graph Transformer with Auto-Correlation Mechanism

The growing interest in Temporal Graph Neural Networks (TGNNs) stems from their ability to model complex dynamics and deliver superior performance. However, TGNNs encounter fundamental challenges in capturing long-term dependencies and identifying periodic patterns. To address these limitations, we propose TGFormer, a novel Transformer architecture specifically designed for temporal graphs. Our model redefines temporal graph learning by establishing a trajectory framework that aligns with time series analysis principles. This approach allows TGFormer to derive node representations through systematic analysis of historical interactions, enabling granular examination of node relationships across sequential timestamps. Building upon stochastic process theory, we develop an auto-correlation mechanism that systematically uncovers periodic dependencies in node interactions. This innovation empowers TGFormer to perform dependency discovery and representation aggregation at sub-interaction levels, demonstrating superior efficiency and accuracy compared to conventional attention mechanisms. Experimental validation across six public benchmarks confirms the effectiveness of our approach, with TGFormer at most achieving 9.35\% precision improvement compared to state-of-the-art approaches.

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arXiv2026

JT-SAFE-V2: Safety-by-Design Foundation Model with World-Context Data

We introduce JT-Safe-V2, a large language model designed to advance the safety and trustworthiness of foundation models, extending our previous JT-Safe model toward a more comprehensive safety-by-design paradigm. JT-Safe-V2 emphasizes the joint optimization of general intelligence and safety-by-design through several key innovations: enriching pre-training data with contextual world knowledge, high-certainty pre-training procedures, and safety strengthening post-training mechanisms for enterprise-oriented agentic capabilities. Building on these safety-enhanced foundation models, we propose Safe-MoMA (Safe Mixture of Models and Agents), a framework that enables traceable and efficient inference through the orchestrated deployment of multiple models and agents. Extensive evaluations demonstrate that JT-Safe-V2 achieves state-of-the-art performance across both general intelligence and safety benchmarks. Moreover, Safe-MoMA reduces inference costs by more than 30\% compared to using the largest standalone model baseline while maintaining comparable performance. To facilitate future research on safety-by-design foundation models, we publicly release the post-trained JT-Safe-V2-35B model checkpoint.

cs.AI↗

arXiv2026

GP2F: Cross-Domain Graph Prompting with Adaptive Fusion of Pre-trained Graph Neural Networks

Graph Prompt Learning (GPL) has recently emerged as a promising paradigm for downstream adaptation of pre-trained graph models, mitigating the misalignment between pre-training objectives and downstream tasks. Recently, the focus of GPL has shifted from in-domain to cross-domain scenarios, which is closer to the real world applications, where the pre-training source and downstream target often differ substantially in data distribution. However, why GPLs remain effective under such domain shifts is still unexplored. Empirically, we observe that representative GPL methods are competitive with two simple baselines in cross-domain settings: full fine-tuning (FT) and linear probing (LP), motivating us to explore a deeper understanding of the prompting mechanism. We provide a theoretical analysis demonstrating that jointly leveraging these two complementary branches yields a smaller estimation error than using either branch alone, formally proving that cross-domain GPL benefits from the integration between pre-trained knowledge and task-specific adaptation. Based on this insight, we propose GP2F, a dual-branch GPL method that explicitly instantiates the two extremes: (1) a frozen branch that retains pre-trained knowledge, and (2) an adapted branch with lightweight adapters for task-specific adaptation. We then perform adaptive fusion under topology constraints via a contrastive loss and a topology-consistent loss. Extensive experiments on cross-domain few-shot node and graph classification demonstrate that our method outperforms existing methods.

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