LLMs for Graph Learning

Graphs provide a natural description of the complex relationships among objects, and play a pivotal role in communications, transportation, social computing, the life sciences, etc. Currently, there is strong agreement that Graph Foundation Models (GFMs) are essential for advancing graph learning, yet considerable disagreement persists on how to build a powerful, general-purpose GFM analogous to Large Language Models (LLMs). Graph Neural Networks (GNNs) exhibit limitations in memory retention and principled interpretability when confronted with multi-domain pretraining and adaptation. The challenge of graph serialization hinders the direct application of LLMs, as the words struggle to capture the structural complexity and diversity inherent in graphs. In contrast, Riemannian geometry offers an elegant mathematical framework for modeling structures, while remaining compatible with graph semantic learning, even with LLMs. In this paper, we argue that, for graphs, Riemannian geometry speaks louder than words, and lay out the foundational principles for GFM. Reimagining with Riemannian geometry, we introduce a blue sky idea-Riemannian Foundation Model (RFM)-that opens a new pathway for capturing complex structural patterns and uncovering cross-domain generalities. RFM emphasizes intrinsic graph geometry and embodies endogenous capacities for structural inference and generation, moving beyond mere representation-space switching. Accordingly, we outline a progressive agenda that begins with universal structural understanding through intrinsic geometry, and then rebuilds LLM with a Riemannian engine for general-purpose graph modeling and beyond. Thus, RFM enables a paradigm shift from designing graph models to solving graph-structured applications with RFM agents, unlocking the next-generation graph intelligence.

Text-rich graphs, which integrate complex structural dependencies with abundant textual information, are ubiquitous yet remain challenging for existing learning paradigms. Conventional methods and even LLM-hybrids compress rich text into static embeddings or summaries before structural reasoning, creating an information bottleneck and detaching updates from the raw content. We argue that in text-rich graphs, the text is not merely a node attribute but the primary medium through which structural relationships are manifested. We introduce RAMP, a Raw-text Anchored Message Passing approach that moves beyond using LLMs as mere feature extractors and instead recasts the LLM itself as a graph-native aggregation operator. RAMP exploits the text-rich nature of the graph via a novel dual-representation scheme: it anchors inference on each node's raw text during each iteration while propagating dynamically optimized messages from neighbors. It further handles both discriminative and generative tasks under a single unified generative formulation. Extensive experiments show that RAMP effectively bridges the gap between graph propagation and deep text reasoning, achieving competitive performance and offering new insights into the role of LLMs as graph kernels for general-purpose graph learning.

Dynamic graph clustering aims to detect and track time-varying clusters in dynamic graphs, revealing how complex real-world systems evolve over time. However, existing methods are predominantly black-box models. They lack interpretability in their clustering decisions and fail to provide semantic explanations of why clusters form or how they evolve, severely limiting their use in safety-critical domains such as healthcare or transportation. To address these limitations, we propose an end-to-end interpretable framework that maps continuous graph embeddings into discrete semantic concepts through learnable prototypes. Specifically, we first decompose node representations into orthogonal role and clustering subspaces, so that nodes with similar roles (e.g., hubs, bridges) but different cluster affiliations can be properly distinguished. We then introduce five node role prototypes (Leader, Contributor, Wanderer, Connector, Newcomer) in the role subspace as semantic anchors, transforming continuous embeddings into discrete concepts to facilitate LLM understanding of node roles within communities. Finally, we design a hierarchical LLM reasoning mechanism to generate both clustering results and natural language explanations, while providing consistency feedback as weak supervision to refine node representations. Experimental results on four synthetic and six real-world benchmarks demonstrate the effectiveness, interpretability, and robustness of DyG-RoLLM. Code is available at https://github.com/Clearloveyuan/DyG-RoLLM.

Knowledge Graphs (KGs) are widely used to represent structured knowledge, yet their automatic construction, especially with Large Language Models (LLMs), often results in incomplete or noisy outputs. Knowledge Graph Completion (KGC) aims to infer and add missing triples, but most existing methods either rely on structural embeddings that overlook semantics or language models that ignore the graph's structure and depend on external sources. In this work, we present OMNIA, a two-stage approach that bridges structural and semantic reasoning for KGC. It first generates candidate triples by clustering semantically related entities and relations within the KG, then validates them through lightweight embedding filtering followed by LLM-based semantic validation. OMNIA performs on the internal KG, without external sources, and specifically targets implicit semantics that are most frequent in LLM-generated graphs. Extensive experiments on multiple datasets demonstrate that OMNIA significantly improves F1-score compared to traditional embedding-based models. These results highlight OMNIA's effectiveness and efficiency, as its clustering and filtering stages reduce both search space and validation cost while maintaining high-quality completion.

Large Language Models (LLMs) have shown strong performance on text-attributed graphs (TAGs) due to their superior semantic understanding ability on textual node features. However, their effectiveness as predictors in the low-resource setting, where labeled nodes are severely limited and scarce, remains constrained since fine-tuning LLMs usually requires sufficient labeled data, especially when the TAG shows complex structural patterns. In essence, this paper targets two key challenges: (i) the difficulty of generating and selecting reliable pseudo labels on TAGs for LLMs, and (ii) the need to mitigate potential label noise when fine-tuning LLMs with pseudo labels. To counter the challenges, we propose a new framework, GNN-as-Judge, which can unleash the power of LLMs for few-shot semi-supervised learning on TAGs by incorporating the structural inductive bias of Graph Neural Networks (GNNs). Specifically, GNN-as-Judge introduces a collaborative pseudo-labeling strategy that first identifies the most influenced unlabeled nodes from labeled nodes, then exploits both the agreement and disagreement patterns between LLMs and GNNs to generate reliable labels. Furthermore, we develop a weakly-supervised LLM fine-tuning algorithm that can distill the knowledge from informative pseudo labels while mitigating the potential label noise. Experiments on multiple TAG datasets demonstrate that GNN-as-Judge significantly outperforms existing methods, particularly in low-resource regimes where labeled data are scarce.

The rapid rise of large language models (LLMs) and their ability to capture semantic relationships has led to their adoption in a wide range of applications. Text-attributed graphs (TAGs) are a notable example where LLMs can be combined with Graph Neural Networks to improve the performance of node classification. In TAGs, each node is associated with textual content and such graphs are commonly seen in various domains such as social networks, citation graphs, recommendation systems, etc. Effectively learning from TAGs would enable better representations of both structural and textual representations of the graph and improve decision-making in relevant domains. We present GaLoRA, a parameter-efficient framework that integrates structural information into LLMs. GaLoRA demonstrates competitive performance on node classification tasks with TAGs, performing on par with state-of-the-art models with just 0.24% of the parameter count required by full LLM fine-tuning. We experiment with three real-world datasets to showcase GaLoRA's effectiveness in combining structural and semantical information on TAGs.

Scholarly web is a vast network of knowledge connected by citations. However, this system is increasingly compromised by miscitation, where references do not support or even contradict the claims they are cited for. Current miscitation detection methods, which primarily rely on semantic similarity or network anomalies, struggle to capture the nuanced relationship between a citation's context and its place in the wider network. While large language models (LLMs) offer powerful capabilities in semantic reasoning for this task, their deployment is hindered by hallucination risks and high computational costs. In this work, we introduce LLM-Augmented Graph Learning-based Miscitation Detector (LAGMiD), a novel framework that leverages LLMs for deep semantic reasoning over citation graphs and distills this knowledge into graph neural networks (GNNs) for efficient and scalable miscitation detection. Specifically, LAGMiD introduces an evidence-chain reasoning mechanism, which uses chain-of-thought prompting, to perform multi-hop citation tracing and assess semantic fidelity. To reduce LLM inference costs, we design a knowledge distillation method aligning GNN embeddings with intermediate LLM reasoning states. A collaborative learning strategy further routes complex cases to the LLM while optimizing the GNN for structure-based generalization. Experiments on three real-world benchmarks show that LAGMiD achieves state-of-the-art miscitation detection with significantly reduced inference cost.

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.

Leveraging Large Language Models (LLMs) for Knowledge Graph Completion (KGC) is promising but hindered by a fundamental granularity mismatch. LLMs operate on fragmented token sequences, whereas entities are the fundamental units in knowledge graphs (KGs) scenarios. Existing approaches typically constrain predictions to limited candidate sets or align entities with the LLM's vocabulary by pooling multiple tokens or decomposing entities into fixed-length token sequences, which fail to capture both the semantic meaning of the text and the structural integrity of the graph. To address this, we propose KGT, a novel framework that uses dedicated entity tokens to enable efficient, full-space prediction. Specifically, we first introduce specialized tokenization to construct feature representations at the level of dedicated entity tokens. We then fuse pre-trained structural and textual features into these unified embeddings via a relation-guided gating mechanism, avoiding training from scratch. Finally, we implement decoupled prediction by leveraging independent heads to separate and combine semantic and structural reasoning. Experimental results show that KGT consistently outperforms state-of-the-art methods across multiple benchmarks.

Knowledge graph reasoning (KGR) infers missing facts, with recent advances increasingly harnessing the semantic priors and reasoning abilities of Large Language Models (LLMs). However, prevailing generative paradigms are prone to memorizing surface-level co-occurrences rather than learning genuine relational semantics, limiting out-of-distribution generalization. To address this, we propose RADAR, which reformulates KGR from generative pattern matching to discriminative relational reasoning. We recast KGR as discriminative entity selection, where reinforcement learning enforces relative entity separability beyond token-likelihood imitation. Leveraging this separability, inference operates directly in representation space, ensuring consistency with the discriminative optimization and bypassing generation-induced hallucinations. Across four benchmarks, RADAR achieves 5-6% relative gains on link prediction and triple classification over strong LLM baselines, while increasing task-relevant mutual information in intermediate representations by 62.9%, indicating more robust and transferable relational reasoning.

Temporal knowledge graphs (TKGs) support reasoning over time-evolving facts, yet state-of-the-art models are often computationally heavy and costly to deploy. Existing compression and distillation techniques are largely designed for static graphs; directly applying them to temporal settings may overlook time-dependent interactions and lead to performance degradation. We propose an LLM-assisted distillation framework specifically designed for temporal knowledge graph reasoning. Beyond a conventional high-capacity temporal teacher, we incorporate a large language model as an auxiliary instructor to provide enriched supervision. The LLM supplies broad background knowledge and temporally informed signals, enabling a lightweight student to better model event dynamics without increasing inference-time complexity. Training is conducted by jointly optimizing supervised and distillation objectives, using a staged alignment strategy to progressively integrate guidance from both teachers. Extensive experiments on multiple public TKG benchmarks with diverse backbone architectures demonstrate that the proposed approach consistently improves link prediction performance over strong distillation baselines, while maintaining a compact and efficient student model. The results highlight the potential of large language models as effective teachers for transferring temporal reasoning capability to resource-efficient TKG systems.

The emergence of large language models (LLMs) has popularized text-attributed graphs (TAGs), creating an urgent need for graph structure learning (GSL) methods that effectively leverage textual information. However, existing GSL approaches are designed for traditional graphs without text, and adapting them to LLMs faces two challenges: defining a suitable optimization objective given LLMs' massive parameters, and designing an efficient architecture without costly fine-tuning. To address these, we propose LLaTA (Large Language and Tree Assistant), which reformulates GSL as a tree optimization framework---shifting from training edge predictors to designing a language-aware tree sampler. LLaTA constructs structural encoding trees via entropy minimization to capture topology, then leverages tree-guided LLM in-context learning to integrate textual semantics without fine-tuning. Extensive experiments on 11 datasets demonstrate LLaTA's flexibility with any backbone, superior scalability over LLM-based GSL methods, and state-of-the-art effectiveness across diverse domains.

Text-Attributed Graphs (TAGs), where each node is associated with text descriptions, are ubiquitous in real-world scenarios. They typically exhibit distinctive structure and domain-specific knowledge, motivating the development of a Graph Foundation Model (GFM) that generalizes across diverse graphs and tasks. Despite large efforts to integrate Large Language Models (LLMs) and Graph Neural Networks (GNNs) for TAGs, existing approaches suffer from decoupled architectures with two-stage alignment, limiting their synergistic potential. Even worse, existing methods assign out-of-vocabulary (OOV) tokens to graph nodes, leading to graph-specific semantics, token explosion, and incompatibility with task-oriented prompt templates, which hinders cross-graph and cross-task transferability. To address these challenges, we propose PromptGFM, a versatile GFM for TAGs grounded in graph vocabulary learning. PromptGFM comprises two key components: (1) Graph Understanding Module, which explicitly prompts LLMs to replicate the finest GNN workflow within the text space, facilitating seamless GNN-LLM integration and elegant graph-text alignment; (2) Graph Inference Module, which establishes a language-based graph vocabulary ensuring expressiveness, transferability, and scalability, enabling readable instructions for LLM fine-tuning. Extensive experiments demonstrate our superiority and transferability across diverse graphs and tasks. The code is available at this: https://github.com/agiresearch/PromptGFM.

Cryptocurrencies are widely used, yet current methods for analyzing transactions often rely on opaque, black-box models. While these models may achieve high performance, their outputs are usually difficult to interpret and adapt, making it challenging to capture nuanced behavioral patterns. Large language models (LLMs) have the potential to address these gaps, but their capabilities in this area remain largely unexplored, particularly in cybercrime detection. In this paper, we test this hypothesis by applying LLMs to real-world cryptocurrency transaction graphs, with a focus on Bitcoin, one of the most studied and widely adopted blockchain networks. We introduce a three-tiered framework to assess LLM capabilities: foundational metrics, characteristic overview, and contextual interpretation. This includes a new, human-readable graph representation format, LLM4TG, and a connectivity-enhanced transaction graph sampling algorithm, CETraS. Together, they significantly reduce token requirements, transforming the analysis of multiple moderately large-scale transaction graphs with LLMs from nearly impossible to feasible under strict token limits. Experimental results demonstrate that LLMs have outstanding performance on foundational metrics and characteristic overview, where the accuracy of recognizing most basic information at the node level exceeds 98.50% and the proportion of obtaining meaningful characteristics reaches 95.00%. Regarding contextual interpretation, LLMs also demonstrate strong performance in classification tasks, even with very limited labeled data, where top-3 accuracy reaches 72.43% with explanations. While the explanations are not always fully accurate, they highlight the strong potential of LLMs in this domain. At the same time, several limitations persist, which we discuss along with directions for future research.