# LLM as GNN: Graph Vocabulary Learning for Text-Attributed Graph Foundation Models

arXiv: https://arxiv.org/abs/2503.03313 · HTML: https://mlsanity.com/paper/2503.03313/

## Key facts

- Cited by 22 papers in the map (data through 14 Oct 2026).
- Builds on 59 of its 77 references that are in the map.
- First posted on arXiv 5 Mar 2025.

## Builds on (most cited first, 30 of 59)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [Finetuned Language Models Are Zero-Shot Learners](https://mlsanity.com/paper/2109.01652/) (2021)
- [Scaling Instruction-Finetuned Language Models](https://mlsanity.com/paper/2210.11416/) (2022)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [Graph Convolutional Neural Networks for Web-Scale Recommender Systems](https://mlsanity.com/paper/1806.01973/) (2018)
- [Deep Graph Infomax](https://mlsanity.com/paper/1809.10341/) (2018)
- [Cross-Task Generalization via Natural Language Crowdsourcing Instructions](https://mlsanity.com/paper/2104.08773/) (2021)
- [Autoregressive Entity Retrieval](https://mlsanity.com/paper/2010.00904/) (2020)
- [Wiki-CS: A Wikipedia-Based Benchmark for Graph Neural Networks](https://mlsanity.com/paper/2007.02901/) (2020)
- [Can Language Models Solve Graph Problems in Natural Language?](https://mlsanity.com/paper/2305.10037/) (2023)
- [One for All: Towards Training One Graph Model for All Classification Tasks](https://mlsanity.com/paper/2310.00149/) (2023)
- [GraphGPT: Graph Instruction Tuning for Large Language Models](https://mlsanity.com/paper/2310.13023/) (2023)
- [Language is All a Graph Needs](https://mlsanity.com/paper/2308.07134/) (2023)
- [NodeFormer: A Scalable Graph Structure Learning Transformer for Node Classification](https://mlsanity.com/paper/2306.08385/) (2023)
- [LLaGA: Large Language and Graph Assistant](https://mlsanity.com/paper/2402.08170/) (2024)
- [Talk like a Graph: Encoding Graphs for Large Language Models](https://mlsanity.com/paper/2310.04560/) (2023)
- [Training Graph Neural Networks with 1000 Layers](https://mlsanity.com/paper/2106.07476/) (2021)
- [Learning on Large-scale Text-attributed Graphs via Variational Inference](https://mlsanity.com/paper/2210.14709/) (2022)
- [Harnessing Explanations: LLM-to-LM Interpreter for Enhanced Text-Attributed Graph Representation Learning](https://mlsanity.com/paper/2305.19523/) (2023)
- [SGFormer: Simplifying and Empowering Transformers for Large-Graph Representations](https://mlsanity.com/paper/2306.10759/) (2023)
- [GraphText: Graph Reasoning in Text Space](https://mlsanity.com/paper/2310.01089/) (2023)
- [GraphLLM: Boosting Graph Reasoning Ability of Large Language Model](https://mlsanity.com/paper/2310.05845/) (2023)

## Built on by (most cited first, 22 of 22)

- [Two Heads are Better Than One: Test-time Scaling of Multi-agent Collaborative Reasoning](https://mlsanity.com/paper/2504.09772/) (2025)
- [MemRec: Collaborative Memory-Augmented Agentic Recommender System](https://mlsanity.com/paper/2601.08816/) (2026)
- [Towards Effective Federated Graph Foundation Model via Mitigating Knowledge Entanglement](https://mlsanity.com/paper/2505.12684/) (2025)
- [GRAVER: Generative Graph Vocabularies for Robust Graph Foundation Models Fine-tuning](https://mlsanity.com/paper/2511.05592/) (2025)
- [DGP: A Dual-Granularity Prompting Framework for Fraud Detection with Graph-Enhanced LLMs](https://mlsanity.com/paper/2507.21653/) (2025)
- [Towards Graph Foundation Models: A Transferability Perspective](https://mlsanity.com/paper/2503.09363/) (2025)
- [Multi-Domain Riemannian Graph Gluing for Building Graph Foundation Models](https://mlsanity.com/paper/2603.00618/) (2026)
- [Dynamic Bundling with Large Language Models for Zero-Shot Inference on Text-Attributed Graphs](https://mlsanity.com/paper/2505.17599/) (2025)
- [When Structure Doesn't Help: LLMs Do Not Read Text-Attributed Graphs as Effectively as We Expected](https://mlsanity.com/paper/2511.16767/) (2025)
- [Node-as-Agent: Graph Agentic Network](https://mlsanity.com/paper/2508.00429/) (2025)
- [From Aggregation to Selection: User-Validated Distributed Social Recommendation](https://mlsanity.com/paper/2505.21388/) (2025)
- [GRIP: In-Parameter Graph Reasoning through Fine-Tuning Large Language Models](https://mlsanity.com/paper/2511.07457/) (2025)
- [Colorful Talks with Graphs: Human-Interpretable Graph Encodings for Large Language Models](https://mlsanity.com/paper/2602.10386/) (2026)
- [LLM as Graph Kernel: Rethinking Message Passing on Text-Rich Graphs](https://mlsanity.com/paper/2603.14937/) (2026)
- [Decoupled and Divergence-Conditioned Prompt for Multi-domain Dynamic Graph Foundation Models](https://mlsanity.com/paper/2605.13540/) (2026)
- [Two Facets of the Same Optimization Coin: Model Degradation and Representation Collapse in Graph Foundation Models](https://mlsanity.com/paper/2509.08401/) (2025)
- [GraphShaper: Geometry-aware Alignment for Improving Transfer Learning in Text-Attributed Graphs](https://mlsanity.com/paper/2510.12085/) (2025)
- [Factual and Edit-Sensitive Graph-to-Sequence Generation via Graph-Aware Adaptive Noising](https://mlsanity.com/paper/2604.24104/) (2026)
- [A Unified Graph Language Model for Multi-Domain Multi-Task Graph Alignment Instruction Tuning](https://mlsanity.com/paper/2605.12197/) (2026)
- [Hypergraph as Language](https://mlsanity.com/paper/2605.21858/) (2026)
- [PromptGNN-sim: Deep Fusion and Alignment of GNN and LLMs for Text-Attributed Graph Learning](https://mlsanity.com/paper/2606.30291/) (2026)
- [Spatial Message Passing in Language Space for Pathology Image Interpretation](https://mlsanity.com/paper/2608.14309/) (2026)

## Abstract (arXiv)

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.