# Beyond One-Size-Fits-All: Adaptive Subgraph Denoising for Zero-Shot Graph Learning with Large Language Models

arXiv: https://arxiv.org/abs/2603.02938 · HTML: https://mlsanity.com/paper/2603.02938/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 34 of its 53 references that are in the map.
- First posted on arXiv 3 Mar 2026.

## Builds on (most cited first, 30 of 34)

- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [HybridFlow: A Flexible and Efficient RLHF Framework](https://mlsanity.com/paper/2409.19256/) (2024)
- [LlamaFactory: Unified Efficient Fine-Tuning of 100+ Language Models](https://mlsanity.com/paper/2403.13372/) (2024)
- [M3-Embedding: Multi-Linguality, Multi-Functionality, Multi-Granularity Text Embeddings Through Self-Knowledge Distillation](https://mlsanity.com/paper/2402.03216/) (2024)
- [Revisiting Semi-Supervised Learning with Graph Embeddings](https://mlsanity.com/paper/1603.08861/) (2016)
- [Wiki-CS: A Wikipedia-Based Benchmark for Graph Neural Networks](https://mlsanity.com/paper/2007.02901/) (2020)
- [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)
- [LLaGA: Large Language and Graph Assistant](https://mlsanity.com/paper/2402.08170/) (2024)
- [A Survey of Graph Neural Networks for Recommender Systems: Challenges, Methods, and Directions](https://mlsanity.com/paper/2109.12843/) (2021)
- [Harnessing Explanations: LLM-to-LM Interpreter for Enhanced Text-Attributed Graph Representation Learning](https://mlsanity.com/paper/2305.19523/) (2023)
- [ZeroG: Investigating Cross-dataset Zero-shot Transferability in Graphs](https://mlsanity.com/paper/2402.11235/) (2024)
- [GIMLET: A Unified Graph-Text Model for Instruction-Based Molecule Zero-Shot Learning](https://mlsanity.com/paper/2306.13089/) (2023)
- [GraphTranslator: Aligning Graph Model to Large Language Model for Open-ended Tasks](https://mlsanity.com/paper/2402.07197/) (2024)
- [Augmenting Low-Resource Text Classification with Graph-Grounded Pre-training and Prompting](https://mlsanity.com/paper/2305.03324/) (2023)
- [LLMs as Zero-shot Graph Learners: Alignment of GNN Representations with LLM Token Embeddings](https://mlsanity.com/paper/2408.14512/) (2024)
- [GOFA: A Generative One-For-All Model for Joint Graph Language Modeling](https://mlsanity.com/paper/2407.09709/) (2024)
- [InstructGraph: Boosting Large Language Models via Graph-centric Instruction Tuning and Preference Alignment](https://mlsanity.com/paper/2402.08785/) (2024)
- [A Survey of Graph Neural Networks in Real world: Imbalance, Noise, Privacy and OOD Challenges](https://mlsanity.com/paper/2403.04468/) (2024)
- [GLBench: A Comprehensive Benchmark for Graph with Large Language Models](https://mlsanity.com/paper/2407.07457/) (2024)
- [Beyond Text: A Deep Dive into Large Language Models' Ability on Understanding Graph Data](https://mlsanity.com/paper/2310.04944/) (2023)
- [GraphICL: Unlocking Graph Learning Potential in LLMs through Structured Prompt Design](https://mlsanity.com/paper/2501.15755/) (2025)
- [Can LLMs Convert Graphs to Text-Attributed Graphs?](https://mlsanity.com/paper/2412.10136/) (2024)
- [LangGFM: A Large Language Model Alone Can be a Powerful Graph Foundation Model](https://mlsanity.com/paper/2410.14961/) (2024)
- [Are Large Language Models In-Context Graph Learners?](https://mlsanity.com/paper/2502.13562/) (2025)
- [Graph Neural Networks in Modern AI-aided Drug Discovery](https://mlsanity.com/paper/2506.06915/) (2025)
- [Graph Agent: Explicit Reasoning Agent for Graphs](https://mlsanity.com/paper/2310.16421/) (2023)
- [UniGTE: Unified Graph-Text Encoding for Zero-Shot Generalization across Graph Tasks and Domains](https://mlsanity.com/paper/2510.16885/) (2025)
- [Challenges of Generating Structurally Diverse Graphs](https://mlsanity.com/paper/2409.18859/) (2024)

## Built on by (most cited first, 1 of 1)

- [A Unified Graph Language Model for Multi-Domain Multi-Task Graph Alignment Instruction Tuning](https://mlsanity.com/paper/2605.12197/) (2026)

## Abstract (arXiv)

Graph-based tasks in the zero-shot setting remain a significant challenge due to data scarcity and the inability of traditional Graph Neural Networks (GNNs) to generalize to unseen domains or label spaces. While recent advancements have transitioned toward leveraging Large Language Models (LLMs) as predictors to enhance GNNs, these methods often suffer from cross-modal alignment issues. A recent paradigm (i.e., Graph-R1) overcomes the aforementioned architectural dependencies by adopting a purely text-based format and utilizing LLM-based graph reasoning, showing improved zero-shot generalization. However, it employs a task-agnostic, one-size-fits-all subgraph extraction strategy, which inevitably introduces significant structural noise--irrelevant neighbors and edges--that distorts the LLMs' receptive field and leads to suboptimal predictions. To address this limitation, we introduce GraphSSR, a novel framework designed for adaptive subgraph extraction and denoising in zero-shot LLM-based graph reasoning. Specifically, we propose the SSR pipeline, which dynamically tailors subgraph extraction to specific contexts through a "Sample-Select-Reason" process, enabling the model to autonomously filter out task-irrelevant neighbors and overcome the one-size-fits-all issue. To internalize this capability, we develop SSR-SFT, a data synthesis strategy that generates high-quality SSR-style graph reasoning traces for supervised fine-tuning of LLMs. Furthermore, we propose SSR-RL, a two-stage reinforcement learning framework that explicitly regulates sampling and selection operations within the proposed SSR pipeline designed for adaptive subgraph denoising. By incorporating Authenticity-Reinforced and Denoising-Reinforced RL, we guide the model to achieve accurate predictions using parsimonious, denoised subgraphs for reasoning.