# GraphTOP: Graph Topology-Oriented Prompting for Graph Neural Networks

arXiv: https://arxiv.org/abs/2510.22451 · HTML: https://mlsanity.com/paper/2510.22451/

## Key facts

- Cited by 5 papers in the map (data through 14 Oct 2026).
- Builds on 52 of its 65 references that are in the map.
- First posted on arXiv 25 Oct 2025.

## Builds on (most cited first, 30 of 52)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Categorical Reparameterization with Gumbel-Softmax](https://mlsanity.com/paper/1611.01144/) (2016)
- [Learning to Prompt for Vision-Language Models](https://mlsanity.com/paper/2109.01134/) (2021)
- [Dynamic Graph CNN for Learning on Point Clouds](https://mlsanity.com/paper/1801.07829/) (2018)
- [Visual Prompt Tuning](https://mlsanity.com/paper/2203.12119/) (2022)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [The Concrete Distribution: A Continuous Relaxation of Discrete Random Variables](https://mlsanity.com/paper/1611.00712/) (2016)
- [Deep Graph Infomax](https://mlsanity.com/paper/1809.10341/) (2018)
- [Revisiting Semi-Supervised Learning with Graph Embeddings](https://mlsanity.com/paper/1603.08861/) (2016)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Simple and Deep Graph Convolutional Networks](https://mlsanity.com/paper/2007.02133/) (2020)
- [Hyperband: A Novel Bandit-Based Approach to Hyperparameter Optimization](https://mlsanity.com/paper/1603.06560/) (2016)
- [MaPLe: Multi-modal Prompt Learning](https://mlsanity.com/paper/2210.03117/) (2022)
- [GraphSAINT: Graph Sampling Based Inductive Learning Method](https://mlsanity.com/paper/1907.04931/) (2019)
- [Temporal Graph Networks for Deep Learning on Dynamic Graphs](https://mlsanity.com/paper/2006.10637/) (2020)
- [GraphMAE: Self-Supervised Masked Graph Autoencoders](https://mlsanity.com/paper/2205.10803/) (2022)
- [InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization](https://mlsanity.com/paper/1908.01000/) (2019)
- [Composition-based Multi-Relational Graph Convolutional Networks](https://mlsanity.com/paper/1911.03082/) (2019)
- [Graph Structure Learning for Robust Graph Neural Networks](https://mlsanity.com/paper/2005.10203/) (2020)
- [A critical look at the evaluation of GNNs under heterophily: Are we really making progress?](https://mlsanity.com/paper/2302.11640/) (2023)
- [Iterative Deep Graph Learning for Graph Neural Networks: Better and Robust Node Embeddings](https://mlsanity.com/paper/2006.13009/) (2020)
- [Is Homophily a Necessity for Graph Neural Networks?](https://mlsanity.com/paper/2106.06134/) (2021)
- [SimGRACE: A Simple Framework for Graph Contrastive Learning without Data Augmentation](https://mlsanity.com/paper/2202.03104/) (2022)
- [GraphPrompt: Unifying Pre-Training and Downstream Tasks for Graph Neural Networks](https://mlsanity.com/paper/2302.08043/) (2023)
- [Knowledge Graph Prompting for Multi-Document Question Answering](https://mlsanity.com/paper/2308.11730/) (2023)
- [All in One: Multi-task Prompting for Graph Neural Networks](https://mlsanity.com/paper/2307.01504/) (2023)
- [Self-supervised Learning on Graphs: Contrastive, Generative,or Predictive](https://mlsanity.com/paper/2105.07342/) (2021)

## Built on by (most cited first, 5 of 5)

- [GraphFlow: A Graph-Based Workflow Management for Efficient LLM-Agent Serving](https://mlsanity.com/paper/2605.22566/) (2026)
- [MAGPrompt: Message-Adaptive Graph Prompt Tuning for Graph Neural Networks](https://mlsanity.com/paper/2602.05567/) (2026)
- [Unified Graph Prompt Learning via Low-Rank Graph Message Prompting](https://mlsanity.com/paper/2604.11257/) (2026)
- [Signed Graph Pre-Training and Prompt Learning](https://mlsanity.com/paper/2609.25722/) (2026)
- [Spectral Reversal: Counteracting Singular Value Bias for Graph Prompting](https://mlsanity.com/paper/2609.32143/) (2026)

## Abstract (arXiv)

Graph Neural Networks (GNNs) have revolutionized the field of graph learning by learning expressive graph representations from massive graph data. As a common pattern to train powerful GNNs, the "pre-training, adaptation" scheme first pre-trains GNNs over unlabeled graph data and subsequently adapts them to specific downstream tasks. In the adaptation phase, graph prompting is an effective strategy that modifies input graph data with learnable prompts while keeping pre-trained GNN models frozen. Typically, existing graph prompting studies mainly focus on *feature-oriented* methods that apply graph prompts to node features or hidden representations. However, these studies often achieve suboptimal performance, as they consistently overlook the potential of *topology-oriented* prompting, which adapts pre-trained GNNs by modifying the graph topology. In this study, we conduct a pioneering investigation of graph prompting in terms of graph topology. We propose the first **Graph** **T**opology-**O**riented **P**rompting (GraphTOP) framework to effectively adapt pre-trained GNN models for downstream tasks. More specifically, we reformulate topology-oriented prompting as an edge rewiring problem within multi-hop local subgraphs and relax it into the continuous probability space through reparameterization while ensuring tight relaxation and preserving graph sparsity. Extensive experiments on five graph datasets under four pre-training strategies demonstrate that our proposed GraphTOP outshines six baselines on multiple node classification datasets. Our code is available at https://github.com/xbfu/GraphTOP.