# P2GNN: Two Prototype Sets to boost GNN Performance

arXiv: https://arxiv.org/abs/2603.09195 · HTML: https://mlsanity.com/paper/2603.09195/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 38 of its 58 references that are in the map.
- First posted on arXiv 10 Mar 2026.

## Builds on (most cited first, 30 of 38)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [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)
- [Prototypical Networks for Few-shot Learning](https://mlsanity.com/paper/1703.05175/) (2017)
- [Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering](https://mlsanity.com/paper/1606.09375/) (2016)
- [Simplifying Graph Convolutional Networks](https://mlsanity.com/paper/1902.07153/) (2019)
- [Predict then Propagate: Graph Neural Networks meet Personalized PageRank](https://mlsanity.com/paper/1810.05997/) (2018)
- [Representation Learning on Graphs with Jumping Knowledge Networks](https://mlsanity.com/paper/1806.03536/) (2018)
- [Simple and Deep Graph Convolutional Networks](https://mlsanity.com/paper/2007.02133/) (2020)
- [Geom-GCN: Geometric Graph Convolutional Networks](https://mlsanity.com/paper/2002.05287/) (2020)
- [Adaptive Universal Generalized PageRank Graph Neural Network](https://mlsanity.com/paper/2006.07988/) (2020)
- [Multi-scale Attributed Node Embedding](https://mlsanity.com/paper/1909.13021/) (2019)
- [MixHop: Higher-Order Graph Convolutional Architectures via Sparsified Neighborhood Mixing](https://mlsanity.com/paper/1905.00067/) (2019)
- [Beyond Low-frequency Information in Graph Convolutional Networks](https://mlsanity.com/paper/2101.00797/) (2021)
- [A critical look at the evaluation of GNNs under heterophily: Are we really making progress?](https://mlsanity.com/paper/2302.11640/) (2023)
- [Large Scale Learning on Non-Homophilous Graphs: New Benchmarks and Strong Simple Methods](https://mlsanity.com/paper/2110.14446/) (2021)
- [Enhancing Graph Neural Network-based Fraud Detectors against Camouflaged Fraudsters](https://mlsanity.com/paper/2008.08692/) (2020)
- [Graph Neural Networks with Heterophily](https://mlsanity.com/paper/2009.13566/) (2020)
- [BernNet: Learning Arbitrary Graph Spectral Filters via Bernstein Approximation](https://mlsanity.com/paper/2106.10994/) (2021)
- [Rethinking Graph Neural Networks for Anomaly Detection](https://mlsanity.com/paper/2205.15508/) (2022)
- [Two Sides of the Same Coin: Heterophily and Oversmoothing in Graph Convolutional Neural Networks](https://mlsanity.com/paper/2102.06462/) (2021)
- [Is Homophily a Necessity for Graph Neural Networks?](https://mlsanity.com/paper/2106.06134/) (2021)
- [Finding Global Homophily in Graph Neural Networks When Meeting Heterophily](https://mlsanity.com/paper/2205.07308/) (2022)
- [Revisiting Heterophily For Graph Neural Networks](https://mlsanity.com/paper/2210.07606/) (2022)
- [ProtGNN: Towards Self-Explaining Graph Neural Networks](https://mlsanity.com/paper/2112.00911/) (2021)
- [Breaking the Limit of Graph Neural Networks by Improving the Assortativity of Graphs with Local Mixing Patterns](https://mlsanity.com/paper/2106.06586/) (2021)
- [Non-Local Graph Neural Networks](https://mlsanity.com/paper/2005.14612/) (2020)
- [GBK-GNN: Gated Bi-Kernel Graph Neural Networks for Modeling Both Homophily and Heterophily](https://mlsanity.com/paper/2110.15777/) (2021)
- [New Benchmarks for Learning on Non-Homophilous Graphs](https://mlsanity.com/paper/2104.01404/) (2021)

## Abstract (arXiv)

Message Passing Graph Neural Networks (MP-GNNs) have garnered attention for addressing various industry challenges, such as user recommendation and fraud detection. However, they face two major hurdles: (1) heavy reliance on local context, often lacking information about the global context or graph-level features, and (2) assumption of strong homophily among connected nodes, struggling with noisy local neighborhoods. To tackle these, we introduce P2GNN, a plug-and-play technique leveraging prototypes to optimize message passing, enhancing the performance of the base GNN model. Our approach views the prototypes in two ways: (1) as universally accessible neighbors for all nodes, enriching global context, and (2) aligning messages to clustered prototypes, offering a denoising effect. We demonstrate the extensibility of our proposed method to all message-passing GNNs and conduct extensive experiments across 18 datasets, including proprietary e-commerce datasets and open-source datasets, on node recommendation and node classification tasks. Results show that P2GNN outperforms production models in e-commerce and achieves the top average rank on open-source datasets, establishing it as a leading approach. Qualitative analysis supports the value of global context and noise mitigation in the local neighborhood in enhancing performance.