Graph Pointer Neural Networks
Abstract
Graph Neural Networks (GNNs) have shown advantages in various graph-based applications. Most existing GNNs assume strong homophily of graph structure and apply permutation-invariant local aggregation of neighbors to learn a representation for each node. However, they fail to generalize to heterophilic graphs, where most neighboring nodes have different labels or features, and the relevant nodes are distant. Few recent studies attempt to address this problem by combining multiple hops of hidden representations of central nodes (i.e., multi-hop-based approaches) or sorting the neighboring nodes based on attention scores (i.e., ranking-based approaches). As a result, these approaches have some apparent limitations. On the one hand, multi-hop-based approaches do not explicitly distinguish relevant nodes from a large number of multi-hop neighborhoods, leading to a severe over-smoothing problem. On the other hand, ranking-based models do not joint-optimize node ranking with end tasks and result in sub-optimal solutions. In this work, we present Graph Pointer Neural Networks (GPNN) to tackle the challenges mentioned above. We leverage a pointer network to select the most relevant nodes from a large amount of multi-hop neighborhoods, which constructs an ordered sequence according to the relationship with the central node. 1D convolution is then applied to extract high-level features from the node sequence. The pointer-network-based ranker in GPNN is joint-optimized with other parts in an end-to-end manner. Extensive experiments are conducted on six public node classification datasets with heterophilic graphs. The results show that GPNN significantly improves the classification performance of state-of-the-art methods. In addition, analyses also reveal the privilege of the proposed GPNN in filtering out irrelevant neighbors and reducing over-smoothing.
Benchmark Results
Tested on 3 datasets 1 baseline value reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9672
±0.0147 | |
| 2 | DoG | 0.9660
±0.0210 | |
| 3 | GPF-plus | 0.9583
±0.0419 | |
| 34 | MLP | 0.9230
±0.0070 best reported | best at pub: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) |
| 40 | H2GCN | 0.9189
±0.0393 best reported | best at pub: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 53 | GraphSAGE | 0.9000
±0.0365 best reported | best at pub: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) best today: Graph Neural Networks Need Cluster-Normalize-Activate Modules (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 142 | GPNN | 0.8523
±0.0640 | This paper |
| 189 | SAGE | 0.8269 | |
| 211 | GAT | 0.5945
±0.0637 | prev best: Heterophilic Graphs (ICLR 2020) best today: Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models (2025) Improvement within reported uncertainty; not highlighted. |
| 257 | GCN | 0.7933
±0.0447 best reported | best at pub: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) best today: Graph Wave Networks (WWW 2025) |
| 276 | MixHop | 0.7784
±0.0773 | This paper |
| 455 | Node2Seq | 0.6370
±0.0610 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 24 | MLP | 0.9136
±0.0070 best reported | best at pub: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) best today: Node-oriented Spectral Filtering for Graph Neural Networks (2022) Difference within reported uncertainty; not counted as underperformance. |
| 68 | H2GCN | 0.8623
±0.0471 best reported | best at pub: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Difference within reported uncertainty; not counted as underperformance. |
| 89 | GPNN | 0.8514
±0.0600 | This paper |
| 138 | SAGE | 0.8269 | |
| 157 | GraphSAGE | 0.8196
±0.0739 best reported | best at pub: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) best today: Heterophily-Aware Graph Attention Network (2023) Difference within reported uncertainty; not counted as underperformance. |
| 158 | GAT | 0.8190
±0.0540 best reported | best at pub: NCGNN: Node-Level Capsule Graph Neural Network for Semisupervised Classification (2020) best today: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 170 | GCN | 0.8082
±0.0360 best reported | best at pub: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) |
| 183 | MixHop | 0.7950
±0.0630 best reported | best today: Label-Wise Graph Convolutional Network for Heterophilic Graphs (2021) Difference within reported uncertainty; not counted as underperformance. |
| 392 | Node2Seq | 0.5870
±0.0680 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 42 | MLP | 0.4026
±0.0108 best reported | best at pub: Is Homophily a Necessity for Graph Neural Networks? (ICLR 2021) best today: Heterophily-Aware Graph Attention Network (2023) |
| 68 | GraphSAGE | 0.3899
±0.0085 best reported | best at pub: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) best today: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 71 | H2GCN | 0.3885
±0.0117 best reported | best at pub: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 133 | GPNN | 0.3708
±0.0141 | This paper |
| 135 | GCN | 0.3690 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 162 | MixHop | 0.3648
±0.0120 best reported | best today: Towards Deep Attention in Graph Neural Networks: Problems and Remedies (ICML 2023) |
| 182 | GAT | 0.2974
±0.0146 | prev best: Non-Local Graph Neural Networks (2020) best today: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) Improvement within reported uncertainty; not highlighted. |
| 266 | GIN | 0.3410
±0.0030 | |
| 315 | Node2Seq | 0.3140
±0.0100 | This paper |
