Bundle Neural Networks for message diffusion on graphs
Abstract
The dominant paradigm for learning on graph-structured data is message passing. Despite being a strong inductive bias, the local message passing mechanism suffers from pathological issues such as over-smoothing, over-squashing, and limited node-level expressivity. To address these limitations we propose Bundle Neural Networks (BuNN), a new type of GNN that operates via message diffusion over flat vector bundles - structures analogous to connections on Riemannian manifolds that augment the graph by assigning to each node a vector space and an orthogonal map. A BuNN layer evolves the features according to a diffusion-type partial differential equation. When discretized, BuNNs are a special case of Sheaf Neural Networks (SNNs), a recently proposed MPNN capable of mitigating over-smoothing. The continuous nature of message diffusion enables BuNNs to operate on larger scales of the graph and, therefore, to mitigate over-squashing. Finally, we prove that BuNN can approximate any feature transformation over nodes on any (potentially infinite) family of graphs given injective positional encodings, resulting in universal node-level expressivity. We support our theory via synthetic experiments and showcase the strong empirical performance of BuNNs over a range of real-world tasks, achieving state-of-the-art results on several standard benchmarks in transductive and inductive settings.
Benchmark Results
Tested on 8 datasets
Tables show presented results in global context (best 3 papers + GCN + MLP).
LRGB
| # | Model | MAE ↓ | Paper |
|---|---|---|---|
| 1 | GCN | 0.2421
±0.0016 best reported | best at pub: Where Did the Gap Go? Reassessing the Long-Range Graph Benchmark (TMLR 2023) best today: From Message-Passing to Linearized Graph Sequence Models (2026) |
| 2 | IPR-MPNN | 0.2422
±0.0007 | |
| 3 | TANGO-GPS | 0.2422
±0.0014 | |
| 5 | GIN | 0.2429
±0.0019 | |
| 7 | GatedGCN | 0.2431
±0.0020 best reported | best at pub: Where Did the Gap Go? Reassessing the Long-Range Graph Benchmark (TMLR 2023) best today: From Message-Passing to Linearized Graph Sequence Models (2026) |
| 21 | GAPH ViT | 0.2449
±0.0016 | This paper |
| 36 | BuNN | 0.2463
±0.0012 | This paper |
| 49 | GINE | 0.2473
±0.0017 | This paper |
| 66 | Exphormer | 0.2481
±0.0007 | This paper |
| 85 | GPS | 0.2500
±0.0005 best reported | best at pub: Recurrent Distance Filtering for Graph Representation Learning (ICML 2023) best today: Bridging Input Feature Spaces Towards Graph Foundation Models (ICLR 2026) Difference within reported uncertainty; not counted as underperformance. |
| 115 | DRew | 0.2536
±0.0015 | This paper |
| 124 | SAN | 0.2545
±0.0012 | This paper |
| 201 | MLP | 0.4351
±0.0008 |
| # | Model | AP ↑ | Paper |
|---|---|---|---|
| 1 | S^2GCN | 0.7311
±0.0066 | |
| 2 | S4G | 0.7293
±0.0004 | |
| 3 | BuNN | 0.7276
±0.0065 | This paper |
| 4 | GCN | 0.7261
±0.0011 best reported | best at pub: Where Did the Gap Go? Reassessing the Long-Range Graph Benchmark (TMLR 2023) best today: From Message-Passing to Linearized Graph Sequence Models (2026) |
| 13 | DRew | 0.7150
±0.0044 | prev best: Recurrent Distance Filtering for Graph Representation Learning (ICML 2023) |
| 26 | GIN | 0.7059
±0.0089 | |
| 34 | GatedGCN | 0.7006
±0.0033 best reported | best at pub: Where Did the Gap Go? Reassessing the Long-Range Graph Benchmark (TMLR 2023) best today: From Message-Passing to Linearized Graph Sequence Models (2026) |
| 45 | GAPH ViT | 0.6942
±0.0075 | This paper |
| 78 | GINE | 0.6621
±0.0067 | This paper |
| 87 | GPS | 0.6562
±0.0115 best reported | best at pub: A Generalization of ViT/MLP-Mixer to Graphs (ICML 2022) Difference within reported uncertainty; not counted as underperformance. |
| 95 | Exphormer | 0.6527
±0.0043 | This paper |
| 112 | SAN | 0.6439
±0.0075 | This paper |
| 181 | MLP | 0.4060
±0.0021 |
| # | Model | F1 ↑ | Paper |
|---|---|---|---|
| 1 | NeuralWalker | 0.4912
±0.0042 | |
| 2 | PPGT | 0.4641
±0.0033 | |
| 3 | CRaWl | 0.4588
±0.0079 | |
| 14 | GPS | 0.4440
±0.0065 | This paper |
| 19 | Exphormer | 0.4242
±0.0044 best reported | best today: Benchmarking Positional Encodings for GNNs and Graph Transformers (KDD 2024) |
| 31 | BuNN | 0.4049
±0.0046 | This paper |
| 41 | GatedGCN | 0.3880
±0.0040 | This paper |
| 42 | Gated-GCN | 0.3880
±0.0040 | |
| 65 | DRew | 0.3314
±0.0024 | This paper |
| 66 | SAN | 0.3230
±0.0039 | This paper |
| 75 | GINE | 0.2718
±0.0054 | This paper |
| 81 | GCN | 0.2380
±0.0160 best reported | best at pub: Where Did the Gap Go? Reassessing the Long-Range Graph Benchmark (TMLR 2023) best today: When Graph Neural Networks Meet Dynamic Mode Decomposition (ICLR 2024) |
| 93 | MLP | 0.1140
±0.0230 |
Heterophily Benchmark
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Dir-Poly | 0.9451
±0.0022 | |
| 2 | D-CDE | 0.9387
±0.0041 | |
| 3 | LargeScaleNet | 0.9358
±0.0024 | |
| 15 | BuNN | 0.9175
±0.0039 | This paper |
| 26 | GraphSAGE | 0.9106
±0.0027 | |
| 40 | GAT-sep | 0.8875
±0.0041 | This paper |
| 54 | GT-sep | 0.8732
±0.0039 | This paper |
| 59 | GT | 0.8651
±0.0073 | This paper |
| 64 | SAGE | 0.8574
±0.0067 | This paper |
| 77 | GCN | 0.8272
±0.0082 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) best today: HyperAggregation: Aggregating over Graph Edges with Hypernetworks (2024) |
| 83 | GAT | 0.8145
±0.0009 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) best today: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) |
| 88 | NSD | 0.8041
±0.0072 | This paper |
| 135 | MLP | 0.6665
±0.0047 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | UniGAP | 0.6375
±0.0110 | |
| 2 | H2GCN + HalfHop | 0.5961
±0.0100 | |
| 3 | GraphSAGE + HalfHop | 0.5897
±0.0150 | |
| 12 | SAGE | 0.5569
±0.0023 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) |
| 14 | GAT | 0.5559
±0.0027 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) |
| 15 | GraphSAGE | 0.5540
±0.0020 | |
| 24 | GCN | 0.5411
±0.0034 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) |
| 28 | BuNN | 0.5374
±0.0051 | This paper |
| 52 | GAT-sep | 0.5270
±0.0062 | This paper |
| 62 | GT-sep | 0.5218
±0.0080 | This paper |
| 72 | GT | 0.5117
±0.0066 | This paper |
| 84 | MLP | 0.5058 | |
| 170 | NSD | 0.4276
±0.0054 | This paper |
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | BuNN | 0.9899
±0.0016 | This paper |
| 2 | DC-GNN | 0.9850
±0.0021 | |
| 3 | Tango -GPS | 0.9839
±0.0054 | |
| 36 | GAT | 0.9391
±0.0035 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) best today: Relieving the Over-Aggregating Effect in Graph Transformers (NeurIPS 2025) |
| 37 | GAT-sep | 0.9391
±0.0035 | This paper |
| 42 | GraphSAGE | 0.9358
±0.0005 | |
| 46 | SAGE | 0.9351
±0.0057 | This paper |
| 57 | GT-sep | 0.9229
±0.0047 | This paper |
| 60 | NSD | 0.9215
±0.0084 | This paper |
| 63 | GT | 0.9185
±0.0076 | This paper |
| 68 | GCN | 0.9150
±0.0006 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) best today: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) |
| 156 | MLP | 0.5099
±0.0147 |
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | Polynormer-r | 0.8591
±0.0074 | |
| 2 | DC-GNN | 0.8588
±0.0081 | |
| 3 | TANGO-GPS | 0.8566
±0.0101 | |
| 21 | BuNN | 0.8478
±0.0080 | This paper |
| 28 | GAT | 0.8443
±0.0100 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) best today: TopoBench: A Framework for Benchmarking Topological Deep Learning (2024) Difference within reported uncertainty; not counted as underperformance. |
| 41 | GAT-sep | 0.8378
±0.0043 | This paper |
| 50 | GCN | 0.8364
±0.0067 | This paper |
| 61 | GT | 0.8323
±0.0064 | prev best: Data Augmentation for Supervised Graph Outlier Detection via Latent Diffusion Models (LoG 2023) |
| 73 | GT-sep | 0.8252
±0.0092 | This paper |
| 76 | SAGE | 0.8243
±0.0044 | This paper |
| 77 | GraphSAGE | 0.8243
±0.0044 | |
| 103 | NSD | 0.7883
±0.0076 | This paper |
| 139 | MLP | 0.7362
±0.0020 |
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | NID_GAT | 0.9703
±0.0002 | |
| 2 | NID_GCN | 0.9685
±0.0010 | |
| 3 | UniGAP | 0.8421
±0.0080 | |
| 16 | GCN | 0.7902
±0.0060 best reported | best at pub: Evolving Computation Graphs (ICML 2023) |
| 22 | BuNN | 0.7875
±0.0109 | This paper |
| 26 | GAT | 0.7743
±0.0120 | prev best: Data Augmentation for Supervised Graph Outlier Detection via Latent Diffusion Models (LoG 2023) |
| 29 | GT-sep | 0.7805
±0.0093 | This paper |
| 30 | GT | 0.7795
±0.0068 | prev best: Data Augmentation for Supervised Graph Outlier Detection via Latent Diffusion Models (LoG 2023) |
| 46 | GraphSAGE | 0.7721
±0.0130 | |
| 54 | GAT-sep | 0.7679
±0.0071 | This paper |
| 58 | SAGE | 0.7644
±0.0062 | This paper |
| 96 | MLP | 0.7082
±0.0010 | |
| 109 | NSD | 0.6969
±0.0146 | This paper |
