Understanding Virtual Nodes: Oversquashing and Node Heterogeneity
Abstract
While message passing neural networks (MPNNs) have convincing success in a range of applications, they exhibit limitations such as the oversquashing problem and their inability to capture long-range interactions. Augmenting MPNNs with a virtual node (VN) removes the locality constraint of the layer aggregation and has been found to improve performance on a range of benchmarks. We provide a comprehensive theoretical analysis of the role of VNs and benefits thereof, through the lenses of oversquashing and sensitivity analysis. First, we characterize, precisely, how the improvement afforded by VNs on the mixing abilities of the network and hence in mitigating oversquashing, depends on the underlying topology. We then highlight that, unlike Graph-Transformers (GTs), classical instantiations of the VN are often constrained to assign uniform importance to different nodes. Consequently, we propose a variant of VN with the same computational complexity, which can have different sensitivity to nodes based on the graph structure. We show that this is an extremely effective and computationally efficient baseline for graph-level tasks.
Benchmark Results
Tested on 1 dataset 3 baseline values reported too low
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) |
| 29 | GatedGCN+PE+VN_G | 0.2458
±0.0006 | This paper |
| 32 | GRIT | 0.2460
±0.0012 | This paper |
| 41 | GatedGCN+PE-ViT | 0.2465
±0.0015 | This paper |
| 49 | GINE | 0.2473
±0.0017 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) |
| 58 | GatedGCN+PE | 0.2477
±0.0009 | 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. |
| 93 | CRaWl | 0.2506
±0.0022 | This paper |
| 95 | GatedGCN+PE-Mixer | 0.2508
±0.0007 | This paper |
| 115 | DRew | 0.2536
±0.0015 | prev best: Recurrent Distance Filtering for Graph Representation Learning (ICML 2023) |
| 123 | SAN+RWSE | 0.2545
±0.0012 | This paper |
| 201 | MLP | 0.4351
±0.0008 |
