Graph Ladling: Shockingly Simple Parallel GNN Training without Intermediate Communication
Abstract
Graphs are omnipresent and GNNs are a powerful family of neural networks for learning over graphs. Despite their popularity, scaling GNNs either by deepening or widening suffers from prevalent issues of unhealthy gradients, over-smoothening, information squashing, which often lead to sub-standard performance. In this work, we are interested in exploring a principled way to scale GNNs capacity without deepening or widening, which can improve its performance across multiple small and large graphs. Motivated by the recent intriguing phenomenon of model soups, which suggest that fine-tuned weights of multiple large-language pre-trained models can be merged to a better minima, we argue to exploit the fundamentals of model soups to mitigate the aforementioned issues of memory bottleneck and trainability during GNNs scaling. More specifically, we propose not to deepen or widen current GNNs, but instead present a data-centric perspective of model soups tailored for GNNs, i.e., to build powerful GNNs. By dividing giant graph data, we build multiple independently and parallelly trained weaker GNNs (soup ingredient) without any intermediate communication, and combine their strength using a greedy interpolation soup procedure to achieve state-of-the-art performance. Compared to concurrent distributed GNN training works such as, we train each soup ingredient by sampling different subgraphs per epoch and their respective sub-models are merged only after being fully trained (rather than intermediately so). Moreover, we provide a wide variety of model soup preparation techniques by leveraging state-of-the-art graph sampling and graph partitioning approaches that can handle large graphs. Extensive experiments across many real-world small and large graphs, illustrate the effectiveness of our approach and point towards a promising orthogonal direction for GNN scaling. Codes are available at:.
Benchmark Results
Tested on 10 datasets 33 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSAGE+CNA | 0.9418
±0.0033 | |
| 2 | GCN+CNA | 0.9366
±0.0048 | |
| 3 | TransformerConv | 0.9350
±0.0058 | |
| 21 | GCN | 0.9004 | |
| 333 | APPNP Our Soup | 0.8370 | This paper |
| 339 | APPNP Vanilla | 0.8364 | This paper |
| 363 | GCN Our Soup | 0.8352 | This paper |
| 380 | DAGNN Our Soup | 0.8345 | This paper |
| 388 | DAGNN Vanilla | 0.8339 | This paper |
| 447 | GCNII Our Soup | 0.8277 | This paper |
| 483 | GCN vanilla | 0.8239 | This paper |
| 514 | GCNII Vanilla | 0.8219 | This paper |
| 649 | SGC Our Soup | 0.8022 | This paper |
| 664 | JKNet Our Soup | 0.7989 | This paper |
| 686 | SGC Vanilla | 0.7931 | This paper |
| 693 | JKNet Vanilla | 0.7906 | This paper |
| 724 | MLP | 0.7768 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 20 | APPNP | 0.8142
±0.0026 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 36 | GCNII | 0.8076
±0.0030 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 61 | GraphSAGE | 0.7923
±0.0053 | |
| 62 | JKNet | 0.7920 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 75 | DAGNN | 0.7860 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 96 | SGC | 0.7765
±0.0012 best reported | |
| 350 | MLP | 0.7289
±0.0010 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LGTL | 0.9518
±0.0011 | |
| 2 | MixHop (LO) | 0.9513
±0.0038 | |
| 3 | GraphSAGE (LO) | 0.9511
±0.0036 | |
| 17 | APPNP | 0.9355
±0.0060 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 18 | GCN | 0.9296
±0.0015 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 24 | JKNet | 0.9160 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 58 | GCNII | 0.9030
±0.0043 best reported | best at pub: Graph Neural Networks Inspired by Classical Iterative Algorithms (ICML 2021) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 141 | SGC | 0.8832
±0.0055 best reported | |
| 210 | MLP | 0.8690
±0.0074 | |
| 226 | DAGNN | 0.8640 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 377 | BTM | 0.8092 | This paper |
Default metric is F1. The paper reports 6 values on F1 , 1 value on accuracy (percent, no explicit header; source follows benchmark metrics per L381) and 4 values on accuracy (percent, no explicit header) .
| # | Model | F1 ↑ default | accuracy (percent, no explicit header; source follows benchmark metrics per L381) ↑ | accuracy (percent, no explicit header) ↑ | Paper |
|---|---|---|---|---|---|
| 1 | Node Sampled Soup | —
| — | 0.9728
±
0.0008 | accuracy (percent, no explicit header; source follows benchmark metrics per L381)
— accuracy (percent, no explicit header)
0.9728
±
0.0008 |
| 1 | EnGCN | 0.9714
±
0.0003 | — | — | accuracy (percent, no explicit header; source follows benchmark metrics per L381)
— accuracy (percent, no explicit header)
— |
| 2 | SAGN+SLE | 0.9710
±
0.0000 | — | — | accuracy (percent, no explicit header; source follows benchmark metrics per L381)
— accuracy (percent, no explicit header)
— |
| 3 | GAMLP(JK) | 0.9704
±
0.0001 | — | — | accuracy (percent, no explicit header; source follows benchmark metrics per L381)
— accuracy (percent, no explicit header)
— |
| 4 | GraphSAINT | 0.9700 best reported | — | — | accuracy (percent, no explicit header; source follows benchmark metrics per L381)
— accuracy (percent, no explicit header)
— best at pub: LMC: Fast Training of GNNs via subgraph-wise sampling with Provable Convergence (ICLR 2023) |
| 13 | GraphSAGE Ensemble | 0.9661 | — | — | accuracy (percent, no explicit header; source follows benchmark metrics per L381)
— accuracy (percent, no explicit header)
— |
| 14 | GraphSAGE | 0.9660 best reported | — | — | accuracy (percent, no explicit header; source follows benchmark metrics per L381)
— accuracy (percent, no explicit header)
— best at pub: Accelerating Large Scale Real-Time GNN Inference using Channel Pruning (2021) |
| 22 | Our Data Partition Soup | —
| — | 0.9641
±
0.0008 | accuracy (percent, no explicit header; source follows benchmark metrics per L381)
— accuracy (percent, no explicit header)
0.9641
±
0.0008 |
| 48 | ClusterGCN | 0.9570 best reported | — | — | accuracy (percent, no explicit header; source follows benchmark metrics per L381)
— accuracy (percent, no explicit header)
— best at pub: PaSca: a Graph Neural Architecture Search System under the Scalable Paradigm (WWW 2022) Difference within reported uncertainty; not counted as underperformance. |
| 49 | ClusterGCN Ensemble | 0.9570 | — | — | accuracy (percent, no explicit header; source follows benchmark metrics per L381)
— accuracy (percent, no explicit header)
— |
| 58 | GCN | 0.9530
±
0.0010 | — | — | accuracy (percent, no explicit header; source follows benchmark metrics per L381)
— accuracy (percent, no explicit header)
— |
| 91 | FastGCN | 0.9370 best reported | — | — | accuracy (percent, no explicit header; source follows benchmark metrics per L381)
— accuracy (percent, no explicit header)
— best at pub: FastGCN: Fast Learning with Graph Convolutional Networks via Importance Sampling (ICLR 2018) |
| 111 | Edge Sampled Soup | —
| — | 0.9266
±
0.0034 | accuracy (percent, no explicit header; source follows benchmark metrics per L381)
— accuracy (percent, no explicit header)
0.9266
±
0.0034 |
| 119 | Layer Sampled Soup | —
| — | 0.8601
±
0.0017 | accuracy (percent, no explicit header; source follows benchmark metrics per L381)
— accuracy (percent, no explicit header)
0.8601
±
0.0017 |
| 104 | LADIES | —
| 0.6278
±
0.0089 | — | accuracy (percent, no explicit header; source follows benchmark metrics per L381)
0.6278
±
0.0089 accuracy (percent, no explicit header)
— |
OGB
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Jacobi | 0.8968 | |
| 2 | GPR | 0.8953 | |
| 3 | LEMP4HG | 0.8939 | |
| 4 | SAGE | 0.8933 | |
| 64 | GraphSAINT | 0.8383
±0.0014 best reported | best at pub: Node Feature Extraction by Self-Supervised Multi-scale Neighborhood Prediction (ICLR 2021) |
| 83 | GraphSAGE | 0.8287 best reported | best at pub: A Comprehensive Study on Large-Scale Graph Training: Benchmarking and Rethinking (NeurIPS 2022) best today: Clustering as Reasoning: A $k$-Means Interpretation of Chain-of-Thought Graph Learning (ICML 2026) |
| 114 | Node Sampled Soup | 0.8134
±0.0028 | This paper |
| 130 | GraphSAGE Ensemble | 0.8085 | This paper |
| 170 | Our Data Partition Soup | 0.7934
±0.0028 | This paper |
| 190 | ClusterGCN | 0.7897
±0.0033 best reported | best at pub: SIGN: Scalable Inception Graph Neural Networks (2020) best today: From Node Interaction to Hop Interaction: New Effective and Scalable Graph Learning Paradigm (2022) Difference within reported uncertainty; not counted as underperformance. |
| 198 | ClusterGCN Ensemble | 0.7874 | This paper |
| 256 | Edge Sampled Soup | 0.7558
±0.0045 | This paper |
| 262 | LADIES | 0.7531
±0.0056 | This paper |
| 270 | Layer Sampled Soup | 0.7495
±0.0038 | This paper |
| 308 | FastGCN | 0.7346
±0.0020 | This paper |
| 351 | MLP | 0.6605
±0.0020 |
ogbn-arxiv
Global leaderboard →Default metric is Accuracy. The paper reports 6 values on Accuracy and 5 values on accuracy (percent, no explicit header) .
| # | Model | Accuracy ↑ default | accuracy (percent, no explicit header) ↑ | Paper |
|---|---|---|---|---|
| 1 | GIANT-XRT | 0.7612
±
0.0016 | — | accuracy (percent, no explicit header)
— |
| 2 | GEGCN | 0.7576
±
0.0064 | — | accuracy (percent, no explicit header)
— |
| 3 | AGDN | 0.7522
±
0.0007 | — | accuracy (percent, no explicit header)
— |
| 23 | GCN | 0.7300
±
0.0017 | — | accuracy (percent, no explicit header)
— |
| 25 | Node Sampled Soup | —
| 0.7283
±
0.0021 | accuracy (percent, no explicit header)
0.7283
±
0.0021 |
| 31 | Our Data Partition Soup | 0.7235
±
0.0019 | — | accuracy (percent, no explicit header)
— |
| 57 | GraphSAGE Ensemble | 0.7158 | — | accuracy (percent, no explicit header)
— |
| 25 | GraphSAGE | —
| 0.7155
±
0.0041 | accuracy (percent, no explicit header)
0.7155
±
0.0041 |
| 63 | ClusterGCN Ensemble | 0.7143 | — | accuracy (percent, no explicit header)
— |
| 67 | ClusterGCN | 0.7129
±
0.0044 | — | accuracy (percent, no explicit header)
— |
| 79 | GraphSAINT | 0.7055
±
0.0026 | — | accuracy (percent, no explicit header)
— |
| 82 | Edge Sampled Soup | —
| 0.7045
±
0.0029 | accuracy (percent, no explicit header)
0.7045
±
0.0029 |
| 91 | Layer Sampled Soup | 0.6830
±
0.0054 | — | accuracy (percent, no explicit header)
— |
| 100 | FastGCN | —
| 0.6610
±
0.0106 | accuracy (percent, no explicit header)
0.6610
±
0.0106 |
| 105 | LADIES | —
| 0.6278
±
0.0089 | accuracy (percent, no explicit header)
0.6278
±
0.0089 |
| 107 | MLP | 0.5765
±
0.0012 | — | accuracy (percent, no explicit header)
— |
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 | |
| 46 | APPNP | 0.9131
±0.0197 best reported | best at pub: Node-oriented Spectral Filtering for Graph Neural Networks (2022) best today: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 53 | GraphSAGE | 0.9000
±0.0365 | |
| 70 | GCNII | 0.8918
±0.0443 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: Piecewise Constant Spectral Graph Neural Network (TMLR 2025) |
| 257 | GCN | 0.7933
±0.0447 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Graph Wave Networks (WWW 2025) |
| 330 | SGC | 0.7440
±0.0600 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 385 | BTM | 0.7045
±0.0277 | This paper |
| 392 | JKNet | 0.7000
±0.0549 best reported | best at pub: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) Difference within reported uncertainty; not counted as underperformance. |
| 401 | GradientGCN | 0.6919
±0.0656 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | P^2GNN | 0.9541
±0.0272 | |
| 2 | ACM-GCN | 0.9480
±0.0380 | |
| 3 | RF-GCN | 0.9429 | |
| 21 | APPNP | 0.9181
±0.0196 best reported | best at pub: LON-GNN: Spectral GNNs with Learnable Orthonormal Basis (2023) |
| 24 | MLP | 0.9136
±0.0070 | |
| 35 | GCNII | 0.8918
±0.0396 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 138 | SAGE | 0.8269 | |
| 170 | GCN | 0.8082
±0.0360 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) |
| 223 | BTM | 0.7590
±0.0476 | This paper |
| 241 | JKNet | 0.7443
±0.0830 best reported | best at pub: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) |
| 248 | GradientGCN | 0.7416
±0.0648 | This paper |
| 252 | SGC | 0.7350
±0.0430 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 38 | GCNII | 0.4082
±0.0179 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 41 | APPNP | 0.4046
±0.0064 best reported | best at pub: Feature Expansion for Graph Neural Networks (ICML 2023) best today: A Quasi-Wasserstein Loss for Learning Graph Neural Networks (WWW 2023) |
| 42 | MLP | 0.4026
±0.0108 | |
| 68 | GraphSAGE | 0.3899
±0.0085 | |
| 135 | GCN | 0.3690 best reported | best at pub: Beyond Low-frequency Information in Graph Convolutional Networks (AAAI 2021) |
| 237 | SGC | 0.3490
±0.0070 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 243 | BTM | 0.3469
±0.0051 | This paper |
| 257 | GradientGCN | 0.3428
±0.0112 | This paper |
| 281 | JKNet | 0.3342
±0.0028 best reported | best at pub: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DMD++ | 0.9190
±0.0260 | |
| 2 | F-GREAD-BS | 0.9059
±0.0380 | |
| 3 | APPNP | 0.9010
±0.0350 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: When Graph Neural Networks Meet Dynamic Mode Decomposition (ICLR 2024) |
| 37 | MLP | 0.8629
±0.0450 | |
| 63 | GCN | 0.8310
±0.0320 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 69 | GraphSAGE | 0.8118
±0.0556 | |
| 75 | GCNII | 0.8039
±0.0340 best reported | best at pub: From Node Interaction to Hop Interaction: New Effective and Scalable Graph Learning Paradigm (2022) best today: Graph Navier–Stokes Networks (2026) |
| 91 | SGC | 0.7780
±0.0470 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 118 | BTM | 0.7201
±0.0389 | This paper |
| 126 | GradientGCN | 0.7031
±0.0475 | This paper |
| 166 | JKNet | 0.6098
±0.0297 best reported | best at pub: Optimization-Induced Graph Implicit Nonlinear Diffusion (ICML 2022) Difference within reported uncertainty; not counted as underperformance. |
