Optimization-Induced Graph Implicit Nonlinear Diffusion
Abstract
Due to the over-smoothing issue, most existing graph neural networks can only capture limited dependencies with their inherently finite aggregation layers. To overcome this limitation, we propose a new kind of graph convolution, called Graph Implicit Nonlinear Diffusion (GIND), which implicitly has access to infinite hops of neighbors while adaptively aggregating features with nonlinear diffusion to prevent over-smoothing. Notably, we show that the learned representation can be formalized as the minimizer of an explicit convex optimization objective. With this property, we can theoretically characterize the equilibrium of our GIND from an optimization perspective. More interestingly, we can induce new structural variants by modifying the corresponding optimization objective. To be specific, we can embed prior properties to the equilibrium, as well as introducing skip connections to promote training stability. Extensive experiments show that GIND is good at capturing long-range dependencies, and performs well on both homophilic and heterophilic graphs with nonlinear diffusion. Moreover, we show that the optimization-induced variants of our models can boost the performance and improve training stability and efficiency as well. As a result, our GIND obtains significant improvements on both node-level and graph-level tasks.
Benchmark Results
Tested on 11 datasets 21 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 44 | GCN | 0.8033
±0.0088 | |
| 62 | JKNet | 0.7920 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 111 | H2GCN | 0.7711 | prev best: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) Improvement within reported uncertainty; not highlighted. |
| 115 | GIND | 0.7695
±0.0173 | This paper |
| 168 | EIGNN* | 0.7531 | This paper |
| 171 | IGNN* | 0.7524 | This paper |
| 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 | |
| 16 | H2GCN | 0.8949 | prev best: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) best today: Adaptive Tokenization: On the Hop-Overpriority Problem in Tokenized Graph Learning Models (2025) Improvement within reported uncertainty; not highlighted. |
| 18 | GCN | 0.9296
±0.0015 | |
| 24 | JKNet | 0.9160 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 160 | EIGNN* | 0.8792 | This paper |
| 180 | IGNN* | 0.8766 | This paper |
| 210 | MLP | 0.8690
±0.0074 |
| # | Model | F1 ↑ | Paper |
|---|---|---|---|
| 1 | GAMLP(JK) | 0.9982
±0.0001 | |
| 2 | GraphCON-GCN | 0.9960 | |
| 3 | GCNII | 0.9953
±0.0001 | |
| 21 | GCN | 0.9850 best reported | best at pub: Graph-Coupled Oscillator Networks (ICML 2022) |
| 25 | GIND | 0.9840 | This paper |
| 33 | EIGNN | 0.9800 | This paper |
| 51 | IGNN | 0.9760 best reported | best today: Graph Neural Networks Gone Hogwild (ICLR 2024) |
| 92 | GIN | 0.8724
±0.0002 | |
| 101 | GraphSAGE | 0.7860 | prev best: Graph Neural Networks With Convolutional ARMA Filters (2019) |
| 173 | MLP | 0.4620 |
TU Dortmund
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9910
±0.0030 | |
| 2 | ID-GNN+BEC | 0.9830
±0.0360 | |
| 3 | SupCosine | 0.9830
±0.0250 | |
| 39 | GIN | 0.9330
±0.0290 | |
| 241 | CGS | 0.8940
±0.0560 | This paper |
| 259 | GIND | 0.8930
±0.0740 | This paper |
| 262 | IGNN* | 0.8930
±0.0670 best reported | best at pub: Implicit Graph Neural Networks (NeurIPS 2020) best today: Graph Neural Networks Gone Hogwild (ICLR 2024) |
| 403 | MLP | 0.8660
±0.0495 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 | |
| 3 | GCN | 0.9727 | |
| 131 | GraphSAGE | 0.8200
±0.0100 | |
| 196 | IGNN* | 0.8050
±0.0190 best reported | best at pub: Implicit Graph Neural Networks (NeurIPS 2020) |
| 274 | GIND | 0.7880
±0.0170 | This paper |
| 333 | CGS | 0.7760
±0.0200 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | MSH-GNN | 0.9410
±0.0330 | |
| 2 | GRDL | 0.8260
±0.0120 | |
| 3 | GMN | 0.8225 | |
| 32 | GIN | 0.7880
±0.0410 | |
| 56 | IGNN* | 0.7770
±0.0340 best reported | best today: Graph Neural Networks Gone Hogwild (ICLR 2024) Difference within reported uncertainty; not counted as underperformance. |
| 72 | GIND | 0.7720
±0.0290 | This paper |
| 127 | CGS | 0.7630
±0.0490 | This paper |
| 149 | MLP | 0.7600
±0.0320 |
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 | |
| 40 | H2GCN | 0.9189
±0.0393 best reported | best at pub: Graph-Coupled Oscillator Networks (ICML 2022) best today: GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers (ICML 2024) Difference within reported uncertainty; not counted as underperformance. |
| 46 | APPNP | 0.9131
±0.0197 best reported | best at pub: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 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) |
| 112 | GIND | 0.8622
±0.0519 | This paper |
| 158 | EIGNN | 0.8460
±0.0541 | This paper |
| 211 | GAT | 0.8162
±0.0645 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Equivariance Everywhere All At Once: A Recipe for Graph Foundation Models (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) |
| 392 | JKNet | 0.6378
±0.0630 | prev best: Bag of Tricks for Training Deeper Graph Neural Networks: A Comprehensive Benchmark Study (2021) Improvement within reported uncertainty; not highlighted. |
| 534 | IGNN | 0.5837
±0.0582 | 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: Convolutional Neural Networks on Graphs with Chebyshev Approximation, Revisited (NeurIPS 2022) best today: 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) |
| 68 | H2GCN | 0.8623
±0.0471 best reported | best at pub: Graph-Coupled Oscillator Networks (ICML 2022) best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) Difference within reported uncertainty; not counted as underperformance. |
| 80 | GIND | 0.8568
±0.0383 | This paper |
| 91 | EIGNN | 0.8513
±0.0557 | This paper |
| 138 | SAGE | 0.8269 | |
| 158 | GAT | 0.8190
±0.0540 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 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) |
| 241 | JKNet | 0.5818
±0.0387 | prev best: Bag of Tricks for Training Deeper Graph Neural Networks: A Comprehensive Benchmark Study (2021) best today: Bayesian Neighborhood Adaptation for Graph Neural Networks (TMLR 2025) Improvement within reported uncertainty; not highlighted. |
| 365 | IGNN | 0.6135
±0.0484 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | IBG-NN | 0.7763
±0.0179 | |
| 2 | Dir-GNN+CNA | 0.7747
±0.0128 | |
| 3 | DHGNN | 0.7684
±0.0161 | |
| 39 | H2GCN | 0.4075
±0.0144 | prev best: Block Modeling-Guided Graph Convolutional Neural Networks (AAAI 2021) best today: Efficient Learning on Large Graphs using a Densifying Regularity Lemma (2025) |
| 46 | GCN | 0.6067 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 63 | GIND | 0.5671
±0.0207 | This paper |
| 67 | GAT | 0.5630
±0.0220 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 68 | APPNP | 0.5590
±0.0290 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 106 | EIGNN | 0.4637
±0.0139 | This paper |
| 120 | SAGE | 0.4460
±0.0130 | |
| 156 | JKNet | 0.4081
±0.0260 best reported | |
| 172 | MLP | 0.3930
±0.0079 | |
| 176 | GCNII | 0.3881
±0.0197 best reported | best today: $P^2$GNN: Two Prototype Sets to boost GNN Performance (2026) |
| 263 | IGNN | 0.2499
±0.0211 | This paper |
| # | 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) |
| 19 | GIND | 0.8804
±0.0397 | This paper |
| 22 | H2GCN | 0.8790
±0.0420 best reported | best today: When Graph Neural Networks Meet Dynamic Mode Decomposition (ICLR 2024) Difference within reported uncertainty; not counted as underperformance. |
| 33 | EIGNN | 0.8686
±0.0554 | This paper |
| 37 | MLP | 0.8629
±0.0450 | |
| 53 | GAT | 0.8430
±0.0370 best reported | best at pub: Restructuring Graphs for Higher Homophily via Adaptive Spectral Clustering (AAAI 2022) |
| 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 today: Graph Navier–Stokes Networks (2026) Difference within reported uncertainty; not counted as underperformance. |
| 166 | JKNet | 0.6098
±0.0297 | This paper |
| 193 | IGNN | 0.5353
±0.0649 | This paper |
