GCCM: Enhancing Generative Graph Prediction via Contrastive Consistency Model
Abstract
Conditional generative models, particularly diffusion-based methods, have recently been applied to graph prediction by modeling the target as a conditional distribution given the input graph, yielding competitive results compared to deterministic predictor. However, existing diffusion-based prediction methods typically require expensive iterative denoising at inference and often suffer from unstable sampling, which motivates recent efforts to reduce inference denoising steps and enable stable sampling via techniques such as consistency training. Despite this progress, we find that existing consistency training methods for graph prediction could potentially fall into a shortcut solution: the model may attempt to satisfy the self-consistency constraint by ignoring the noisy target (i.e., assigning it negligible weight), ultimately collapsing into a purely deterministic predictor. To mitigate such shortcut solution, we propose GCCM, a graph contrastive consistency model that goes beyond isolated pairwise matching between the same target at different noise levels by introducing negative pairs into a contrastive consistency objective. This adds an additional separation requirement, making the shortcut solution no longer trivially sufficient to satisfy the proposed objective. Moreover, we apply feature perturbation to the input node/edge features to break identical conditioning on the input graph, so that the shortcut no longer yields the same predictions across noise levels and becomes less attractive. Extensive experiments on benchmark datasets demonstrate that GCCM mitigates the shortcut solution and yields consistent performance improvements in graph prediction compared to deterministic predictors.
Benchmark Results
Tested on 6 datasets 18 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
LRGB
| # | 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 best reported | best at pub: Where Did the Gap Go? Reassessing the Long-Range Graph Benchmark (TMLR 2023) best today: Plain Transformers Can be Powerful Graph Learners (2025) |
| 21 | GCCM | 0.4219
±0.0102 | This paper |
| 25 | GPS-PCL | 0.4196
±0.0086 | This paper |
| 39 | GPS-LGD | 0.3912
±0.0207 | This paper |
| 41 | GatedGCN | 0.3880
±0.0040 best reported | best at pub: Where Did the Gap Go? Reassessing the Long-Range Graph Benchmark (TMLR 2023) best today: Plain Transformers Can be Powerful Graph Learners (2025) |
| 42 | Gated-GCN | 0.3880
±0.0040 | |
| 66 | SAN | 0.3230
±0.0039 | This paper |
| 81 | GCN | 0.2380
±0.0160 best reported | best at pub: When Graph Neural Networks Meet Dynamic Mode Decomposition (ICLR 2024) |
| 93 | MLP | 0.1140
±0.0230 |
| # | Model | F1 ↑ | Paper |
|---|---|---|---|
| 1 | FloydNet | 0.4901 | |
| 2 | CRaWl | 0.4588
±0.0079 | |
| 3 | GPS | 0.4440
±0.0065 best reported | best at pub: Where Did the Gap Go? Reassessing the Long-Range Graph Benchmark (TMLR 2023) |
| 16 | GatedGCN | 0.3880
±0.0040 best reported | best at pub: Where Did the Gap Go? Reassessing the Long-Range Graph Benchmark (TMLR 2023) |
| 20 | GCCM | 0.3856
±0.0021 | This paper |
| 21 | GPS-PCL | 0.3816
±0.0058 | This paper |
| 33 | Gated-GCN | 0.2922
±0.0018 | |
| 37 | SAN | 0.2592
±0.0158 | This paper |
| 45 | GCN | 0.2078
±0.0031 best reported | best at pub: Where Did the Gap Go? Reassessing the Long-Range Graph Benchmark (TMLR 2023) |
| 74 | MLP | 0.0310
±0.0160 |
GNNBenchmark
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | Schrödinger | 0.9913
±0.0004 | |
| 2 | CNN | 0.9907
±0.0007 | |
| 3 | MPNN | 0.9895
±0.0006 | |
| 11 | GatedGCN | 0.9855
±0.0002 best reported | best at pub: RandAlign: A Parameter-Free Method for Regularizing Graph Convolutional Networks (2024) |
| 32 | GIN | 0.9833
±0.0011 best reported | best at pub: Graph-Coupled Oscillator Networks (ICML 2022) |
| 37 | GCCM | 0.9824
±0.0006 | This paper |
| 47 | EGT | 0.9817
±0.0009 | This paper |
| 55 | GPS-PCL | 0.9811
±0.0018 | This paper |
| 56 | GRIT | 0.9811
±0.0011 | This paper |
| 59 | GPS | 0.9808
±0.0011 | prev best: Recipe for a General, Powerful, Scalable Graph Transformer (NeurIPS 2022) Improvement within reported uncertainty; not highlighted. |
| 75 | PNA | 0.9794
±0.0012 | This paper |
| 86 | GAT | 0.9755
±0.0003 best reported | best at pub: RandAlign: A Parameter-Free Method for Regularizing Graph Convolutional Networks (2024) |
| 95 | GraphSAGE | 0.9731
±0.0010 | |
| 125 | GPS-LGD | 0.9546
±0.0061 | This paper |
| 126 | MLP | 0.9534
±0.0014 | |
| 135 | GCN | 0.9405
±0.0005 best reported | best at pub: RandAlign: A Parameter-Free Method for Regularizing Graph Convolutional Networks (2024) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | RandAlign | 0.7942
±0.0007 | |
| 2 | differential encoding | 0.7907
±0.0027 | |
| 3 | PPGT | 0.7856
±0.0070 | |
| 7 | GRIT | 0.7647
±0.0088 | This paper |
| 38 | PNA | 0.7311
±0.0011 best reported | best at pub: From Stars to Subgraphs: Uplifting Any GNN with Local Structure Awareness (ICLR 2021) |
| 40 | DGN | 0.7284
±0.0042 best reported | best at pub: From Stars to Subgraphs: Uplifting Any GNN with Local Structure Awareness (ICLR 2021) Difference within reported uncertainty; not counted as underperformance. |
| 43 | GCCM | 0.7250
±0.0029 | This paper |
| 44 | GIN-AK+ | 0.7239
±0.0038 best reported | best at pub: Improving Subgraph-GNNs via Edge-Level Ego-Network Encodings (TMLR 2023) Difference within reported uncertainty; not counted as underperformance. |
| 46 | GPS | 0.7236
±0.0032 | prev best: Recipe for a General, Powerful, Scalable Graph Transformer (NeurIPS 2022) Improvement within reported uncertainty; not highlighted. |
| 58 | GPS-PCL | 0.7183
±0.0022 | This paper |
| 62 | GatedGCN | 0.7133
±0.0039 best reported | best at pub: Formatting Instructions for ICLR 2021 Conference Submissions (2020) |
| 68 | GPS-LGD | 0.7016
±0.0036 | This paper |
| 82 | EGT | 0.6870
±0.0041 | This paper |
| 92 | GraphSAGE | 0.6690
±0.0020 | |
| 101 | GAT | 0.6611
±0.0098 best reported | best at pub: Formatting Instructions for ICLR 2021 Conference Submissions (2020) |
| 109 | GIN | 0.6510
±0.0050 best reported | best at pub: Beyond Low-pass Filtering: Graph Convolutional Networks with Automatic Filtering (2021) |
| 124 | GCN | 0.5839
±0.0073 best reported | best at pub: From Stars to Subgraphs: Uplifting Any GNN with Local Structure Awareness (ICLR 2021) |
| 126 | MLP | 0.5634
±0.0018 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GRPE-Small | 0.8159
±0.0019 | |
| 2 | TANGO-GPS | 0.8011
±0.0014 | |
| 3 | GRIT | 0.8003
±0.0028 | This paper |
| 6 | EGT | 0.7923
±0.0035 | This paper |
| 9 | GCCM | 0.7882
±0.0019 | This paper |
| 17 | GPS-PCL | 0.7817
±0.0023 | This paper |
| 22 | GPS | 0.7802
±0.0018 best reported | best at pub: Recipe for a General, Powerful, Scalable Graph Transformer (NeurIPS 2022) best today: DARTS-GT: Differentiable Architecture Search for Graph Transformers with Quantifiable Instance-Specific Interpretability Analysis (2025) Difference within reported uncertainty; not counted as underperformance. |
| 48 | GPS-LGD | 0.7677
±0.0030 | This paper |
| 50 | SAN | 0.7669
±0.0065 | This paper |
| 54 | GatedGCN | 0.7608
±0.0020 best reported | best at pub: GRPE: Relative Positional Encoding for Graph Transformer (2022) |
| 67 | GAT | 0.7059
±0.0045 | This paper |
| 70 | GCN | 0.6903
±0.0137 best reported | best at pub: Recurrent Distance Filtering for Graph Representation Learning (ICML 2023) Difference within reported uncertainty; not counted as underperformance. |
| 79 | GIN | 0.6472
±0.0155 | This paper |
| 80 | GraphSAGE | 0.6388
±0.0011 | |
| 114 | MLP | 0.2097
±0.0000 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DeepGraph (48) | 0.9066
±0.0006 | |
| 2 | GRIT (our run) | 0.9041
±0.0023 | |
| 3 | GRIT 2-QiQRW | 0.9016
±0.0045 | |
| 6 | GRIT | 0.8722
±0.0003 best reported | best at pub: Benchmarking Positional Encodings for GNNs and Graph Transformers (KDD 2024) Difference within reported uncertainty; not counted as underperformance. |
| 19 | GIN-AK+ | 0.8685
±0.0006 | This paper |
| 24 | EGT | 0.8682
±0.0002 | This paper |
| 30 | GCCM | 0.8677
±0.0004 | This paper |
| 48 | GPS-PCL | 0.8669
±0.0007 | This paper |
| 50 | GPS | 0.8669
±0.0590 best reported | best at pub: Enhancing Graph Neural Networks with Quantum Computed Encodings (2023) best today: DARTS-GT: Differentiable Architecture Search for Graph Transformers with Quantifiable Instance-Specific Interpretability Analysis (2025) Difference within reported uncertainty; not counted as underperformance. |
| 51 | DGN | 0.8668
±0.0003 | This paper |
| 58 | SAN | 0.8658
±0.0004 | This paper |
| 66 | GatedGCN | 0.8651
±0.0008 best reported | best at pub: IJCAI--23 Formatting Instructions (IJCAI 2023) |
| 84 | GPS-LGD | 0.8566
±0.0018 | This paper |
| 88 | GCN | 0.8561
±0.0003 best reported | best at pub: Recurrent Distance Filtering for Graph Representation Learning (ICML 2023) |
| 89 | GIN | 0.8559
±0.0001 best reported | best at pub: Factorizable Graph Convolutional Networks (NeurIPS 2020) best today: GNNBenchmark (JMLR 2023) Difference within reported uncertainty; not counted as underperformance. |
| 107 | GAT | 0.7827
±0.0019 | This paper |
| 123 | MLP | 0.5052 | |
| 124 | GraphSAGE | 0.5052
±0.0000 |
