Evolving Computation Graphs
Abstract
Graph neural networks (GNNs) have demonstrated success in modeling relational data, especially for data that exhibits homophily: when a connection between nodes tends to imply that they belong to the same class. However, while this assumption is true in many relevant situations, there are important real-world scenarios that violate this assumption, and this has spurred research into improving GNNs for these cases. In this work, we propose Evolving Computation Graphs (ECGs), a novel method for enhancing GNNs on heterophilic datasets. Our approach builds on prior theoretical insights linking node degree, high homophily, and inter vs intra-class embedding similarity by rewiring the GNNs’ computation graph towards adding edges that connect nodes that are likely to be in the same class. We utilise weaker classifiers to identify these edges, ultimately improving GNN performance on non-homophilic data as a result. We evaluate ECGs on a diverse set of recently-proposed heterophilous datasets and demonstrate improvements over the relevant baselines. ECG presents a simple, intuitive and elegant approach for improving GNN performance on heterophilic datasets without requiring prior domain knowledge.
Benchmark Results
Tested on 5 datasets
Tables show presented results in global context (best 3 papers + GCN + MLP).
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 | |
| 26 | GraphSAGE | 0.9106
±0.0027 | |
| 30 | ECG-GAT-sep | 0.8962
±0.0018 | This paper |
| 31 | BGRL-ECG-GAT-sep | 0.8962
±0.0018 | This paper |
| 32 | ECG-GT-sep | 0.8956
±0.0016 | This paper |
| 33 | BGRL-ECG-GT-sep | 0.8956
±0.0016 | This paper |
| 40 | GAT-sep | 0.8875
±0.0041 | This paper |
| 41 | MLPBGRL-GAT-sep | 0.8873
±0.0037 | This paper |
| 42 | MLPBGRL-GT-sep | 0.8870
±0.0030 | This paper |
| 43 | MLP->GNN-ECG-GT-sep | 0.8862
±0.0046 | This paper |
| 44 | MLP-ECG-GT-sep | 0.8856
±0.0035 | This paper |
| 46 | MLP-ECG-GAT-sep | 0.8822
±0.0036 | This paper |
| 48 | MLP->GNN-ECG-GAT-sep | 0.8804
±0.0032 | This paper |
| 49 | ECG-SAGE | 0.8788
±0.0025 | This paper |
| 50 | BGRL-ECG-SAGE | 0.8788
±0.0025 | This paper |
| 54 | GT-sep | 0.8732
±0.0039 | This paper |
| 60 | MLPBGRL-ECG-SAGE | 0.8650
±0.0034 | This paper |
| 62 | MLP->GNN-ECG-SAGE | 0.8594
±0.0057 | This paper |
| 63 | MLP-ECG-SAGE | 0.8582
±0.0062 | This paper |
| 64 | SAGE | 0.8574
±0.0067 | This paper |
| 68 | ECG-GCN | 0.8453
±0.0026 | This paper |
| 69 | MLPBGRL-ECG-GCN | 0.8453
±0.0026 | This paper |
| 71 | MLP->GNN-ECG-GCN | 0.8439
±0.0022 | This paper |
| 74 | MLP-ECG-GCN | 0.8355
±0.0039 | 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) |
| 86 | BGRL-ECG-GCN | 0.8059
±0.0048 | This paper |
| 92 | FSGNN | 0.7992
±0.0056 | This paper |
| 107 | GBK-GNN | 0.7587
±0.0043 best reported | best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) |
| 108 | FAGCN | 0.7571
±0.0139 best reported | |
| 114 | GPR-GNN | 0.7337
±0.0068 best reported | best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) |
| 122 | JacobiConv | 0.7114
±0.0042 | This paper |
| 129 | H2GCN | 0.6809
±0.0029 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) |
| 135 | MLP | 0.6665
±0.0047 best reported | best today: HyperAggregation: Aggregating over Graph Edges with Hypernetworks (2024) |
| 141 | ResNet | 0.6588
±0.0038 | This paper |
| 152 | CPGNN | 0.6396
±0.0062 | This paper |
| 154 | GloGNN | 0.6385
±0.0049 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | UniGAP | 0.6375
±0.0110 | |
| 2 | H2GCN + HalfHop | 0.5961
±0.0100 | |
| 3 | GraphSAGE + HalfHop | 0.5897
±0.0150 | |
| 7 | H2GCN | 0.5681
±0.0090 best reported | |
| 12 | SAGE | 0.5569
±0.0023 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) |
| 29 | ECG-GAT-sep | 0.5365
±0.0039 | This paper |
| 30 | MLP->GNN-ECG-GAT-sep | 0.5365
±0.0039 | This paper |
| 36 | ECG-SAGE | 0.5345
±0.0027 | This paper |
| 37 | MLP->GNN-ECG-SAGE | 0.5345
±0.0027 | This paper |
| 38 | MLP-ECG-SAGE | 0.5332
±0.0039 | This paper |
| 41 | ECG-GT-sep | 0.5325
±0.0039 | This paper |
| 42 | MLP->GNN-ECG-GT-sep | 0.5325
±0.0039 | This paper |
| 44 | BGRL-ECG-SAGE | 0.5312
±0.0032 | This paper |
| 46 | MLP-ECG-GAT-sep | 0.5298
±0.0030 | This paper |
| 50 | FSGNN | 0.5274
±0.0083 | This paper |
| 52 | GAT-sep | 0.5270
±0.0062 | This paper |
| 54 | MLP-ECG-GT-sep | 0.5268
±0.0065 | This paper |
| 57 | BGRL-ECG-GT-sep | 0.5237
±0.0030 | This paper |
| 58 | MLPBGRL-ECG-SAGE | 0.5234
±0.0092 | This paper |
| 59 | MLPBGRL-GT-sep | 0.5229
±0.0060 | This paper |
| 60 | BGRL-ECG-GAT-sep | 0.5220
±0.0057 | This paper |
| 62 | GT-sep | 0.5218
±0.0080 | This paper |
| 73 | ECG-GCN | 0.5112
±0.0038 | This paper |
| 74 | MLP->GNN-ECG-GCN | 0.5112
±0.0038 | This paper |
| 76 | MLPBGRL-GAT-sep | 0.5106
±0.0073 | This paper |
| 78 | MLP-ECG-GCN | 0.5099
±0.0064 | This paper |
| 84 | MLP | 0.5058 best reported | best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 90 | MLPBGRL-ECG-GCN | 0.5011
±0.0060 | This paper |
| 103 | GPR-GNN | 0.4937
±0.0071 best reported | best today: Piecewise Constant Spectral Graph Neural Network (TMLR 2025) |
| 107 | BGRL-ECG-GCN | 0.4899
±0.0028 | This paper |
| 114 | JacobiConv | 0.4853
±0.0096 best reported | best today: Piecewise Constant Spectral Graph Neural Network (TMLR 2025) |
| 137 | FAGCN | 0.4632
±0.0250 best reported | best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 140 | GBK-GNN | 0.4598
±0.0071 | This paper |
| 141 | ResNet | 0.4590
±0.0052 | This paper |
| 154 | CPGNN | 0.4436
±0.0035 best reported | best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) |
| 196 | GloGNN | 0.3728
±0.0066 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | BuNN | 0.9899
±0.0016 | |
| 2 | DC-GNN | 0.9850
±0.0021 | |
| 3 | Tango -GPS | 0.9839
±0.0054 | |
| 21 | ECG-GAT-sep | 0.9452
±0.0020 | This paper |
| 22 | MLP-ECG-GAT-sep | 0.9452
±0.0020 | This paper |
| 23 | MLPBGRL-GAT-sep | 0.9439
±0.0020 | This paper |
| 27 | BGRL-ECG-GAT-sep | 0.9424
±0.0015 | This paper |
| 29 | ECG-SAGE | 0.9411
±0.0007 | This paper |
| 30 | BGRL-ECG-SAGE | 0.9411
±0.0007 | This paper |
| 31 | MLP-ECG-SAGE | 0.9410
±0.0008 | This paper |
| 33 | MLPBGRL-ECG-SAGE | 0.9401
±0.0007 | This paper |
| 35 | MLP->GNN-ECG-GAT-sep | 0.9397
±0.0019 | This paper |
| 37 | GAT-sep | 0.9391
±0.0035 | This paper |
| 39 | MLP->GNN-ECG-SAGE | 0.9377
±0.0012 | This paper |
| 40 | ECG-GT-sep | 0.9362
±0.0027 | This paper |
| 41 | MLP-ECG-GT-sep | 0.9362
±0.0027 | This paper |
| 42 | GraphSAGE | 0.9358
±0.0005 | |
| 43 | BGRL-ECG-GT-sep | 0.9355
±0.0018 | This paper |
| 44 | MLPBGRL-GT-sep | 0.9352
±0.0025 | This paper |
| 46 | SAGE | 0.9351
±0.0057 | This paper |
| 50 | MLP->GNN-ECG-GT-sep | 0.9269
±0.0034 | This paper |
| 51 | ECG-GCN | 0.9263
±0.0010 | This paper |
| 52 | MLP-ECG-GCN | 0.9263
±0.0010 | This paper |
| 54 | MLP->GNN-ECG-GCN | 0.9256
±0.0023 | This paper |
| 55 | MLPBGRL-ECG-GCN | 0.9247
±0.0050 | This paper |
| 56 | BGRL-ECG-GCN | 0.9235
±0.0010 | This paper |
| 57 | GT-sep | 0.9229
±0.0047 | 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) |
| 76 | GBK-GNN | 0.9085
±0.0058 | This paper |
| 83 | FSGNN | 0.9008
±0.0070 | This paper |
| 85 | H2GCN | 0.8995
±0.0038 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 91 | FAGCN | 0.8969
±0.0060 best reported | best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) |
| 93 | JacobiConv | 0.8966
±0.0040 | This paper |
| 110 | GPR-GNN | 0.8624
±0.0061 | This paper |
| 137 | CPGNN | 0.7127
±0.0114 best reported | best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) |
| 148 | GloGNN | 0.6253
±0.0134 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) |
| 156 | MLP | 0.5099
±0.0147 best reported | best today: Graph Homophily Booster: Rethinking the Role of Discrete Features on Heterophilic Graphs (2025) Difference within reported uncertainty; not counted as underperformance. |
| 157 | ResNet | 0.5095
±0.0112 best reported | best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| # | 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 | |
| 18 | ECG-GCN | 0.8481
±0.0025 | This paper |
| 19 | MLP-ECG-GCN | 0.8481
±0.0025 | This paper |
| 22 | MLPBGRL-ECG-GCN | 0.8473
±0.0023 | This paper |
| 31 | MLP->GNN-ECG-GCN | 0.8435
±0.0031 | This paper |
| 32 | BGRL-ECG-GCN | 0.8425
±0.0022 | This paper |
| 33 | ECG-GAT-sep | 0.8423
±0.0025 | This paper |
| 34 | BGRL-ECG-GAT-sep | 0.8423
±0.0025 | This paper |
| 36 | MLPBGRL-GAT-sep | 0.8411
±0.0023 | This paper |
| 37 | ECG-GT-sep | 0.8400
±0.0024 | This paper |
| 38 | MLPBGRL-GT-sep | 0.8400
±0.0024 | This paper |
| 40 | MLP-ECG-GAT-sep | 0.8391
±0.0032 | This paper |
| 41 | GAT-sep | 0.8378
±0.0043 | This paper |
| 45 | MLP->GNN-ECG-GAT-sep | 0.8375
±0.0030 | This paper |
| 49 | MLP-ECG-GT-sep | 0.8365
±0.0029 | This paper |
| 50 | GCN | 0.8364
±0.0067 | This paper |
| 57 | MLP->GNN-ECG-GT-sep | 0.8341
±0.0044 | This paper |
| 63 | BGRL-ECG-GT-sep | 0.8297
±0.0026 | This paper |
| 66 | FSGNN | 0.8276
±0.0061 | This paper |
| 68 | ECG-SAGE | 0.8261
±0.0029 | This paper |
| 69 | BGRL-ECG-SAGE | 0.8261
±0.0029 | This paper |
| 70 | MLP-ECG-SAGE | 0.8260
±0.0023 | This paper |
| 71 | MLPBGRL-ECG-SAGE | 0.8255
±0.0018 | This paper |
| 73 | GT-sep | 0.8252
±0.0092 | This paper |
| 74 | MLP->GNN-ECG-SAGE | 0.8252
±0.0022 | This paper |
| 76 | SAGE | 0.8243
±0.0044 | This paper |
| 77 | GraphSAGE | 0.8243
±0.0044 | |
| 85 | GBK-GNN | 0.8101
±0.0067 | This paper |
| 113 | H2GCN | 0.7815 best reported | best at pub: Graph Neural Networks for Graphs with Heterophily: A Survey (2022) |
| 116 | FAGCN | 0.7812 best reported | best today: Language Models as Messengers: Enhancing Message Passing in Heterophilic Graph Learning (2025) Difference within reported uncertainty; not counted as underperformance. |
| 139 | MLP | 0.7362
±0.0020 best reported | best today: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) Difference within reported uncertainty; not counted as underperformance. |
| 140 | GloGNN | 0.7339
±0.0117 | This paper |
| 141 | CPGNN | 0.7336
±0.0101 | This paper |
| 142 | ResNet | 0.7295
±0.0106 | This paper |
| 143 | GPR-GNN | 0.7294
±0.0097 | This paper |
| 154 | JacobiConv | 0.6866
±0.0065 | This paper |
| # | Model | ROC-AUC ↑ | Paper |
|---|---|---|---|
| 1 | NID_GAT | 0.9703
±0.0002 | |
| 2 | NID_GCN | 0.9685
±0.0010 | |
| 3 | UniGAP | 0.8421
±0.0080 | |
| 13 | H2GCN | 0.7928
±0.0080 best reported | |
| 16 | GCN | 0.7902
±0.0060 best reported | |
| 21 | FSGNN | 0.7886
±0.0092 | This paper |
| 27 | ECG-GT-sep | 0.7812
±0.0032 | This paper |
| 28 | BGRL-ECG-GT-sep | 0.7812
±0.0032 | This paper |
| 29 | GT-sep | 0.7805
±0.0093 | This paper |
| 32 | MLPBGRL-GT-sep | 0.7785
±0.0045 | This paper |
| 35 | MLP-ECG-GT-sep | 0.7782
±0.0043 | This paper |
| 37 | ECG-GCN | 0.7750
±0.0035 | This paper |
| 38 | BGRL-ECG-GCN | 0.7750
±0.0035 | This paper |
| 39 | ECG-GAT-sep | 0.7738
±0.0018 | This paper |
| 40 | BGRL-ECG-GAT-sep | 0.7738
±0.0018 | This paper |
| 41 | MLPBGRL-ECG-GCN | 0.7732
±0.0031 | This paper |
| 42 | MLP-ECG-GAT-sep | 0.7730
±0.0047 | This paper |
| 43 | FAGCN | 0.7724
±0.0126 | This paper |
| 44 | ECG-SAGE | 0.7723
±0.0036 | This paper |
| 45 | BGRL-ECG-SAGE | 0.7723
±0.0036 | This paper |
| 46 | GraphSAGE | 0.7721
±0.0130 | |
| 49 | MLPBGRL-GAT-sep | 0.7697
±0.0045 | This paper |
| 54 | GAT-sep | 0.7679
±0.0071 | This paper |
| 57 | MLPBGRL-ECG-SAGE | 0.7655
±0.0033 | This paper |
| 58 | SAGE | 0.7644
±0.0062 | This paper |
| 60 | MLP-ECG-GCN | 0.7625
±0.0059 | This paper |
| 62 | MLP-ECG-SAGE | 0.7613
±0.0041 | This paper |
| 69 | MLP->GNN-ECG-GAT-sep | 0.7561
±0.0074 | This paper |
| 71 | MLP->GNN-ECG-SAGE | 0.7553
±0.0064 | This paper |
| 72 | MLP->GNN-ECG-GT-sep | 0.7550
±0.0113 | This paper |
| 77 | MLP->GNN-ECG-GCN | 0.7516
±0.0087 | This paper |
| 81 | GBK-GNN | 0.7447
±0.0086 | This paper |
| 85 | JacobiConv | 0.7388
±0.0116 | This paper |
| 86 | GPR-GNN | 0.7341
±0.0124 best reported | best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) |
| 96 | MLP | 0.7082
±0.0010 best reported | best today: Gumbel-MPNN: Graph Rewiring with Gumbel-Softmax (2025) Difference within reported uncertainty; not counted as underperformance. |
| 101 | ResNet | 0.7034
±0.0076 | This paper |
| 119 | GloGNN | 0.6715
±0.0192 best reported | best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
| 120 | CPGNN | 0.6709
±0.0263 best reported | best today: Distributed-Order Fractional Graph Operating Network (NeurIPS 2024) Difference within reported uncertainty; not counted as underperformance. |
