Uncertainty-Aware Graph Neural Networks: A Multi-Hop Evidence Fusion Approach
Abstract
Graph neural networks (GNNs) excel in graph representation learning by integrating graph structure and node features. Existing GNNs, unfortunately, fail to account for the uncertainty of class probabilities that vary with the depth of the model, leading to unreliable and risky predictions in real-world scenarios. To bridge the gap, in this paper, we propose a novel vidence using raph eural etwork (EFGNN for short) to achieve trustworthy prediction, enhance node classification accuracy, and make explicit the risk of wrong predictions. In particular, we integrate the evidence theory with multi-hop propagation-based GNN architecture to quantify the prediction uncertainty of each node with the consideration of multiple receptive fields. Moreover, a parameter-free cumulative belief fusion (CBF) mechanism is developed to leverage the changes in prediction uncertainty and fuse the evidence to improve the trustworthiness of the final prediction. To effectively optimize the EFGNN model, we carefully design a joint learning objective composed of evidence cross-entropy, dissonance coefficient, and false confident penalty. The experimental results on various datasets and theoretical analyses demonstrate the effectiveness of the proposed model in terms of accuracy and trustworthiness, as well as its robustness to potential attacks. The source code of EFGNN is available at https://github.com/Shiy-Li/EFGNN.
Benchmark Results
Tested on 4 datasets 18 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | 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: LOGIN: A Large Language Model Consulted Graph Neural Network Training Framework (2024) |
| 18 | GCN | 0.9296
±0.0015 best reported | |
| 20 | GAT | 0.9233
±0.0018 best reported | |
| 36 | ResGCN | 0.9110 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 135 | JK-Net | 0.8841
±0.0001 best reported | best at pub: LOGIN: A Large Language Model Consulted Graph Neural Network Training Framework (2024) |
| 210 | MLP | 0.8690
±0.0074 | |
| 320 | EFGNN | 0.8240
±0.0020 | This paper |
| 390 | GAMLP | 0.8080
±0.0050 | This paper |
| 444 | AP-GCN | 0.8010
±0.0070 best reported | best at pub: Adversarial Graph Disentanglement with Component-specific Aggregation (2021) Difference within reported uncertainty; not counted as underperformance. |
| 466 | S²GC | 0.7990
±0.0030 | This paper |
| 465 | AGNN | 0.7990
±0.0700 best reported | best at pub: Attention-based Graph Neural Network for Semi-supervised Learning (2018) Difference within reported uncertainty; not counted as underperformance. |
| 478 | Flip-APPNP | 0.7980
±0.0060 | This paper |
| 484 | SIGN | 0.7970
±0.0043 best reported | best at pub: PaSca: a Graph Neural Architecture Search System under the Scalable Paradigm (WWW 2022) best today: Gauge-Equivariant Graph Networks via Self-Interference Cancellation (2025) Difference within reported uncertainty; not counted as underperformance. |
| 548 | CaGCN | 0.7930
±0.0150 | This paper |
| 579 | S-BGCN-T | 0.7910
±0.0020 | This paper |
| 580 | GKDE | 0.7910
±0.0020 | This paper |
| 594 | Drop-GCN | 0.7900
±0.0030 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9703
±0.0019 | |
| 2 | GAT | 0.9669
±0.0014 best reported | |
| 3 | GAT+T | 0.9660
±0.0007 | |
| 7 | SAGE | 0.9643
±0.0027 | |
| 8 | GCN | 0.9632
±0.0008 best reported | |
| 21 | APPNP | 0.9573
±0.0012 best reported | best at pub: NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification (2024) |
| 50 | SGC | 0.9511
±0.0009 best reported | |
| 117 | EFGNN | 0.9380
±0.0010 | This paper |
| 271 | GAMLP | 0.9260
±0.0080 | This paper |
| 313 | CaGCN | 0.9230
±0.0060 | This paper |
| 332 | AP-GCN | 0.9210
±0.0030 | This paper |
| 343 | Drop-GCN | 0.9200
±0.0010 | This paper |
| 349 | JK-Net | 0.9190
±0.0070 | This paper |
| 350 | Flip-APPNP | 0.9190
±0.0030 | This paper |
| 363 | SIGN | 0.9170
±0.0070 | This paper |
| 388 | ResGCN | 0.9130
±0.0090 | This paper |
| 390 | MLP | 0.9128
±0.0063 | |
| 478 | AGNN | 0.8890
±0.0150 | This paper |
| 487 | GKDE | 0.8830
±0.0160 | This paper |
| 525 | S-BGCN-T | 0.8180
±0.0130 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphTARIF | 0.9461
±0.0017 | |
| 2 | GCN | 0.9412
±0.0008 best reported | best at pub: Diss-l-ECT: Dissecting Graph Data with local Euler Characteristic Transforms (ICML 2024) |
| 3 | GAT | 0.9398
±0.0022 best reported | best at pub: Diss-l-ECT: Dissecting Graph Data with local Euler Characteristic Transforms (ICML 2024) |
| 8 | SAGE | 0.9351
±0.0006 | |
| 58 | APPNP | 0.9093
±0.0018 best reported | best at pub: NTFormer: A Composite Node Tokenized Graph Transformer for Node Classification (2024) |
| 82 | SGC | 0.9022
±0.0021 best reported | |
| 308 | AP-GCN | 0.8518
±0.0023 best reported | best at pub: Adaptive Propagation Graph Convolutional Network (2020) |
| 320 | MLP | 0.8463 | |
| 326 | EFGNN | 0.8450
±0.0040 | This paper |
| 343 | GAMLP | 0.8420
±0.0050 | |
| 378 | SIGN | 0.8310
±0.0080 | This paper |
| 380 | S2GC | 0.8310
±0.0070 | This paper |
| 404 | JK-Net | 0.8200
±0.0060 | This paper |
| 406 | CaGCN | 0.8200
±0.0160 | This paper |
| 417 | Drop-GCN | 0.8120
±0.0050 | This paper |
| 418 | ResGCN | 0.8110
±0.0070 | This paper |
| 423 | Flip-APPNP | 0.8080
±0.0010 | This paper |
| 440 | S-BGCN-T | 0.7830
±0.0150 | This paper |
| 442 | GKDE | 0.7810
±0.0200 | This paper |
| 449 | AGNN | 0.7570
±0.0240 | This paper |
Heterophilic Graphs
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | DiGGR | 0.4535
±0.0353 | |
| 2 | TRIGON | 0.4402
±0.0028 | |
| 3 | DoG | 0.4320
±0.0120 | |
| 33 | SIGN | 0.4122
±0.0096 best reported | best at pub: Optimizing Polynomial Graph Filters: A Novel Adaptive Krylov Subspace Approach (WWW 2024) |
| 41 | APPNP | 0.4046
±0.0064 best reported | best at pub: 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) |
| 182 | GAT | 0.3605
±0.0035 best reported | best at pub: Hierarchical Graph Transformer with Adaptive Node Sampling (NeurIPS 2022) |
| 298 | AGNN | 0.3220 best reported | |
| 353 | EFGNN | 0.3000
±0.0030 | This paper |
| 355 | Flip-APPNP | 0.2990
±0.0110 | This paper |
| 422 | CaGCN | 0.2570
±0.0100 | This paper |
| 436 | JK-Net | 0.2490
±0.0040 | This paper |
| 445 | ResGCN | 0.2380
±0.0280 | This paper |
| 450 | S²GC | 0.2350
±0.0020 | This paper |
| 468 | GAMLP | 0.2220
±0.0140 | This paper |
| 475 | S-BGCN-T | 0.2160
±0.0060 | This paper |
| 484 | AP-GCN | 0.2070
±0.0290 | This paper |
| 487 | Drop-GCN | 0.2050
±0.0060 | This paper |
| 489 | GKDE | 0.1970
±0.0110 | This paper |
