AutoGEL: An Automated Graph Neural Network with Explicit Link Information
Abstract
Recently, Graph Neural Networks (GNNs) have gained popularity in a variety of real-world scenarios. Despite the great success, the architecture design of GNNs heavily relies on manual labor. Thus, automated graph neural network (AutoGNN) has attracted interest and attention from the research community, which makes significant performance improvements in recent years. However, existing AutoGNN works mainly adopt an implicit way to model and leverage the link information in the graphs, which is not well regularized to the link prediction task on graphs, and limits the performance of AutoGNN for other graph tasks. In this paper, we present a novel AutoGNN work that explicitly models the link information, abbreviated to AutoGEL. In such a way, AutoGEL can handle the link prediction task and improve the performance of AutoGNNs on the node classification and graph classification task. Specifically, AutoGEL proposes a novel search space containing various design dimensions at both intra-layer and inter-layer designs and adopts a more robust differentiable search algorithm to further improve efficiency and effectiveness. Experimental results on benchmark data sets demonstrate the superiority of AutoGEL on several tasks.
Benchmark Results
Tested on 4 datasets 3 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
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 best reported | best at pub: ProtGNN: Towards Self-Explaining Graph Neural Networks (AAAI 2021) Difference within reported uncertainty; not counted as underperformance. |
| 54 | PatchySan | 0.9260
±0.0420 best reported | best at pub: How Powerful are Graph Neural Networks? (ICLR 2018) best today: Simplifying Graph Convolutional Networks with Redundancy-Free Neighbors (2025) |
| 63 | GCN | 0.9220
±0.0440 best reported | best at pub: Breaking the Limits of Message Passing Graph Neural Networks (ICML 2021) best today: Depth-Adaptive Graph Neural Networks via Learnable Bakry-Émery Curvature (KDD 2025) Difference within reported uncertainty; not counted as underperformance. |
| 158 | GraphSAGE | 0.9040
±0.0780 best reported | best at pub: Graph Neural Networks With Convolutional ARMA Filters (2019) best today: Asynchronous Neural Networks for Learning in Graphs (2022) Difference within reported uncertainty; not counted as underperformance. |
| 403 | MLP | 0.8660
±0.0495 | |
| 425 | DGCNN | 0.8583
±0.0116 best reported | best at pub: Deep Learning on Attributed Graphs: A Journey from Graphs to Their Embeddings and Back (2018) best today: Graph Structure Refinement with Energy-based Contrastive Learning (AAAI 2024) |
| 718 | SAGE | 0.7490
±0.0870 | |
| 799 | NAS-GCN | 0.4780 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSNN | 0.7790
±0.0360 | |
| 2 | SIN | 0.7560
±0.0320 | |
| 3 | CIN | 0.7560
±0.0370 | |
| 5 | GIN | 0.7510
±0.0510 best reported | best at pub: Graph Homomorphism Convolution (ICML 2020) best today: Empowering GNNs via Edge-Aware Weisfeiler-Leman Algorithm (TMLR 2022) |
| 38 | GCN | 0.5190 | This paper |
| 46 | GraphSAGE | 0.5090 | This paper |
| 78 | DGCNN | 0.4900
±0.0356 best reported | best at pub: Pooling Architecture Search for Graph Classification (2021) Difference within reported uncertainty; not counted as underperformance. |
| 86 | SAGE | 0.4853
±0.0543 | |
| 91 | NAS-GCN | 0.4780 | This paper |
| 106 | PatchySan | 0.4520 | This paper |
Knowledge Graphs
| # | Model | MRR ↑ | Paper |
|---|---|---|---|
| 1 | FedSage | 0.8426
±0.0026 | |
| 2 | FED-PUB | 0.8348
±0.0025 | |
| 3 | FedAvg | 0.8252
±0.0023 | |
| 7 | GCN | 0.8171
±0.0030 | |
| 61 | AutoGEL | 0.4790 | This paper |
| 60 | CompGCN | 0.4790 | This paper |
| 62 | RotatE | 0.4770 best reported | best at pub: RotatE: Knowledge Graph Embedding by Relational Rotation in Complex Space (ICLR 2018) best today: KnowFormer: Revisiting Transformers for Knowledge Graph Reasoning (ICML 2024) |
| 63 | ConvR | 0.4750 | This paper |
| 69 | SACN | 0.4700 | This paper |
| 73 | HyperER | 0.4650 | This paper |
| 84 | ComplEx | 0.4400 | This paper |
| 88 | DisMult | 0.4300 | This paper |
| 89 | ConvE | 0.4300 | This paper |
| 98 | ConvKB | 0.2650 best reported | best at pub: Composition-based Multi-Relational Graph Convolutional Networks (ICLR 2019) |
| 100 | TransE | 0.2310 best reported | best at pub: RotatE: Knowledge Graph Embedding by Relational Rotation in Complex Space (ICLR 2018) |
| # | Model | MRR ↑ | Paper |
|---|---|---|---|
| 1 | sum, Msg_r^3, f(t)=0 | 0.8500 | |
| 2 | sum, Msg_r^3, f(t)=t | 0.8440 | |
| 3 | PNA, Msg_r^1, f(t)=0 | 0.8010 | |
| 34 | AutoGEL | 0.3570 | This paper |
| 35 | CompGCN | 0.3550 | This paper |
| 44 | ConvR | 0.3500 | This paper |
| 45 | SACN | 0.3500 | This paper |
| 47 | ComplEx | 0.3460 best reported | best at pub: Knowledge Graphs (AAAI 2017) |
| 57 | HyperER | 0.3410 | This paper |
| 58 | RotatE | 0.3380 | This paper |
| 67 | TransE | 0.3300 best reported | best at pub: Composition-based Multi-Relational Graph Convolutional Networks (ICLR 2019) best today: KnowFormer: Revisiting Transformers for Knowledge Graph Reasoning (ICML 2024) |
| 71 | ConvE | 0.3250 | This paper |
| 83 | ConvKB | 0.2890 best reported | best at pub: Composition-based Multi-Relational Graph Convolutional Networks (ICLR 2019) |
| 89 | R-GCN | 0.2490 best reported | best at pub: Multi-hop Attention Graph Neural Networks (IJCAI 2020) |
| 91 | VR-GCN | 0.2480 | This paper |
| 92 | DisMult | 0.2430 best reported |
