Automated Graph Machine Learning: Approaches, Libraries, Benchmarks and Directions
Abstract
Graph machine learning has been extensively studied in both academic and industry. However, as the literature on graph learning booms with a vast number of emerging methods and techniques, it becomes increasingly difficult to manually design the optimal machine learning algorithm for different graph-related tasks. To tackle the challenge, automated graph machine learning, which aims at discovering the best hyper-parameter and neural architecture configuration for different graph tasks/data without manual design, is gaining an increasing number of attentions from the research community. In this paper, we extensively discuss automated graph machine learning approaches, covering hyper-parameter optimization (HPO) and neural architecture search (NAS) for graph machine learning. We briefly overview existing libraries designed for either graph machine learning or automated machine learning respectively, and further in depth introduce AutoGL, our dedicated and the world's first open-source library for automated graph machine learning. Also, we describe a tailored benchmark that supports unified, reproducible, and efficient evaluations. Last but not least, we share our insights on future research directions for automated graph machine learning. This paper is the first systematic and comprehensive discussion of approaches, libraries as well as directions for automated graph machine learning.
Benchmark Results
Tested on 5 datasets 10 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | GraphSAGE+CNA | 0.9418
±0.0033 | |
| 2 | GCN+CNA | 0.9366
±0.0048 | |
| 3 | TransformerConv | 0.9350
±0.0058 | |
| 21 | GCN | 0.9004 best reported | best at pub: SplineCNN: Fast Geometric Deep Learning with Continuous B-Spline Kernels (2017) best today: Understanding Heterophily for Graph Neural Networks (ICML 2024) |
| 39 | SAGE | 0.8911
±0.0012 | |
| 44 | GAT | 0.8897
±0.0014 best reported | best at pub: Learned Low Precision Graph Neural Networks (2020) |
| 141 | GraphSAGE | 0.8708
±0.0085 best reported | best at pub: The Impact of Global Structural Information in Graph Neural Networks Applications (2020) best today: Large Language Model Meets Graph Neural Network in Knowledge Distillation (AAAI 2024) |
| 403 | AutoGL | 0.8320
±0.0060 | This paper |
| 511 | Ensemble | 0.8220
±0.0040 | This paper |
| 518 | TPE (50 trials) | 0.8210
±0.0100 | This paper |
| 724 | MLP | 0.7768 |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | CNA | 0.9575
±0.0058 | |
| 2 | IS-GIB | 0.9390
±0.0187 | |
| 3 | EERM | 0.9112
±0.0145 | |
| 35 | GAT | 0.8080
±0.0026 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) best today: Feature Expansion for Graph Neural Networks (ICML 2023) |
| 44 | GCN | 0.8033
±0.0088 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 61 | GraphSAGE | 0.7923
±0.0053 best reported | best at pub: Gophormer: Ego-Graph Transformer for Node Classification (2021) |
| 259 | SAGE | 0.7361
±0.0190 | |
| 350 | MLP | 0.7289
±0.0010 | |
| 407 | Ensemble | 0.7243
±0.0026 best reported | best at pub: AutoGL: A Library for Automated Graph Learning (ICLR 2021) best today: Boosting Graph Neural Networks via Adaptive Knowledge Distillation (AAAI 2022) |
| 414 | AutoGL | 0.7240
±0.0060 | This paper |
| 421 | TPE (50 trials, GCN) | 0.7240
±0.0060 | This paper |
| 442 | random (10 trials, GAT) | 0.7220
±0.0070 | This paper |
| 471 | None (GAT) | 0.7190
±0.0060 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | LGTL | 0.9518
±0.0011 | |
| 2 | MixHop (LO) | 0.9513
±0.0038 | |
| 3 | GraphSAGE (LO) | 0.9511
±0.0036 | |
| 18 | GCN | 0.9296
±0.0015 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 20 | GAT | 0.9233
±0.0018 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) |
| 116 | SAGE | 0.8881
±0.0015 | |
| 125 | GraphSAGE | 0.8864
±0.0030 best reported | best at pub: Tackling Over-Smoothing for General Graph Convolutional Networks (2020) best today: Non-backtracking Graph Neural Networks (TMLR 2023) |
| 210 | MLP | 0.8690
±0.0074 | |
| 546 | AutoGL | 0.7930
±0.0040 | This paper |
| 638 | Ensemble | 0.7850
±0.0040 | This paper |
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 | |
| 357 | GIN (random) | 0.8760
±0.0600 | This paper |
| 358 | AutoGL | 0.8760
±0.0600 | This paper |
| 403 | MLP | 0.8660
±0.0495 | |
| 493 | Top-K Pooling (TPE) | 0.8390
±0.1010 | 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 best reported | best at pub: Breaking the Limits of Message Passing Graph Neural Networks (ICML 2021) |
| 67 | SAGE | 0.7726
±0.0228 | |
| 149 | MLP | 0.7600
±0.0320 | |
| 351 | AutoGL | 0.7330
±0.0440 | This paper |
| 399 | TPE | 0.7230
±0.0550 | This paper |
| 462 | Top-K Pooling | 0.6950
±0.0440 | This paper |
