CogDL: A Comprehensive Library for Graph Deep Learning
Abstract
Graph neural networks (GNNs) have attracted tremendous attention from the graph learning community in recent years. It has been widely adopted in various real-world applications from diverse domains, such as social networks and biological graphs. The research and applications of graph deep learning present new challenges, including the sparse nature of graph data, complicated training of GNNs, and non-standard evaluation of graph tasks. To tackle the issues, we present CogDL, a comprehensive library for graph deep learning that allows researchers and practitioners to conduct experiments, compare methods, and build applications with ease and efficiency. In CogDL, we propose a unified design for the training and evaluation of GNN models for various graph tasks, making it unique among existing graph learning libraries. By utilizing this unified trainer, CogDL can optimize the GNN training loop with several training techniques, such as mixed precision training. Moreover, we develop efficient sparse operators for CogDL, enabling it to become the most competitive graph library for efficiency. Another important CogDL feature is its focus on ease of use with the aim of facilitating open and reproducible research of graph learning. We leverage CogDL to report and maintain benchmark results on fundamental graph tasks, which can be reproduced and directly used by the community.
Benchmark Results
Tested on 4 datasets 5 baseline values reported too low
Tables show presented results in global context (best 3 papers + GCN + MLP).
Classic
| # | Model | F1 ↑ | Paper |
|---|---|---|---|
| 1 | GAMLP(JK) | 0.9982
±0.0001 | |
| 2 | GraphCON-GCN | 0.9960 | |
| 3 | GCNII | 0.9650
±0.0020 | prev best: Hierarchical message-passing graph neural networks (2020) |
| 4 | GraphSAINT | 0.9930
±0.0010 | prev best: SIGN: Scalable Inception Graph Neural Networks (2020) |
| 21 | GCN | 0.9850 best reported | best at pub: Graph Neural Networks With Convolutional ARMA Filters (2019) best today: Graph-Coupled Oscillator Networks (ICML 2022) |
| 38 | Cluster-SAGE | 0.9790
±0.0010 | This paper |
| 57 | GAT | 0.9732
±0.0032 best reported | best at pub: GaAN: Gated Attention Networks for Learning on Large and Spatiotemporal Graphs (2018) best today: HAT-GAE: Self-Supervised Graph Auto-encoders with Hierarchical Adaptive Masking and Trainable Corruption (2023) Difference within reported uncertainty; not counted as underperformance. |
| 90 | SGC | 0.8920
±0.0150 best reported | |
| 92 | GIN | 0.8724
±0.0002 | |
| 151 | APPNP | 0.6230
±0.0010 | This paper |
| 168 | PPRGo | 0.4860
±0.0010 | This paper |
| 173 | MLP | 0.4620 |
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 | 0.9206 | prev best: Provably Powerful Graph Networks (NeurIPS 2019) Improvement within reported uncertainty; not highlighted. |
| 63 | GCN | 0.9220
±0.0440 | |
| 190 | SortPool | 0.8725 | prev best: Graph Information Bottleneck for Subgraph Recognition (ICLR 2020) Improvement within reported uncertainty; not highlighted. |
| 239 | DiffPool | 0.8518 | prev best: Fast Graph Representation Learning with PyTorch Geometric (ICLR 2019) best today: Graph Classification via Reference Distribution Learning: Theory and Practice (NeurIPS 2024) Improvement within reported uncertainty; not highlighted. |
| 257 | InfoGraph | 0.8930
±0.0514 best reported | best at pub: Contrastive Multi-View Representation Learning on Graphs (ICML 2020) best today: Improving Expressivity of GNNs with Subgraph-specific Factor Embedded Normalization (KDD 2023) Difference within reported uncertainty; not counted as underperformance. |
| 365 | DGK | 0.8744
±0.0272 best reported | best at pub: Provably Powerful Graph Networks (NeurIPS 2019) best today: Model-Driven Graph Contrastive Learning (2025) Difference within reported uncertainty; not counted as underperformance. |
| 403 | MLP | 0.8660
±0.0495 | |
| 407 | graph2vec | 0.8368 | prev best: Contrastive Multi-View Representation Learning on Graphs (ICML 2020) best today: Graph Masked Autoencoders with Transformers (2022) Improvement within reported uncertainty; not highlighted. |
| 417 | PATCHY_SAN | 0.8612 | This paper |
| 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) |
| 623 | SAGPool | 0.7986
±0.0236 best reported | best at pub: Graph Neural Networks in TensorFlow and Keras with Spektral (2020) best today: Embedding Graphs on Grassmann Manifold (2022) |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9954 | |
| 2 | GIN | 0.9934 best reported | best at pub: Provably Powerful Graph Networks (NeurIPS 2019) best today: 1-WL Expressiveness Is (Almost) All You Need (2022) |
| 3 | GCN | 0.9727 | |
| 5 | DiffPool | 0.9210
±0.0260 best reported | best at pub: Contrastive Self-supervised Learning for Graph Classification (AAAI 2020) best today: Where to Mask: Structure-Guided Masking for Graph Masked Autoencoders (IJCAI 2024) |
| 131 | GraphSAGE | 0.8200
±0.0100 | |
| 259 | SAGPool | 0.7910
±0.0300 best reported | best at pub: Contrastive Self-supervised Learning for Graph Classification (AAAI 2020) best today: The expressive power of pooling in Graph Neural Networks (NeurIPS 2023) |
| 338 | InfoGraph | 0.7664 | prev best: Contrastive Self-supervised Learning for Graph Classification (AAAI 2020) |
| 373 | DGCNN | 0.7650
±0.0190 best reported | best at pub: GraphCrop: Subgraph Cropping for Graph Classification (2020) |
| 406 | graph2vec | 0.7540
±0.0120 best reported | best today: InfoGCL: Information-Aware Graph Contrastive Learning (NeurIPS 2021) |
| 415 | SortPool | 0.7399 | prev best: Multi-grained Semantics-aware Graph Neural Networks (2020) Improvement within reported uncertainty; not highlighted. |
| 484 | PATCHY_SAN | 0.6982 | This paper |
| # | Model | Accuracy ↑ | Paper |
|---|---|---|---|
| 1 | WL-MLP | 0.9792 | |
| 2 | MSH-GNN | 0.9640
±0.0070 | |
| 3 | CoCN | 0.8722
±0.0013 | |
| 6 | graph2vec | 0.8558 | This paper |
| 23 | GCN | 0.8260
±0.0220 | |
| 30 | GIN | 0.8220
±0.0210 best reported | best at pub: On the Equivalence between Graph Isomorphism Testing and Function Approximation with GNNs (NeurIPS 2019) best today: Scalable Expressiveness through Preprocessed Graph Perturbations (2024) Difference within reported uncertainty; not counted as underperformance. |
| 33 | DiffPool | 0.7927 | prev best: Fast Graph Representation Learning with PyTorch Geometric (ICLR 2019) best today: Scalable Graph Compressed Convolutions (2024) Improvement within reported uncertainty; not highlighted. |
| 125 | SortPool | 0.8007 | prev best: Fast Graph Representation Learning with PyTorch Geometric (ICLR 2019) |
| 146 | InfoGraph | 0.7940 | This paper |
| 151 | MLP | 0.7920
±0.0240 | |
| 191 | DGCNN | 0.7745 | prev best: Graph U-Nets (2019) |
| 258 | PATCHY_SAN | 0.7434 | This paper |
