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Awesome Graph Level Learning

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A collection of papers, implementations, datasets, and tools for graph-level learning.

A Timeline of Graph-level Learning

timeline

Surveys

Paper Title Venue Year Materials
State of the Art and Potentialities of Graph-level Learning Acm Comput. Surv. 2024 [Paper]
Graph Pooling for Graph Neural Networks: Progress, Challenges, and Opportunities arXiv 2022 [Paper]
Graph-level Neural Networks: Current Progress and Future Directions arXiv 2022 [Paper]
A Survey on Graph Kernels Appl. Netw. Sci. 2020 [Paper]
Deep Learning on Graphs: A Survey IEEE Trans. Knowl. Data Eng. 2020 [Paper]
A Comprehensive Survey on Graph Neural Networks IEEE Trans. Neural Netw. Learn. Syst. 2020 [Paper]

Traditional Graph-level Learning

Graph Kernels

Message Passing Kernels

Paper Title Venue Year Method Materials
A Persistent Weisfeiler-lehman Procedure for Graph Classification ICML 2019 P-WL [Paper] [Code]
Glocalized Weisfeiler-lehman Graph Kernels: Global-local Feature Maps of Graphs ICDM 2017 Global-WL [Paper] [Code]
Propagation kernels: Efficient Graph Kernels from Propagated Information Mach. Learn. 2016 PK [Paper] [Code]
Weisfeiler-lehman Graph Kernels J. Mach. Learn. Res. 2011 WL [Paper] [Code]
A linear-time graph kernel ICDM 2009 NHK [Paper] [Code]

Shortest Path Kernels

Paper Title Venue Year Method Materials
Shortest-path Graph Kernels for Document Similarity EMNLP 2017 SPK-DS [Paper]
Shortest-path Kernels on Graphs ICDM 2005 SPK [Paper] [Code]

Random Walk Kernels

Paper Title Venue Year Method Materials
Graph Kernels J. Mach. Learn. Res. 2010 SOMRWK [Paper] [Code]
Extensions of Marginalized Graph Kernels ICML 2004 ERWK [Paper] [Code]
On Graph Kernels: Hardness Results and Efficient Alternatives LNAI 2003 RWK [Paper] [Code]

Optimal Assignment Kernels

Paper Title Venue Year Method Materials
Transitive Assignment Kernels for Structural Classification SIMBAD 2015 TAK [Paper]
Learning With Similarity Functions on Graphs Using Matchings of Geometric Embeddings KDD 2015 GE-OAK [Paper]
Solving the Multi-way Matching Problem by Permutation Synchronization NeurIPS 2013 PS-OAK [Paper] [Code]
Optimal Assignment Kernels for Attributed Molecular Graphs ICML 2005 OAK [Paper]

Subgraph Kernels

Paper Title Venue Year Method Materials
Subgraph Matching Kernels for Attributed Graphs ICML 2012 SMK [Paper] [Code]
Fast Neighborhood Subgraph Pairwise Distance Kernel ICML 2010 NSPDK [Paper] [Code]
Efficient Graphlet Kernels for Large Graph Comparison AISTATS 2009 Graphlet [Paper] [Code]

Subgraph Mining

Frequent Subgraph Mining

Paper Title Venue Year Method Materials
gspan: Graph-based Substructure Pattern Mining ICDM 2002 gspan [Paper] [Code]
Frequent Subgraph Discovery ICDM 2001 FSG [Paper] [Code]
An Apriori-based Algorithmfor Mining Frequent Substructures from Graph Data ECML-PKDD 2000 AGM [Paper] [Code]

Discriminative Subgraph Mining

Paper Title Venue Year Method Materials
Multi-graph-view Learning for Graph Classification ICDM 2014 gCGVFL [Paper]
Positive and Unlabeled Learning for Graph Classification ICDM 2011 gPU [Paper]
Semi-supervised Feature Selection for Graph Classification KDD 2010 gSSC [Paper]
Multi-label Feature Selection for Graph Classification ICDM 2010 gMLC [Paper]
Near-optimal Supervised Feature Selection Among Frequent Subgraphs SDM 2009 CORK [Paper]
Mining Significant Graph Patterns by Leap Search SIGMOD 2008 LEAP [Paper]

Graph Embedding

Deterministic Graph Embedding

Paper Title Venue Year Method Materials
Fast Attributed Graph Embedding via Density of States ICDM 2021 A-DOGE [Paper] [Code]
Bridging the Gap Between Von Neumann Graph Entropy and Structural Information: Theory and Applications WWW 2021 VNGE [Paper] [Code]
Just SLaQ When You Approximate: Accurate Spectral Distances for Web-Scale Graphs WWW 2021 SLAQ [Paper] [Code]
A Simple Yet Effective Baseline for Non-attributed Graph Classification ICLR-RLGM 2019 LDP [Paper] [Code]
Anonymous Walk Embeddings ICML 2018 AWE [Paper] [Code]
Hunt For The Unique, Stable, Sparse And Fast Feature Learning On Graphs NeurIPS 2017 FGSD [Paper] [Code]

Learnable Graph Embedding

Paper Title Venue Year Method Materials
Learning Graph Representation via Frequent Subgraphs SDM 2018 GE-FSG [Paper] [Code]
graph2vec: Learning Distributed Representations of Graphs KDD-MLG 2017 graph2vec [Paper] [Code]
subgraph2vec: Learning Distributed Representations of Rooted Sub-graphs from Large Graphs KDD-MLG 2016 subgraph2vec [Paper] [Code]

Graph-Level Deep Neural Networks

Recurrent Neural Network-based Graph-level Learning

Paper Title Venue Year Method Materials
GraphRNN: Generating Realistic Graphs with Deep Auto-regressive Models ICML 2018 GraphRNN [Paper] [Code]
NetGAN: Generating Graphs via Random Walks ICML 2018 NetGAN [Paper] [Code]
Substructure Assembling Network for Graph Classification AAAI 2018 SAN [Paper]
Graph Classification using Structural Attention KDD 2018 GAM [Paper] [Code]
Gated Graph Sequence Neural Networks ICLR 2016 GGNN [Paper] [Code]

Convolution Neural Network-based Graph-level Learning

Paper Title Venue Year Method Materials
Kernel Graph Convolutional Neural Networks ICANN 2018 KCNN [Paper] [Code]
Dynamic Edge-Conditioned Filters in Convolutional Neural Networks on Graphs CVPR 2017 ECC [Paper] [Code]
Diffusion-Convolutional Neural Networks NeurIPS 2016 DCNN [Paper] [Code]
Learning Convolutional Neural Networks for Graphs ICML 2016 PATCHYSAN [Paper] [Code]

Capsule Neural Network-based Graph-level Learning

Paper Title Venue Year Method Materials
Capsule Neural Networks for Graph Classification using Explicit Tensorial Graph Representations arXiv 2019 PATCHYCaps [Paper] [Code]
Capsule Graph Neural Network ICLR 2019 CapsGNN [Paper] [Code]
Graph Capsule Convolutional Neural Networks WCB 2018 GCAPSCNN [Paper] [Code]

Graph-Level Graph Neural Networks

Message Passing Neural Networks

Paper Title Venue Year Method Materials
The Surprising Power of Graph Neural Networks with Random Node Initialization IJCAI 2021 RNI [Paper]
Weisfeiler and Lehman Go Cellular: CW Networks NeurIPS 2021 CWN [Paper] [Code]
Weisfeiler and Lehman Go Topological: Message Passing Simplicial Networks ICML 2021 SWL [Paper] [Code]
Expressive Power of Invariant and Equivariant Graph Neural Networks ICLR 2021 FGNN [Paper] [Code]
Relational Pooling for Graph Representations ICML 2019 RP [Paper] [Code]
Provably Powerful Graph Networks NeurIPS 2019 PPGN [Paper] [Code]
Weisfeiler and Leman Go Neural: Higher-Order Graph Neural Networks AAAI 2019 K-GNN [Paper] [Code]
How Powerful are Graph Neural Networks? ICLR 2019 GIN [Paper] [Code]
Quantum-chemical Insights from Deep Tensor Neural Networks Nat. Commun. 2017 DTNN [Paper] [Code]
Neural Message Passing for Quantum Chemistry ICML 2017 MPNN [Paper] [Code]
Interaction Networks for Learning about Objects, Relations and Physics NeurIPS 2016 GraphSim [Paper] [Code]
Convolutional Networks on Graphs for Learning Molecular Fingerprints NeurIPS 2015 Fingerprint [Paper] [Code]

Subgraph-based GL-GNNs

Paper Title Venue Year Method Materials
Equivariant Subgraph Aggregation Networks ICLR 2021 ESAN [Paper] [Code]
SUGAR: Subgraph Neural Network with Reinforcement Pooling and Self-Supervised Mutual Information Mechanism WWW 2021 SUGAR [Paper] [Code]
A New Perspective on "How Graph Neural Networks Go Beyond Weisfeiler-Lehman?" ICLR 2021 GraphSNN [Paper] [Code]
Nested Graph Neural Network NeurIPS 2021 NGNN [Paper] [Code]
From Stars to Subgraphs: Uplifting Any GNN with Local Structure Awareness ICLR 2021 GNN-AK [Paper] [Code]
Subgraph Neural Networks NeurIPS 2020 SubGNN [Paper] [Code]
Improving Graph Neural Network Expressivity via Subgraph Isomorphism Counting IEEE Trans. Pattern Anal. Mach. Intell. 2020 GSN [Paper] [Code]

Kernel-based GL-GNNs

Paper Title Venue Year Method Materials
Theoretically Improving Graph Neural Networks via Anonymous Walk Graph Kernels WWW 2021 GSKN [Paper] [Code]
Random Walk Graph Neural Networks NeurIPS 2020 RWNN [Paper] [Code]
Convolutional Kernel Networks for Graph-Structured Data ICML 2020 GCKN [Paper] [Code]
DDGK: Learning Graph Representations for Deep Divergence Graph Kernels WWW 2019 DDGK [Paper] [Code]
Graph Neural Tangent Kernel: Fusing Graph Neural Networks with Graph Kernels NeurIPS 2019 GNTK [Paper] [Code]

Contrastive-based GL-GNNs

Paper Title Venue Year Method Materials
Graph Contrastive Learning Automated ICML 2021 JOAO [Paper] [Code]
Contrastive Multi-View Representation Learning on Graphs ICML 2020 MVGRL [Paper] [Code]
GCC: Graph Contrastive Coding for Graph Neural Network Pre-Training KDD 2020 ESAN [Paper] [Code]
InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization ICLR 2020 InfoGraph [Paper] [Code]
Graph Contrastive Learning with Augmentations NeurIPS 2020 GraphCL [Paper] [Code]

Spectral-based GL-GNNs

Paper Title Venue Year Method Materials
How Framelets Enhance Graph Neural Networks ICML 2021 UFG [Paper] [Code]
Graph Neural Networks With Convolutional ARMA Filters IEEE Trans. Pattern Anal. Mach. Intell. 2021 ARMA [Paper] [Code]
Breaking the Limits of Message Passing Graph Neural Networks ICML 2021 GNNMatlang [Paper] [Code]
Transferability of Spectral Graph Convolutional Neural Networks J. Mach. Learn. Res. 2021 GNNTFS [Paper]
Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering NeurIPS 2016 ChebNet [Paper] [Code]

Graph Pooling

Global Graph Pooling

Numeric Operation Pooling

Paper Title Venue Year Method Materials
Second-Order Pooling for Graph Neural Networks IEEE Trans. Pattern Anal. Mach. Intell 2020 SOPOOL [Paper] [Code]
Every Document Owns Its Structure: Inductive Text Classification via Graph Neural Networks ACL 2020 TextING [Paper] [Code]
Principal Neighbourhood Aggregation for Graph Nets NeurIPS 2020 PNA [Paper] [Code]

Attention-based Pooling

Paper Title Venue Year Method Materials
Order Matters: Sequence to Sequence for Sets ICLR 2021 Set2Set [Paper] [Code]

Convolution Neural Network-based Pooling

Paper Title Venue Year Method Materials
Kernel Graph Convolutional Neural Networks ICANN 2018 KCNN [Paper] [Code]
Learning Convolutional Neural Networks for Graphs ICML 2016 PATCHYSAN [Paper] [Code]

Global Top-K Pooling

Paper Title Venue Year Method Materials
Structure-Feature based Graph Self-adaptive Pooling WWW 2020 GSAPool [Paper] [Code]
An End-to-End Deep Learning Architecture for Graph Classification AAAI 2018 SortPool [Paper] [Code]

Hierarchical Graph Pooling

Clustering-based Pooling

Paper Title Venue Year Method Materials
Accurate Learning of Graph Representations with Graph Multiset Pooling ICLR 2020 GMT [Paper] [Code]
Spectral Clustering with Graph Neural Networks for Graph Pooling ICML 2020 MinCutPool [Paper] [Code]
StructPool: Structured Graph Pooling via Conditional Random Fields ICLR 2020 StructPool [Paper] [Code]
Graph Convolutional Networks with EigenPooling KDD 2019 EigenPool [Paper] [Code]
Hierarchical Graph Representation Learning with Differentiable Pooling NeurIPS 2018 DiffPool [Paper] [Code]
Deep Convolutional Networks on Graph-Structured Data arXiv 2015 GraphCNN [Paper] [Code]
Spectral Networks and Locally Connected Networks on Graphs ICLR 2014 DLCN [Paper]

Hierarchical Top-K Pooling

Paper Title Venue Year Method Materials
ASAP: Adaptive Structure Aware Pooling for Learning Hierarchical Graph Representations AAAI 2020 ASAP [Paper] [Code]
Self-Attention Graph Pooling ICML 2019 SAGPool [Paper] [Code]
Graph U-Nets ICML 2019 U-Nets [Paper] [Code]
Towards Sparse Hierarchical Graph Classifiers arXiv 2018 SHGC [Paper] [Code]

Hierarchical Tree-based Pooling

Paper Title Venue Year Method Materials
A Simple yet Effective Method for Graph Classification IJCAI 2022 HRN [Paper] [Code]
Edge Contraction Pooling for Graph Neural Networks arXiv 2019 EdgePool [Paper] [Code]
Geometric Deep Learning on Graphs and Manifolds Using Mixture Model CNNs CVPR 2017 MoNet [Paper] [Code]

Datasets

Biology

Dataset Size Graphs Classes Link
ENZYMES Small 600 6 Link
PROTEINS Small 1113 2 Link
D&D Small 1178 2 Link
BACE Small 1513 2 Link
MUV Medium 93087 2 Link
ppa Medium 158100 37 Link

Chemistry

Dataset Size Graphs Classes Link
MUTAG Small 188 2 Link
SIDER Small 1427 2 Link
ClinTox Small 1477 2 Link
BBBP Small 2039 2 Link
Tox21 Small 7831 2 Link
ToxCast Small 8576 2 Link
molhiv Small 41127 2 Link
molpcba Medium 437929 2 Link
FreeSolv Small 642 - Link
ESOL Small 1128 - Link
Lipophilicity Small 4200 - Link
AQSOL Small 9823 - Link
ZINC Small 12000 - Link
QM9 Medium 129433 - Link

Social Networks

Dataset Size Graphs Classes Link
IMDB-BINARY Small 1000 2 Link
IMDB-MULTI Small 1500 3 Link
DBLP_v1 Small 19456 2 Link
COLLAB Medium 5000 3 Link
REDDIT-BINARY Small 2000 2 Link
REDDIT-MULTI-5K Medium 4999 5 Link
REDDIT-MULTI-12K Medium 11929 11 Link

Computer Science

Dataset Size Graphs Classes Link
CIFAR10 Medium 60000 10 Link
MNIST Medium 70000 10 Link
code2 Medium 452741 - Link
MALNET Large 1262024 696 Link

Dataset Library

Tools

Disclaimer

If you have any questions, please feel free to contact us. Emails: zhenyu.yang3@hdr.mq.edu.au, ge.zhang5@students.mq.edu.au, jia.wu@mq.edu.au