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ENZYMES

Introduced in Protein function prediction via graph kernels1 Jan 2005 archive 2025-07-28

ENZYMES is a dataset of 600 protein tertiary structures obtained from the BRENDA enzyme database. The ENZYMES dataset contains 6 enzymes.

Source: When Work Matters: Transforming Classical Network Structures to Graph CNN

HomepageBenchmarksPapers JSON

Benchmarks archive 2025-07-28

All 1 leaderboard whose dataset resolves to this page shown (sort by any header). "First row" is the archive's own first row at snapshot, in the archive's row order; nothing here re-ranks and metric direction is not asserted.

First row (archive order)PaperCode
Graph Classification ENZYMES ESA (Edge set attention, no positional encodings) Accuracy 79.423±1.658 An end-to-end attention-based approach for learning on graphs davidbuterez/edge-set-attention 54 Compare

Papers archive 2025-07-28

30 shown of 47 papers with a leaderboard row on this dataset's benchmarks, newest first. The archive's own "papers using this dataset" list was never published, so this is the benchmark-backed subset; the archive's count for this dataset is 202. The Syntology column is from Syntology's graph (read 2026-09-24), stated per sample; it is not part of any archive number.

DateSamples run Syntology
PANDA: Expanded Width-Aware Message Passing Beyond Rewiring 1 4 6 Jun 2024 ran 7 of 9 samples (2 unverified)
An end-to-end attention-based approach for learning on graphs 1 1 16 Feb 2024 not harvested
Fine-tuning Graph Neural Networks by Preserving Graph Generative Patterns 1 1 21 Dec 2023 ran 13 of 13 samples (0 unverified; 13 pointer-only for licence)
Graph isomorphism UNet 1 1 23 Aug 2023 not harvested
Transitivity-Preserving Graph Representation Learning for Bridging Local Connectivity and Role-based Similarity 3 1 18 Aug 2023 ran 5 of 26 samples (21 unverified)
Strengthening structural baselines for graph classification using Local Topological Profile 1 1 1 May 2023 not harvested
TREE-G: Decision Trees Contesting Graph Neural Networks 1 1 6 Jul 2022 ran 0 of 10 samples (10 unverified)
Template based Graph Neural Network with Optimal Transport Distances 1 1 31 May 2022 not harvested
Recipe for a General, Powerful, Scalable Graph Transformer 4 1 25 May 2022 ran 3 of 21 samples (18 unverified)
A New Perspective on the Effects of Spectrum in Graph Neural Networks 1 1 14 Dec 2021 ran 0 of 2 samples (2 unverified)
DropGNN: Random Dropouts Increase the Expressiveness of Graph Neural Networks 1 1 11 Nov 2021 ran 0 of 3 samples (3 unverified)
Fea2Fea: Exploring Structural Feature Correlations via Graph Neural Networks 1 1 24 Jun 2021 not harvested
How Attentive are Graph Attention Networks? 8 1 30 May 2021 ran 6 of 16 samples (10 unverified; 1 pointer-only for licence)
Online Graph Dictionary Learning 1 1 12 Feb 2021 not harvested
Wasserstein Embedding for Graph Learning 1 1 16 Jun 2020 not harvested
Principal Neighbourhood Aggregation for Graph Nets 8 1 12 Apr 2020 ran 33 of 55 samples (22 unverified; 48 pointer-only for licence)
Bridging the Gap Between Spectral and Spatial Domains in Graph Neural Networks 2 2 26 Mar 2020 not harvested
A Fair Comparison of Graph Neural Networks for Graph Classification 5 2 20 Dec 2019 not harvested
Hierarchical Graph Pooling with Structure Learning 3 1 14 Nov 2019 not harvested
Hierarchical Representation Learning in Graph Neural Networks with Node Decimation Pooling 1 1 24 Oct 2019 ran 1 of 1 samples (0 unverified; 1 pointer-only for licence)
Evolution of Graph Classifiers 1 1 4 Oct 2019 not harvested
Learning Universal Graph Neural Network Embeddings With Aid Of Transfer Learning 1 1 22 Sep 2019 not harvested
A Non-Negative Factorization approach to node pooling in Graph Convolutional Neural Networks 0 1 7 Sep 2019 not harvested
Improving Attention Mechanism in Graph Neural Networks via Cardinality Preservation 1 1 4 Jul 2019 ran 0 of 1 samples (1 unverified)
Graph Star Net for Generalized Multi-Task Learning 1 1 21 Jun 2019 ran 1 of 6 samples (5 unverified)
DEMO-Net: Degree-specific Graph Neural Networks for Node and Graph Classification 1 1 5 Jun 2019 not harvested
Wasserstein Weisfeiler-Lehman Graph Kernels 2 1 4 Jun 2019 ran 0 of 11 samples (11 unverified)
Are Powerful Graph Neural Nets Necessary? A Dissection on Graph Classification 1 2 11 May 2019 not harvested
Capsule Graph Neural Network 1 1 1 May 2019 not harvested
Graph Convolutional Networks with EigenPooling 1 1 30 Apr 2019 not harvested

The full list of 47 is in the JSON twin.

Dataset loaders archive 2025-07-28

docs.dgl.ai/api/python/dgl.data.html#dgl.data.TUDatasetdmlc/dglpytorchtfmxnet
graphneural.network/datasets/#tudatasetdanielegrattarola/spektraltf
snap-stanford/GraphRNNpytorch

3 loaders as listed in the archive; links are outbound and not re-checked here.

Tasks archive 2025-07-28

Graph Classification

License archive 2025-07-28

Unknown

Modalities archive 2025-07-28

Graphs

Languages archive 2025-07-28

No language tagged.

Variants archive 2025-07-28

  • ENZYMES

1 variant name, as the archive lists them.

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