Datasets › PROTEINS

PROTEINS

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

PROTEINS is a dataset of proteins that are classified as enzymes or non-enzymes. Nodes represent the amino acids and two nodes are connected by an edge if they are less than 6 Angstroms apart.

Source: Fast and Deep Graph Neural Networks

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 PROTEINS HGP-SL Accuracy 84.91 Hierarchical Graph Pooling with Structure Learning dmlc/dgl +2 103 Compare

Papers archive 2025-07-28

30 shown of 85 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 371. 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
FIT-GNN: Faster Inference Time for GNNs Using Coarsening 1 1 19 Oct 2024 not harvested
PANDA: Expanded Width-Aware Message Passing Beyond Rewiring 1 4 6 Jun 2024 ran 7 of 9 samples (2 unverified)
Multi-hop Attention-based Graph Pooling: A Personalized PageRank Perspective 1 1 4 Mar 2024 not harvested
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-level Representation Learning with Joint-Embedding Predictive Architectures 1 1 27 Sep 2023 ran 10 of 11 samples (1 unverified)
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)
Weisfeiler and Lehman Go Paths: Learning Topological Features via Path Complexes 0 1 13 Aug 2023 not harvested
Randomized Schur Complement Views for Graph Contrastive Learning 1 1 6 Jun 2023 ran 0 of 2 samples (2 unverified)
CIN++: Enhancing Topological Message Passing 1 1 6 Jun 2023 not harvested
Strengthening structural baselines for graph classification using Local Topological Profile 1 1 1 May 2023 not harvested
Cell Attention Networks 1 1 16 Sep 2022 ran 0 of 5 samples (5 unverified)
TREE-G: Decision Trees Contesting Graph Neural Networks 1 1 6 Jul 2022 ran 0 of 10 samples (10 unverified)
0/1 Deep Neural Networks via Block Coordinate Descent 0 1 19 Jun 2022 not harvested
DiffWire: Inductive Graph Rewiring via the Lovász Bound 2 4 15 Jun 2022 not harvested
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)
Relational Reasoning Over Spatial-Temporal Graphs for Video Summarization 0 1 6 Apr 2022 not harvested
DropGNN: Random Dropouts Increase the Expressiveness of Graph Neural Networks 1 1 11 Nov 2021 ran 0 of 3 samples (3 unverified)
Maximum Entropy Weighted Independent Set Pooling for Graph Neural Networks 1 1 3 Jul 2021 ran 2 of 2 samples (0 unverified; 2 pointer-only for licence)
Fea2Fea: Exploring Structural Feature Correlations via Graph Neural Networks 1 1 24 Jun 2021 not harvested
Relation order histograms as a network embedding tool 1 1 9 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)
Accurate Learning of Graph Representations with Graph Multiset Pooling 1 1 23 Feb 2021 ran 4 of 5 samples (1 unverified; 5 pointer-only for licence)
Online Graph Dictionary Learning 1 1 12 Feb 2021 not harvested
A Novel Higher-order Weisfeiler-Lehman Graph Convolution 1 1 1 Jul 2020 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)
Segmented Graph-Bert for Graph Instance Modeling 1 1 9 Feb 2020 not harvested

The full list of 85 is in the JSON twin.

Dataset loaders archive 2025-07-28

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

Tasks archive 2025-07-28

License archive 2025-07-28

Various

Modalities archive 2025-07-28

Languages archive 2025-07-28

No language tagged.

Variants archive 2025-07-28

  • PROTEINS

1 variant name, as the archive lists them.

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