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Datasets › PPI

PPI (Protein-Protein Interactions (PPI))

Introduced by William L. Hamilton et al. in Inductive Representation Learning on Large Graphs7 Jun 2017 archive 2025-07-28

protein roles—in terms of their cellular functions from gene ontology—in various protein-protein interaction (PPI) graphs, with each graph corresponding to a different human tissue [41]. positional gene sets are used, motif gene sets and immunological signatures as features and gene ontology sets as labels (121 in total), collected from the Molecular Signatures Database [34]. The average graph contains 2373 nodes, with an average degree of 28.8.

HomepageBenchmarksPapers JSON

Benchmarks archive 2025-07-28

All 2 leaderboards 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
Node Classification PPI g2-MLP F1 99.71 A Proposal of Multi-Layer Perceptron with Graph Gating... nnaakkaaii/g2-MLP 24 Compare
Link Prediction PPI PPPNE AP 84.1% PPPNE: Personalized proximity preserved network embedding — 2 Compare

Papers archive 2025-07-28

22 shown of 22 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 309. 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
The Split Matters: Flat Minima Methods for Improving the Performance of GNNs 1 2 15 Jun 2023 not harvested
A Proposal of Multi-Layer Perceptron with Graph Gating Unit for Graph Representation Learning and its Application to Surrogate Model for FEM 1 1 11 Jul 2022 not harvested
Graph Representation Learning Beyond Node and Homophily 1 1 3 Mar 2022 not harvested
PPPNE: Personalized proximity preserved network embedding 0 1 1 Feb 2022 not harvested
VQ-GNN: A Universal Framework to Scale up Graph Neural Networks using Vector Quantization 1 1 27 Oct 2021 not harvested
Simple and Deep Graph Convolutional Networks 4 1 4 Jul 2020 ran 5 of 7 samples (2 unverified; 4 pointer-only for licence)
Deep Graph Contrastive Representation Learning 3 1 7 Jun 2020 ran 1 of 1 samples (0 unverified; 1 pointer-only for licence)
SIGN: Scalable Inception Graph Neural Networks 5 1 23 Apr 2020 ran 2 of 7 samples (5 unverified)
Bridging the Gap Between Spectral and Spatial Domains in Graph Neural Networks 2 1 26 Mar 2020 not harvested
SGAS: Sequential Greedy Architecture Search 1 1 30 Nov 2019 ran 1 of 7 samples (6 unverified)
Hyperbolic Graph Convolutional Neural Networks 3 1 28 Oct 2019 ran 2 of 3 samples (1 unverified; 3 pointer-only for licence)
DeepGCNs: Making GCNs Go as Deep as CNNs 4 2 15 Oct 2019 ran 1 of 9 samples (8 unverified; 1 pointer-only for licence)
GraphSAINT: Graph Sampling Based Inductive Learning Method 8 1 10 Jul 2019 not harvested
Graph Star Net for Generalized Multi-Task Learning 1 1 21 Jun 2019 ran 1 of 6 samples (5 unverified)
Cluster-GCN: An Efficient Algorithm for Training Deep and Large Graph Convolutional Networks 6 2 20 May 2019 not harvested
GraphNAS: Graph Neural Architecture Search with Reinforcement Learning 1 1 22 Apr 2019 ran 0 of 8 samples (8 unverified)
Large-Scale Learnable Graph Convolutional Networks 1 1 12 Aug 2018 not harvested
Representation Learning on Graphs with Jumping Knowledge Networks 5 1 9 Jun 2018 ran 0 of 1 samples (1 unverified)
GaAN: Gated Attention Networks for Learning on Large and Spatiotemporal Graphs 1 1 20 Mar 2018 not harvested
Graph Attention Networks 93 1 30 Oct 2017 ran 50 of 106 samples (56 unverified; 43 pointer-only for licence)
Inductive Representation Learning on Large Graphs 20 1 7 Jun 2017 ran 3 of 5 samples (2 unverified; 5 pointer-only for licence)
node2vec: Scalable Feature Learning for Networks 20 2 3 Jul 2016 ran 8 of 25 samples (17 unverified; 3 pointer-only for licence)

Dataset loaders archive 2025-07-28

pytorch-geometric.readthedocs.io/en/latest/modules/datasets.htmlrusty1s/pytorch_geometricpytorch
docs.dgl.ai/api/python/dgl.data.html#dgl.data.PPIDatasetdmlc/dglpytorchtfmxnet
graphneural.network/datasets/#ppidanielegrattarola/spektraltf

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

Tasks archive 2025-07-28

Node ClassificationLink Prediction

License archive 2025-07-28

No licence recorded in the archive. Absence here is not a statement about the dataset's terms.

Modalities archive 2025-07-28

No modality tagged.

Languages archive 2025-07-28

No language tagged.

Variants archive 2025-07-28

  • PPI

1 variant name, as the archive lists them.

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