Papers › Hierarchical Graph Representation Learning with Differentiable Pooling

Hierarchical Graph Representation Learning with Differentiable Pooling

22 Jun 2018NeurIPS 2018 12arXiv:1806.08804archive 2025-07-28

Rex Ying, Jiaxuan You, Christopher Morris, Xiang Ren, William L. Hamilton, Jure Leskovec

Recently, graph neural networks (GNNs) have revolutionized the field of graph representation learning through effectively learned node embeddings, and achieved state-of-the-art results in tasks such as node classification and link prediction. However, current GNN methods are inherently flat and do not learn hierarchical representations of graphs---a limitation that is especially problematic for the task of graph classification, where the goal is to predict the label associated with an entire graph. Here we propose DiffPool, a differentiable graph pooling module that can generate hierarchical representations of graphs and can be combined with various graph neural network architectures in an end-to-end fashion. DiffPool learns a differentiable soft cluster assignment for nodes at each layer of a deep GNN, mapping nodes to a set of clusters, which then form the coarsened input for the next GNN layer. Our experimental results show that combining existing GNN methods with DiffPool yields an average improvement of 5-10% accuracy on graph classification benchmarks, compared to all existing pooling approaches, achieving a new state-of-the-art on four out of five benchmark data sets.

PaperPDFConference PDFCodeCode Syntology ran

In Syntology Open this paper in Syntology's Atlas, the map of the papers in Syntology's graph and their citations.

For agents, Syntology's MCP tool lists every function and class Syntology harvested from this paper and whether it ran (how to connect): get_harvested_code_for_paper(arxiv_id="1806.08804")

Code

Syntology Ran 1 of 20 code samples harvested from 4 repositories linked to this paper; 19 have no recorded run. Of those that ran: 1 ran with no contract checked.

By repository: community (archive-listed): 20 samples from 4 repositories, 1 ran. The run record, sample by sample. “Ran” means executed on a synthesized input, not that the code is correct or reproduces the paper.

14 repositories listed; official and paper-mentioned ones first.

AaltoPML/Rethinking-pooling-in-GNNs mentioned on GitHubpytorch report
PasqualeAuriemma/GCN-DIFFPOOL mentioned on GitHubtf report
RexYing/diffpool mentioned on GitHubpytorchMIT report
RexYing/graph-pooling mentioned on GitHubpytorchMIT report
Tioz90/DiffPool mentioned on GitHubtf report
Tioz90/GCN mentioned on GitHubtf report
VoVAllen/diffpool mentioned on GitHubpytorch report
basiralab/RG-Select mentioned on GitHubpytorch report
basiralab/reproduciblefedgnn mentioned on GitHubpytorchMIT report
chappers/graph-differential-pooling mentioned on GitHubpytorchMIT report
gospodima/extended-simgnn mentioned on GitHubpytorchMIT report
gitlab.com/cedric_sanders/masterarbeit mentioned on GitHubpytorch report
dmlc/dgl pytorch report

Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.

Code Syntology ran Syntology

20 samples harvested; 1 ran; 0 honoured the contract we drafted; 19 have no recorded run. Read from Syntology's graph 2026-09-24; that is when this build read the record, not when the samples ran.

1ran
19unverified

Licence: 0 of the 20 samples are pointer only, meaning Syntology does not serve that copy's text. This page shows no code text for any sample; each one links to its file in the repository.

Harvested from 4 repositories linked to this paper, official or community; each sample names its own and says which. “Ran” means the sample executed on a synthesized input. It does not mean the output is correct, and nothing here reproduces the paper's results. “Honoured” and “violated” refer to a contract Syntology drafted from the code itself; “our draft was wrong” and “fixture could not drive it” are failures of Syntology's instrument, not of the code.

Each sample ends with its code_sha256, Syntology's identity for that exact code. An agent fetches the stored sample with Syntology's MCP tool get_code(code_sha256="…") (how to connect); click an identity to copy that call.

Repository labels, per sample. official repository: The archive marks this repository official for the paper. named in the paper: The archive records that the paper mentions this repository; it is not marked official. community (archive-listed): In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper. found in paper text by Syntology: Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted. community: Not in the archive's code links for this paper; a community repository Syntology harvested. Samples from a repository marked official are listed first. Licence labels name the repository's licence as recorded at harvest. “Pointer only” means Syntology does not serve that copy's text, for one of four reasons: no licence file was found; the licence was not identified; the licence is recorded as permissive but that copy's record is not marked cleared; or the licence is outside the permissive list Syntology serves text under (MIT, Apache-2.0, BSD and similar). Some licences outside that list permit redistribution, such as WTFPL, and GPL-3.0 under its conditions; they are simply not on the list. Hover a licence label for the reason. File links open the file on GitHub at the default branch, which may have changed since the harvest.

exp_moving_avg RexYing/diffpool/util.py community (archive-listed) ran fingerprinted MIT (permissive) · dd691d00aa5cc146 · report
Mean_W_Cv basiralab/reproduciblefedgnn/federated_reproducibility/Analysis.py community (archive-listed) unverified MIT (permissive) · d13d56b516dc4831 · report
Mean_W_Two_shot basiralab/reproduciblefedgnn/federated_reproducibility/Analysis.py community (archive-listed) unverified MIT (permissive) · a2ab7f58736f25f8 · report
Models_trained basiralab/reproduciblefedgnn/federated_reproducibility/Analysis.py community (archive-listed) unverified MIT (permissive) · 0540a7e365607e63 · report
average_weights basiralab/reproduciblefedgnn/federated_reproducibility/fed_localmodel.py community (archive-listed) unverified MIT (permissive) · 63d220d8b4f8afd5 · report
datasets_splits basiralab/reproduciblefedgnn/federated_reproducibility/cross_val.py community (archive-listed) unverified MIT (permissive) · 1f11f715f1139ba1 · report
dense_diff_pool chappers/graph-differential-pooling/diff_pool.py community (archive-listed) unverified MIT (permissive) · 2cd5bd6f6bc85e88 · report
evaluate basiralab/reproduciblefedgnn/federated_reproducibility/main_diffpool.py community (archive-listed) unverified MIT (permissive) · 1e9d378dbb12714b · report
evaluate basiralab/reproduciblefedgnn/federated_reproducibility/main_gcn.py community (archive-listed) unverified MIT (permissive) · 96903513f7177254 · report
frobenius_norm_tf PasqualeAuriemma/GCN-DIFFPOOL/models.py community (archive-listed) unverified MIT (permissive) · 0b25aff2096336db · report
gen_2community_ba RexYing/diffpool/gen/data.py community (archive-listed) unverified MIT (permissive) · 712b1b3a42060fb0 · report
gen_ba RexYing/diffpool/gen/data.py community (archive-listed) unverified MIT (permissive) · 854d177d079f1cd3 · report
gen_er RexYing/diffpool/gen/data.py community (archive-listed) unverified MIT (permissive) · 9c9fec82cf325ebc · report
get_adjs basiralab/reproduciblefedgnn/federated_reproducibility/dataLoader_medmnist.py community (archive-listed) unverified MIT (permissive) · 07ed65681aebf2db · report
img_to_adj basiralab/reproduciblefedgnn/federated_reproducibility/dataLoader_medmnist.py community (archive-listed) unverified MIT (permissive) · 3a7c82cbbc34ab03 · report
kruskal RexYing/diffpool/partition.py community (archive-listed) unverified MIT (permissive) · eb9659a87e71ae20 · report
minmax_sc basiralab/reproduciblefedgnn/federated_reproducibility/main_diffpool.py community (archive-listed) unverified MIT (permissive) · 81b03223cd6f4d43 · report
node_dict RexYing/diffpool/util.py community (archive-listed) unverified MIT (permissive) · d3550a1e301975aa · report
node_iter RexYing/diffpool/util.py community (archive-listed) unverified MIT (permissive) · f55bf28721abc66d · report
train basiralab/reproduciblefedgnn/federated_reproducibility/main_gcn.py community (archive-listed) unverified MIT (permissive) · 640adefa68f0073d · report

Tasks

General ClassificationGraph ClassificationGraph Neural NetworkGraph Representation LearningLink PredictionNode ClassificationRepresentation Learning

Results from the paper archive 2025-07-28

TaskDatasetModelMetricValueRank at snapshotLeaderboardReport
Graph Classification COLLAB GNN (DiffPool) Accuracy 75.48% #24 of 39 Archive leaderboard report
Graph Classification D&D S2V (with 2 DiffPool) Accuracy 82.07% #7 of 53 Archive leaderboard report
Graph Classification D&D GNN (DiffPool) Accuracy 80.64% #12 of 53 Archive leaderboard report
Graph Classification ENZYMES S2V (with 2 DiffPool) Accuracy 63.33% #24 of 54 Archive leaderboard report
Graph Classification ENZYMES GNN (DiffPool) Accuracy 62.53% #25 of 54 Archive leaderboard report
Graph Classification PROTEINS GNN (DiffPool) Accuracy 76.25% #55 of 103 Archive leaderboard report
Graph Classification REDDIT-MULTI-12K GNN (DiffPool) Accuracy 47.08 #1 of 3 Archive leaderboard report
Graph Property Prediction ogbg-code2 DiffPool w/ graphSAGE Ext. data No #21 of 21 Archive leaderboard report
Graph Property Prediction ogbg-code2 DiffPool w/ graphSAGE Number of params 10095826 #21 of 21 Archive leaderboard report
Graph Property Prediction ogbg-code2 DiffPool w/ graphSAGE Test F1 score 0.1401 ± 0.0012 #21 of 21 Archive leaderboard report
Graph Property Prediction ogbg-code2 DiffPool w/ graphSAGE Validation F1 score 0.1405 ± 0.0012 #21 of 21 Archive leaderboard report

Ranks are positions in the archive's leaderboards as they stood at the 2025-07-28 snapshot. Results published since then are not among these rows, so a rank here is not a current standing.

Methods

Introduced by this paper: DiffPool

DiffPool

Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections