Papers › Masked Label Prediction: Unified Message Passing Model for Semi-Supervised Classification

Masked Label Prediction: Unified Message Passing Model for Semi-Supervised Classification

8 Sep 2020arXiv:2009.03509archive 2025-07-28

Yunsheng Shi, Zhengjie Huang, Shikun Feng, Hui Zhong, Wenjin Wang, Yu Sun

Graph neural network (GNN) and label propagation algorithm (LPA) are both message passing algorithms, which have achieved superior performance in semi-supervised classification. GNN performs feature propagation by a neural network to make predictions, while LPA uses label propagation across graph adjacency matrix to get results. However, there is still no effective way to directly combine these two kinds of algorithms. To address this issue, we propose a novel Unified Message Passaging Model (UniMP) that can incorporate feature and label propagation at both training and inference time. First, UniMP adopts a Graph Transformer network, taking feature embedding and label embedding as input information for propagation. Second, to train the network without overfitting in self-loop input label information, UniMP introduces a masked label prediction strategy, in which some percentage of input label information are masked at random, and then predicted. UniMP conceptually unifies feature propagation and label propagation and is empirically powerful. It obtains new state-of-the-art semi-supervised classification results in Open Graph Benchmark (OGB).

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="2009.03509")

Code

Syntology Ran 3 of 7 code samples harvested from 3 repositories linked to this paper; 4 have no recorded run. Of those that ran: 2 ran · violated contract; 1 ran · our draft was wrong.

By repository: official repository: 3 samples from 1 repository, 0 ran; community (archive-listed): 4 samples from 2 repositories, 3 ran. The run record, sample by sample. “Ran” means executed on a synthesized input, not that the code is correct or reproduces the paper.

PaddlePaddle/PGL officialpaddle report
lucidrains/graph-transformer-pytorch mentioned on GitHubpytorchMIT 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

7 samples harvested; 3 ran; 0 honoured the contract we drafted; 4 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.

2ran · violated contract
1ran · our draft was wrong
4unverified

Licence: 0 of the 7 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 3 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.

get_default_data_dir PaddlePaddle/PGL/pgl/dataset.py official repository unverified Apache-2.0 (permissive) · 7de5d45120be5bcd · report
is_all PaddlePaddle/PGL/legacy/pgl/heter_graph_wrapper.py official repository unverified Apache-2.0 (permissive) · e97bbf7d7b1c2f61 · report
random_partition PaddlePaddle/PGL/pgl/partition.py official repository unverified Apache-2.0 (permissive) · 75f339abee8ab5cf · report
default lucidrains/graph-transformer-pytorch/graph_transformer_pytorch/graph_transformer_pytorch.py community (archive-listed) ran · violated contract fingerprinted MIT (permissive) · 60fff7c3c400d7ff · report
exists lucidrains/graph-transformer-pytorch/graph_transformer_pytorch/graph_transformer_pytorch.py community (archive-listed) ran · violated contract MIT (permissive) · aa5486a3650902d8 · report
softmax willyfh/graph-transformer/graph_transformer/graph_transformer_model.py community (archive-listed) ran · our draft was wrong fingerprinted MIT (permissive) · 2f6500993366c0f7 · report
FeedForward lucidrains/graph-transformer-pytorch/graph_transformer_pytorch/graph_transformer_pytorch.py community (archive-listed) unverified MIT (permissive) · e094fdc0df86ec02 · report

Tasks

General ClassificationGraph Neural NetworkNode ClassificationNode Property Prediction

Results from the paper archive 2025-07-28

TaskDatasetModelMetricValueRank at snapshotLeaderboardReport
Node Property Prediction ogbn-arxiv UniMP_v2 Ext. data No #32 of 86 Archive leaderboard report
Node Property Prediction ogbn-arxiv UniMP_v2 Number of params 687377 #32 of 86 Archive leaderboard report
Node Property Prediction ogbn-arxiv UniMP_v2 Test Accuracy 0.7397 ± 0.0015 #32 of 86 Archive leaderboard report
Node Property Prediction ogbn-arxiv UniMP_v2 Validation Accuracy 0.7506 ± 0.0009 #32 of 86 Archive leaderboard report
Node Property Prediction ogbn-arxiv UniMP_large Ext. data No #36 of 86 Archive leaderboard report
Node Property Prediction ogbn-arxiv UniMP_large Number of params 1162515 #36 of 86 Archive leaderboard report
Node Property Prediction ogbn-arxiv UniMP_large Test Accuracy 0.7379 ± 0.0014 #36 of 86 Archive leaderboard report
Node Property Prediction ogbn-arxiv UniMP_large Validation Accuracy 0.7475 ± 0.0008 #36 of 86 Archive leaderboard report
Node Property Prediction ogbn-arxiv UniMP Ext. data No #48 of 86 Archive leaderboard report
Node Property Prediction ogbn-arxiv UniMP Number of params 473489 #48 of 86 Archive leaderboard report
Node Property Prediction ogbn-arxiv UniMP Test Accuracy 0.7311 ± 0.0020 #48 of 86 Archive leaderboard report
Node Property Prediction ogbn-arxiv UniMP Validation Accuracy 0.7450 ± 0.0005 #48 of 86 Archive leaderboard report
Node Property Prediction ogbn-papers100M TransformerConv Ext. data No #11 of 20 Archive leaderboard report
Node Property Prediction ogbn-papers100M TransformerConv Number of params 883378 #11 of 20 Archive leaderboard report
Node Property Prediction ogbn-papers100M TransformerConv Test Accuracy 0.6736 ± 0.0010 #11 of 20 Archive leaderboard report
Node Property Prediction ogbn-papers100M TransformerConv Validation Accuracy 0.7172 ± 0.0005 #11 of 20 Archive leaderboard report
Node Property Prediction ogbn-products UniMP Ext. data No #32 of 64 Archive leaderboard report
Node Property Prediction ogbn-products UniMP Number of params 1475605 #32 of 64 Archive leaderboard report
Node Property Prediction ogbn-products UniMP Test Accuracy 0.8256 ± 0.0031 #32 of 64 Archive leaderboard report
Node Property Prediction ogbn-products UniMP Validation Accuracy 0.9308 ± 0.0017 #32 of 64 Archive leaderboard report
Node Property Prediction ogbn-proteins UniMP+CrossEdgeFeat Ext. data No #10 of 26 Archive leaderboard report
Node Property Prediction ogbn-proteins UniMP+CrossEdgeFeat Number of params 1959984 #10 of 26 Archive leaderboard report
Node Property Prediction ogbn-proteins UniMP+CrossEdgeFeat Test ROC-AUC 0.8691 ± 0.0018 #10 of 26 Archive leaderboard report
Node Property Prediction ogbn-proteins UniMP+CrossEdgeFeat Validation ROC-AUC 0.9258 ± 0.0009 #10 of 26 Archive leaderboard report
Node Property Prediction ogbn-proteins UniMP Ext. data No #12 of 26 Archive leaderboard report
Node Property Prediction ogbn-proteins UniMP Number of params 1909104 #12 of 26 Archive leaderboard report
Node Property Prediction ogbn-proteins UniMP Test ROC-AUC 0.8642 ± 0.0008 #12 of 26 Archive leaderboard report
Node Property Prediction ogbn-proteins UniMP Validation ROC-AUC 0.9175 ± 0.0006 #12 of 26 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

Absolute Position EncodingsAdamAttentionBPEDense ConnectionsDropoutGCNLabel SmoothingLayer NormalizationLinear LayerMulti-Head AttentionPosition-Wise Feed-Forward LayerResidual ConnectionSoftmaxTransformer

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