Papers › Graph Neural Networks for Link Prediction with Subgraph Sketching

Graph Neural Networks for Link Prediction with Subgraph Sketching

30 Sep 2022arXiv:2209.15486archive 2025-07-28

Benjamin Paul Chamberlain, Sergey Shirobokov, Emanuele Rossi, Fabrizio Frasca, Thomas Markovich, Nils Hammerla, Michael M. Bronstein, Max Hansmire

Many Graph Neural Networks (GNNs) perform poorly compared to simple heuristics on Link Prediction (LP) tasks. This is due to limitations in expressive power such as the inability to count triangles (the backbone of most LP heuristics) and because they can not distinguish automorphic nodes (those having identical structural roles). Both expressiveness issues can be alleviated by learning link (rather than node) representations and incorporating structural features such as triangle counts. Since explicit link representations are often prohibitively expensive, recent works resorted to subgraph-based methods, which have achieved state-of-the-art performance for LP, but suffer from poor efficiency due to high levels of redundancy between subgraphs. We analyze the components of subgraph GNN (SGNN) methods for link prediction. Based on our analysis, we propose a novel full-graph GNN called ELPH (Efficient Link Prediction with Hashing) that passes subgraph sketches as messages to approximate the key components of SGNNs without explicit subgraph construction. ELPH is provably more expressive than Message Passing GNNs (MPNNs). It outperforms existing SGNN models on many standard LP benchmarks while being orders of magnitude faster. However, it shares the common GNN limitation that it is only efficient when the dataset fits in GPU memory. Accordingly, we develop a highly scalable model, called BUDDY, which uses feature precomputation to circumvent this limitation without sacrificing predictive performance. Our experiments show that BUDDY also outperforms SGNNs on standard LP benchmarks while being highly scalable and faster than ELPH.

Code

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

19 samples harvested; 0 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.

Licence: 0 of the 19 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 melifluos/subgraph-sketching. “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.

Tasks

1 archive task tag without a task page not shown.

Results from the paper archive 2025-07-28

No leaderboard rows for this paper in the archive.

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