Papers › Triplet Interaction Improves Graph Transformers: Accurate Molecular Graph Learning...

Triplet Interaction Improves Graph Transformers: Accurate Molecular Graph Learning with Triplet Graph Transformers

7 Feb 2024arXiv:2402.04538archive 2025-07-28

Md Shamim Hussain, Mohammed J. Zaki, Dharmashankar Subramanian

Graph transformers typically lack third-order interactions, limiting their geometric understanding which is crucial for tasks like molecular geometry prediction. We propose the Triplet Graph Transformer (TGT) that enables direct communication between pairs within a 3-tuple of nodes via novel triplet attention and aggregation mechanisms. TGT is applied to molecular property prediction by first predicting interatomic distances from 2D graphs and then using these distances for downstream tasks. A novel three-stage training procedure and stochastic inference further improve training efficiency and model performance. Our model achieves new state-of-the-art (SOTA) results on open challenge benchmarks PCQM4Mv2 and OC20 IS2RE. We also obtain SOTA results on QM9, MOLPCBA, and LIT-PCBA molecular property prediction benchmarks via transfer learning. We also demonstrate the generality of TGT with SOTA results on the traveling salesman problem (TSP).

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

13 samples harvested; 10 ran; 0 honoured the contract we drafted; 3 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 13 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.

Tasks

1 archive task tag without a task page not shown.

Results from the paper archive 2025-07-28

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

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