Papers › Understanding the Capabilities of Molecular Graph Neural Networks in Materials Science...
Understanding the Capabilities of Molecular Graph Neural Networks in Materials Science Through Multimodal Learning and Physical Context Encoding
Can Polat, Hasan Kurban, Erchin Serpedin, Mustafa Kurban
Molecular graph neural networks (GNNs) often focus exclusively on XYZ-based geometric representations and thus overlook valuable chemical context available in public databases like PubChem. This work introduces a multimodal framework that integrates textual descriptors, such as IUPAC names, molecular formulas, physicochemical properties, and synonyms, alongside molecular graphs. A gated fusion mechanism balances geometric and textual features, allowing models to exploit complementary information. Experiments on benchmark datasets indicate that adding textual data yields notable improvements for certain electronic properties, while gains remain limited for others. Furthermore, the GNN architectures display similar performance patterns (improving and deteriorating on analogous targets), suggesting they learn comparable representations rather than distinctly different physical insights.
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="2505.12137")
Code
Syntology Ran 1 of 2 code samples harvested from 1 repository linked to this paper; 1 has no recorded run. Of those that ran: 1 ran · fixture could not drive it.
By repository: official repository: 2 samples from 1 repository, 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.
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
2 samples harvested; 1 ran; 0 honoured the contract we drafted; 1 has 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 2 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 kurbanintelligencelab/understandingmultimodalgnns. “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.
3ac6b7d76e8e3584 · report
e85f83307efc1946 · report
Results from the paper archive 2025-07-28
No leaderboard rows for this paper in the archive.
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