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[Submitted on 24 Sep 2026] Title:Predicting Transmembrane Protein Topology from 3D Structure View a PDF of the paper titled Predicting Transmembrane Protein Topology from 3D Structure, by Sitong Chen and 1 other authors View PDF HTML (experimental) Abstract:This paper presents a novel approach to infer protein topology using the state-of-the-art graph neural network (GNN), SchNet. The model is trained on the same dataset used to develop the recent DeepTMHMM model with 5-fold cross-validation. Unlike the conventional approaches based on using only the protein sequences or the $\alpha$-carbons as features, we have decoded our classifier in this way, so all atom-level embeddings are used. Without applying any pre-trained weight, the final results have shown great potential that GNNs can be used for topological predictions. Subjects: Artificial Intelligence (cs.AI) Cite as: arXiv:2609.30446 [cs.AI] (or arXiv:2609.30446v1 [cs.AI] for this version) https://doi.org/10.48550/arXiv.2609.30446 arXiv-issued DOI via DataCite (pending registration) Submission history From: Xiaopeng Mao [view email] [v1] Thu, 24 Sep 2026 18:38:33 UTC (3,727 KB) Full-text links: Access Paper: View a PDF of the paper titled Predicting Transmembrane Protein Topology from 3D Structure, by Sitong Chen and 1 other authors View PDF HTML (experimental) TeX Source view license Current browse context: cs.AI new | recent | 2026-09 Change to browse by: cs References & Citations NASA ADS Google Scholar Semantic Scholar Loading... Data provided by: Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer (What is the Explorer?) Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps Toggle Litmaps (What is Litmaps?) scite.ai Toggle scite Smart Citations (What are Smart Citations?) Code, Data, Media Code, Data and Media Associated with this Article alphaXiv Toggle alphaXiv (What is alphaXiv?) Links to Code Toggle CatalyzeX Code Finder for Papers (What is CatalyzeX?) DagsHub Toggle DagsHub (What is DagsHub?) GotitPub Toggle Gotit.pub (What is GotitPub?) Huggingface Toggle Hugging Face (What is Huggingface?) ScienceCast Toggle ScienceCast (What is ScienceCast?) Demos Demos Replicate Toggle Replicate (What is Replicate?) Spaces Toggle Hugging Face Spaces (What is Spaces?) Spaces Toggle TXYZ.AI (What is TXYZ.AI?) Related Papers Recommenders and Search Tools Link to Influence Flower Influence Flower (What are Influence Flowers?) Core recommender toggle CORE Recommender (What is CORE?) Author Venue Institution Topic About arXivLabs arXivLabs: experimental projects with community collaborators arXivLabs is a framework that allows collaborators to develop and share new arXiv features directly on our website. Both individuals and organizations that work with arXivLabs have embraced and accepted our values of openness, community, excellence, and user data privacy. arXiv is committed to these values and only works with partners that adhere to them. Have an idea for a project that will add value for arXiv's community? Learn more about arXivLabs. Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)