{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/geom2vec-pretrained-gnns-as-geometric","title":"Using pretrained graph neural networks with token mixers as geometric featurizers for conformational dynamics","arxiv_id":"2409.19838","date":"2024-09-30","proceeding":null,"authors":["Zihan Pengmei","Chatipat Lorpaiboon","Spencer C. Guo","Jonathan Weare","Aaron R. Dinner"],"abstract":"Identifying informative low-dimensional features that characterize dynamics in molecular simulations remains a challenge, often requiring extensive manual tuning and system-specific knowledge. Here, we introduce geom2vec, in which pretrained graph neural networks (GNNs) are used as universal geometric featurizers. By pretraining equivariant GNNs on a large dataset of molecular conformations with a self-supervised denoising objective, we obtain transferable structural representations that are useful for learning conformational dynamics without further fine-tuning. We show how the learned GNN representations can capture interpretable relationships between structural units (tokens) by combining them with expressive token mixers. Importantly, decoupling training the GNNs from training for downstream tasks enables analysis of larger molecular graphs (such as small proteins at all-atom resolution) with limited computational resources. In these ways, geom2vec eliminates the need for manual feature selection and increases the robustness of simulation analyses.","url_abs":"https://arxiv.org/abs/2409.19838v2","url_pdf":"https://arxiv.org/pdf/2409.19838v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"geom2vec-pretrained-gnns-as-geometric","repo_url":"https://github.com/dinner-group/geom2vec","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"NOASSERTION"}},{"paper_slug":"geom2vec-pretrained-gnns-as-geometric","repo_url":"https://github.com/zpengmei/geom2vec","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"denoising","task_name":"Denoising"},{"task_slug":"feature-selection","task_name":"feature selection"}],"methods":[{"method_slug":"feature-selection","method_name":"Feature Selection"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/2409.19838","atlas_url":"https://app.syntology.ai/?focus=2409.19838","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2409.19838"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-25T09:33:49+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. 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