{"paper":{"title":"CoTAR: Topology and Atomic State Reconstruction in Condensed Phases","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":[],"primary_cat":"cond-mat.mtrl-sci","authors_text":"Hodaka Mori, Takechika Kikkawa, Yu Miyazaki","submitted_at":"2026-06-26T01:23:31Z","abstract_excerpt":"Universal machine learning interatomic potentials (uMLIPs) enable condensed-phase molecular dynamics (MD) simulations with near-first-principles accuracy, but their lack of explicit molecular topology limits bond-aware analysis and reconnection to classical force fields. Here, we present CoTAR, a hybrid graph neural network (GNN)--hidden Markov model (HMM) framework that reconstructs molecular topology, formal charges, and unpaired electrons from atomic species, coordinates, and total charge by combining message passing on a proximity graph with a van der Waals prior, chemical constraints, and"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2606.27636","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2606.27636/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}