{"paper":{"title":"DynImmune-BERT: Dynamic Immune Repertoire Modeling with Neural ODE Driven Continuous Transformers","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":[],"primary_cat":"cs.LG","authors_text":"Haoyu Zhao, Long Zhang, Rong Fu, Shuo Yin, Wangyu Wu, Xiaowen Ma, Yiqing Lyu, Yongtai Liu","submitted_at":"2026-07-19T13:25:05Z","abstract_excerpt":"Longitudinal T cell receptor repertoires contain signals of clonal expansion, contraction, disappearance, and reappearance after immune perturbation. Static repertoire language models usually summarize a sample as a bag of sequences, so the sampling interval, sequencing depth, and clone presence pattern are only weakly represented. This paper presents DynImmune-BERT, a continuous time repertoire model for patient level immune status prediction. The method combines depth adaptive centered log ratio initialization, clone presence gated Neural ordinary differential equation dynamics, bounded neig"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2607.17244","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/2607.17244/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"}