DynImmune-BERT: Dynamic Immune Repertoire Modeling with Neural ODE Driven Continuous Transformers

תקציר מקורי באנגליתarXiv:2607.17244v1 Announce Type: new Abstract: 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 neighborhood self attention, event based state restart, and a hybrid transport objective that supervises dominant and rare clone mass. A low rank meta adapt