Stephen Lu @matrixmaster.me · Jun 8 Antibody LMs learn what looks antibody-like, but not how selection turns naive germline antibodies into strong binders. @aakarshv1.bsky.social and I are excited to share CoSiNE, a model that learns this germline-to-mature process for variant effect prediction and antibody design. (1/8)
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Traditional antibody language modeling assumes sequences are i.i.d. — ignoring the time-dependent process of affinity maturation. To address this, CoSiNE explicitly models transitions: how likely is a mature antibody y to arise from a germline precursor x over time t? (2/8)