arXiv: cs.AI preprintsInternational6 November 2026
Local-Frame Rotary Attention for Antibody-Specific Epitope Prediction
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arXiv:2608.01092v2 Announce Type: replace Abstract: Antibody-specific epitope prediction aims to identify which antigen residues are recognized by a given antibody, a task that depends on the three-dimensional complementarity between antibody CDRs and the antigen surface. Existing methods usually leverage PLM embeddings and inject structure through additional graph, surface, or point-cloud encoders, where the positional mechanism inside attention remains largely tied to one-dimensional sequence order. For proteins, the analogue of a token offset is not only sequence separation, but also the th
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