It is shown that conventional random train-test splits inflate retrieval accuracy by 15–28 percentage points owing to clonal leakage, and clone-aware benchmarking as a practical standard of comparison is established, defining the strengths and limitations of frozen zero-shot PLM embeddings for immune receptor retrieval and establishing clone-aware benchmarking as a practical standard of comparison.
This framework models SHM to generate native-like human antibodies, providing a biologically grounded tool for guiding design within the natural sequence space, and explicitly decouples targeting and substitution to enable faithful reproduction of both hotspot localization and amino acid substitution.
Karenna Ng, B. Némoz, Bryan S. Briney· Journal of Immunology· 0 citations
LM-QASAS provides a rapid, high-precision platform for monitoring humoral immunity against emerging threats by mapping sequences into a high-dimensional semantic embedding space, and identifies functionally convergent clusters of sequences that are semantically similar and exhibit transient expansion upon immune stimul...
Genki Masuda, Y. Funakoshi, S. Iizumi et al.· medRxiv· 0 citations
PRISM embeds receptors into a peptide-organized latent space, returns top-k peptides by nearest-neighbor retrieval, and abstains on out-of-distribution receptors by modeling an intrinsic uncertainty that tracks annotation correctness.
Divya Lakshmi Venkatraman, Lydia Mok, N. Rose et al.· bioRxiv· 0 citations
V identity is an emergent, system-level property of the repertoire, set jointly by recombination and selection and invisible in any single rearrangement, so it should be reported as a calibrated group rather than a single gene.
Revising all immune receptor records to produce resolved, standardized, and analysis-ready receptor data will enable researchers to seamlessly query large-scale repertoires for receptors with experimentally verified specificity in the IEDB, link orphan sequences to known targets, and support cross-repository studies of...
Lonneke Scheffer, Eve Richardson, R. Vita et al.· Journal of Immunology· 0 citations
An ensemble approach (enFoldX) that leverages structure prediction models such as AlphaFold3 to build sensitive binding predictors and outperforms the current co-folding methods which rely on predictions from the single top ranked structure.
O. Lyudovyk, Jonathan A. Levine, M. Pathil et al.· Clinical Cancer Research· 0 citations
We use cookies to run the site and, with your consent, for analytics and to show ads.
See our Cookie Policy.
