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<https://discovery.ucl.ac.uk/id/eprint/10205427> <http://purl.org/dc/terms/title> "Contrastive learning of T cell receptor representations"^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/eprint/10205427> <http://purl.org/ontology/bibo/abstract> "Computational prediction of the interaction of T cell receptors (TCRs) and their ligands is a grand challenge in immunology. Despite advances in high-throughput assays, specificity-labeled TCR data remain sparse. In other domains, the pre-training of language models on unlabeled data has been successfully used to address data bottlenecks. However, it is unclear how to best pre-train protein language models for TCR specificity prediction. Here, we introduce a TCR language model called SCEPTR (simple contrastive embedding of the primary sequence of T cell receptors), which is capable of data-efficient transfer learning. Through our model, we introduce a pre-training strategy combining autocontrastive learning and masked-language modeling, which enables SCEPTR to achieve its state-of-the-art performance. In contrast, existing protein language models and a variant of SCEPTR pre-trained without autocontrastive learning are outperformed by sequence alignment-based methods. We anticipate that contrastive learning will be a useful paradigm to decode the rules of TCR specificity. A record of this paper’s transparent peer review process is included in the supplemental information."^^<http://www.w3.org/2001/XMLSchema#string> .
<https://discovery.ucl.ac.uk/id/eprint/10205427> <http://purl.org/dc/terms/date> "2025-01-15" .
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<https://discovery.ucl.ac.uk/id/eprint/10205427> <http://purl.org/ontology/bibo/volume> "16" .
<https://discovery.ucl.ac.uk/id/eprint/10205427> <http://purl.org/ontology/bibo/issue> "1" .
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<https://discovery.ucl.ac.uk/id/person/ext-c45328c1e35480dbefaf4390f4b03653> <http://xmlns.com/foaf/0.1/familyName> "Nagano"^^<http://www.w3.org/2001/XMLSchema#string> .
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<https://discovery.ucl.ac.uk/id/person/ext-935ee9d213ca88c24a56126363870228> <http://xmlns.com/foaf/0.1/givenName> "Andreas"^^<http://www.w3.org/2001/XMLSchema#string> .
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<https://discovery.ucl.ac.uk/id/person/ext-935ee9d213ca88c24a56126363870228> <http://xmlns.com/foaf/0.1/name> "Andreas Tiffeau-Mayer"^^<http://www.w3.org/2001/XMLSchema#string> .
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