{"id":1134440,"date":"2025-03-18T13:34:34","date_gmt":"2025-03-18T20:34:34","guid":{"rendered":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/?post_type=msr-research-item&#038;p=1134440"},"modified":"2025-03-18T13:35:25","modified_gmt":"2025-03-18T20:35:25","slug":"scalable-universal-t-cell-receptor-embeddings-from-adaptive-immune-repertoires","status":"publish","type":"msr-research-item","link":"https:\/\/cm-edgetun.pages.dev\/en-us\/research\/publication\/scalable-universal-t-cell-receptor-embeddings-from-adaptive-immune-repertoires\/","title":{"rendered":"Scalable Universal T-Cell Receptor Embeddings from Adaptive Immune Repertoires"},"content":{"rendered":"<p>T cells are a key component of the adaptive immune system, targeting infections, cancers, and allergens with specificity encoded by their T cell receptors (TCRs), and retaining a memory of their targets. High-throughput TCR repertoire sequencing captures a cross-section of TCRs that encode the immune history of any subject, though the data are heterogeneous, high dimensional, sparse, and mostly unlabeled. Sets of TCRs responding to the same antigen,\u00a0<em>i.e.<\/em>, a protein fragment, co-occur in subjects sharing immune genetics and exposure history. Here, we leverage TCR co-occurrence across a large set of TCR repertoires and employ the GloVe (Pennington et al., 2014) algorithm to derive low-dimensional, dense vector representations (embeddings) of TCRs. We then aggregate these TCR embeddings to generate subject-level embeddings based on observed\u00a0<em>subject-specific<\/em>\u00a0TCR subsets. Further, we leverage random projection theory to improve GloVe&#8217;s computational efficiency in terms of memory usage and training time. Extensive experimental results show that TCR embeddings targeting the same pathogen have high cosine similarity, and subject-level embeddings encode both immune genetics and pathogenic exposure history.<\/p>\n","protected":false},"excerpt":{"rendered":"<p>T cells are a key component of the adaptive immune system, targeting infections, cancers, and allergens with specificity encoded by their T cell receptors (TCRs), and retaining a memory of their targets. High-throughput TCR repertoire sequencing captures a cross-section of TCRs that encode the immune history of any subject, though the data are heterogeneous, high [&hellip;]<\/p>\n","protected":false},"featured_media":0,"template":"","meta":{"msr-url-field":"","msr-podcast-episode":"","msrModifiedDate":"","msrModifiedDateEnabled":false,"ep_exclude_from_search":false,"_classifai_error":"","msr-author-ordering":null,"msr_publishername":"","msr_publisher_other":"","msr_booktitle":"","msr_chapter":"","msr_edition":"","msr_editors":"","msr_how_published":"","msr_isbn":"","msr_issue":"","msr_journal":"","msr_number":"","msr_organization":"","msr_pages_string":"","msr_page_range_start":"","msr_page_range_end":"","msr_series":"","msr_volume":"","msr_copyright":"","msr_conference_name":"ICLR 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