{"id":"https://openalex.org/W4406261956","doi":"https://doi.org/10.1109/bibm62325.2024.10821797","title":"TDLM: A Diffusion Language Model for TCR Sequence Exploration and Generation","display_name":"TDLM: A Diffusion Language Model for TCR Sequence Exploration and Generation","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406261956","doi":"https://doi.org/10.1109/bibm62325.2024.10821797"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10821797","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10821797","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101651173","display_name":"Haoyan Wang","orcid":"https://orcid.org/0000-0001-7688-5915"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haoyan Wang","raw_affiliation_strings":["Faculty of Computing Harbin Institute of Technology,Harbin,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computing Harbin Institute of Technology,Harbin,China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114246636","display_name":"Yuhang Yang","orcid":"https://orcid.org/0009-0002-1220-5524"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuhang Yang","raw_affiliation_strings":["Faculty of Computing Harbin Institute of Technology,Harbin,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computing Harbin Institute of Technology,Harbin,China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018560644","display_name":"Yifei Huang","orcid":"https://orcid.org/0000-0001-8067-6227"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yifei Huang","raw_affiliation_strings":["Faculty of Computing Harbin Institute of Technology,Harbin,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computing Harbin Institute of Technology,Harbin,China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084159324","display_name":"Tianyi Zang","orcid":"https://orcid.org/0000-0003-0195-8731"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tianyi Zang","raw_affiliation_strings":["Faculty of Computing Harbin Institute of Technology,Harbin,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computing Harbin Institute of Technology,Harbin,China","institution_ids":["https://openalex.org/I204983213"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100613438","display_name":"Yadong Liu","orcid":"https://orcid.org/0000-0001-8597-4418"},"institutions":[{"id":"https://openalex.org/I204983213","display_name":"Harbin Institute of Technology","ror":"https://ror.org/01yqg2h08","country_code":"CN","type":"education","lineage":["https://openalex.org/I204983213"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yadong Liu","raw_affiliation_strings":["Faculty of Computing Harbin Institute of Technology,Harbin,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computing Harbin Institute of Technology,Harbin,China","institution_ids":["https://openalex.org/I204983213"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I204983213"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"113","last_page":"120"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10181","display_name":"Natural Language Processing Techniques","score":0.9818999767303467,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10181","display_name":"Natural Language Processing Techniques","score":0.9818999767303467,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10201","display_name":"Speech Recognition and Synthesis","score":0.9376999735832214,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.65663743019104},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6475009322166443},{"id":"https://openalex.org/keywords/diffusion","display_name":"Diffusion","score":0.5994501113891602},{"id":"https://openalex.org/keywords/t-cell-receptor","display_name":"T-cell receptor","score":0.5013911724090576},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.13541880249977112},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.10506659746170044},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.06273016333580017}],"concepts":[{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.65663743019104},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6475009322166443},{"id":"https://openalex.org/C69357855","wikidata":"https://www.wikidata.org/wiki/Q163214","display_name":"Diffusion","level":2,"score":0.5994501113891602},{"id":"https://openalex.org/C19317047","wikidata":"https://www.wikidata.org/wiki/Q412037","display_name":"T-cell receptor","level":4,"score":0.5013911724090576},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.13541880249977112},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.10506659746170044},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.06273016333580017},{"id":"https://openalex.org/C2776090121","wikidata":"https://www.wikidata.org/wiki/Q193529","display_name":"T cell","level":3,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C97355855","wikidata":"https://www.wikidata.org/wiki/Q11473","display_name":"Thermodynamics","level":1,"score":0.0},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.0},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10821797","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10821797","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321543","display_name":"China Postdoctoral Science Foundation","ror":"https://ror.org/0426zh255"},{"id":"https://openalex.org/F4320337504","display_name":"Research and Development","ror":"https://ror.org/027s68j25"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1914202150","https://openalex.org/W2011450442","https://openalex.org/W2043496713","https://openalex.org/W2131375633","https://openalex.org/W2172893229","https://openalex.org/W2523044687","https://openalex.org/W2613978126","https://openalex.org/W2670890989","https://openalex.org/W2671261300","https://openalex.org/W2752126733","https://openalex.org/W2761865621","https://openalex.org/W2797967938","https://openalex.org/W2898389621","https://openalex.org/W3135351475","https://openalex.org/W3146944767","https://openalex.org/W3159882286","https://openalex.org/W3160420762","https://openalex.org/W3177500196","https://openalex.org/W3196007724","https://openalex.org/W3214452197","https://openalex.org/W3217516687","https://openalex.org/W4286631898","https://openalex.org/W4312982034","https://openalex.org/W4323320132","https://openalex.org/W4385564176","https://openalex.org/W4406128352","https://openalex.org/W6779823529","https://openalex.org/W6786375611","https://openalex.org/W6798447524","https://openalex.org/W6838815585","https://openalex.org/W6846930609","https://openalex.org/W6848910240","https://openalex.org/W6850009388","https://openalex.org/W6873365134"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2394822632","https://openalex.org/W1996773663","https://openalex.org/W2390279801","https://openalex.org/W2169237989","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345"],"abstract_inverted_index":{"The":[0,16,199],"adaptive":[1],"immune":[2],"response":[3],"relies":[4],"on":[5,113],"the":[6,44,177],"ability":[7,173],"of":[8,19,28,46,182],"T-cell":[9,87],"receptors":[10],"(TCRs)":[11],"to":[12,23,75,94,120,124,130],"recognize":[13,24],"specific":[14,169],"antigens.":[15],"vast":[17,122],"diversity":[18],"TCRs":[20,152,183],"allows":[21],"T-cells":[22],"a":[25,60,63,86,159],"broad":[26],"spectrum":[27],"antigens,":[29],"but":[30],"this":[31],"complexity":[32],"also":[33],"poses":[34],"challenges":[35],"for":[36,54,62,176],"understanding":[37],"and":[38,50,56,65,101,141,147,168,180,196],"predicting":[39],"TCR-antigen":[40,137],"binding":[41,138],"specificity.":[42,156],"Despite":[43],"development":[45],"various":[47,76,105],"machine":[48],"learning":[49,52],"deep":[51],"methods":[53],"prediction":[55,139],"clustering,":[57],"there":[58],"remains":[59],"need":[61],"versatile":[64],"effective":[66,143],"TCR":[67,99,115,144,170],"language":[68,91],"framework":[69],"that":[70],"can":[71,110,164],"be":[72,111],"flexibly":[73],"applied":[74],"downstream":[77,106],"tasks,":[78],"including":[79],"sequence":[80,116,145],"generation.":[81],"Here":[82],"we":[83],"present":[84],"TDLM,":[85],"Receptor":[88],"(TCR)":[89],"diffusion":[90],"model,":[92,162],"designed":[93],"decode":[95],"complex":[96],"patterns":[97],"within":[98],"sequences":[100],"apply":[102],"them":[103],"across":[104],"tasks.":[107],"Firstly,":[108],"TDLM":[109,134,163],"trained":[112],"unlabeled":[114],"data,":[117],"enabling":[118],"it":[119],"utilize":[121],"datasets":[123],"generate":[125,165],"comprehensive":[126],"embeddings.":[127],"When":[128],"compared":[129],"other":[131],"embedding":[132],"methods,":[133],"embeddings":[135],"enhance":[136],"accuracy":[140],"enable":[142],"clustering":[146],"similarity":[148],"analysis,":[149],"helping":[150],"identify":[151],"with":[153,184],"shared":[154],"antigen":[155,186],"Furthermore,":[157],"as":[158],"diffusion-based":[160],"generative":[161],"highly":[166],"diverse":[167],"sequences.":[171],"This":[172],"is":[174,201],"invaluable":[175],"rapid":[178],"screening":[179],"optimization":[181],"target":[185],"specificities,":[187],"offering":[188],"significant":[189],"potential":[190],"in":[191],"disease":[192],"diagnosis,":[193],"personalized":[194],"immunotherapy,":[195],"vaccine":[197],"research.":[198],"code":[200],"available":[202],"at:":[203],"https://github.com/skybluewhy/TDLM":[204]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}