{"id":"https://openalex.org/W4297433454","doi":"https://doi.org/10.48550/arxiv.2209.12635","title":"ImmunoLingo: Linguistics-based formalization of the antibody language","display_name":"ImmunoLingo: Linguistics-based formalization of the antibody language","publication_year":2022,"publication_date":"2022-09-26","ids":{"openalex":"https://openalex.org/W4297433454","doi":"https://doi.org/10.48550/arxiv.2209.12635"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2209.12635","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2209.12635","pdf_url":"https://arxiv.org/pdf/2209.12635","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2209.12635","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5108295449","display_name":"Mai Ha Vu","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Vu, Mai Ha","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000751357","display_name":"Philippe A. Robert","orcid":"https://orcid.org/0000-0003-1345-5015"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Robert, Philippe A.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017929614","display_name":"Rahmad Akbar","orcid":"https://orcid.org/0000-0002-6692-0876"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Akbar, Rahmad","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074531013","display_name":"Bart\u0142omiej \u015awi\u0105tczak","orcid":"https://orcid.org/0000-0001-6767-3064"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Swiatczak, Bartlomiej","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054500587","display_name":"Geir Kjetil Sandve","orcid":"https://orcid.org/0000-0002-4959-1409"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sandve, Geir Kjetil","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012620009","display_name":"Dag Haug","orcid":"https://orcid.org/0000-0001-5275-8073"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Haug, Dag Trygve Truslew","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5089158926","display_name":"Victor Greiff","orcid":"https://orcid.org/0000-0003-2622-5032"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Greiff, Victor","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5108295449"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9950000047683716,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9950000047683716,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9945999979972839,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11016","display_name":"Monoclonal and Polyclonal Antibodies Research","score":0.9919000267982483,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/lexicon","display_name":"Lexicon","score":0.6658403277397156},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6585620641708374},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.5099834203720093},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5049896836280823},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.48181429505348206},{"id":"https://openalex.org/keywords/grammar","display_name":"Grammar","score":0.4696853458881378},{"id":"https://openalex.org/keywords/natural-language","display_name":"Natural language","score":0.46652230620384216},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.46035927534103394},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4570299983024597},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15628713369369507},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10958424210548401}],"concepts":[{"id":"https://openalex.org/C2778121359","wikidata":"https://www.wikidata.org/wiki/Q8096","display_name":"Lexicon","level":2,"score":0.6658403277397156},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6585620641708374},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.5099834203720093},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5049896836280823},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.48181429505348206},{"id":"https://openalex.org/C26022165","wikidata":"https://www.wikidata.org/wiki/Q8091","display_name":"Grammar","level":2,"score":0.4696853458881378},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.46652230620384216},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.46035927534103394},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4570299983024597},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15628713369369507},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10958424210548401},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2209.12635","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2209.12635","pdf_url":"https://arxiv.org/pdf/2209.12635","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2209.12635","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2209.12635","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2209.12635","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2209.12635","pdf_url":"https://arxiv.org/pdf/2209.12635","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[{"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4","score":0.8700000047683716}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W3195005284","https://openalex.org/W2391730868","https://openalex.org/W2759814045","https://openalex.org/W2118055728","https://openalex.org/W2140536630","https://openalex.org/W3015631708","https://openalex.org/W800231103","https://openalex.org/W2029051126","https://openalex.org/W2024636691","https://openalex.org/W2113143819"],"abstract_inverted_index":{"Apparent":[0],"parallels":[1],"between":[2,119],"natural":[3,120],"language":[4,19,121,179],"and":[5,27,58,68,101,117,122,165,180],"biological":[6,29,40,89,123],"sequence":[7,41,65],"have":[8],"led":[9,71],"to":[10,22,72,162],"a":[11,32,35,111,185],"recent":[12],"surge":[13],"in":[14,166,193,209],"the":[15,23,52,56,61,84,88,96,126,134,146,149,155,174,177,188,201],"application":[16,189],"of":[17,25,34,39,55,76,87,114,128,136,157,176,190,205],"deep":[18],"models":[20,138],"(LMs)":[21],"analysis":[24,197],"antibody":[26,150,158,178],"other":[28,97],"sequences.":[30],"However,":[31],"lack":[33],"rigorous":[36],"linguistic":[37,93,191],"formalization":[38],"languages,":[42],"which":[43,78,130],"would":[44,109],"define":[45],"basic":[46],"components,":[47],"such":[48,144],"as":[49,145],"lexicon":[50],"(i.e.,":[51,60],"discrete":[53],"units":[54],"language)":[57],"grammar":[59],"rules":[62,156],"that":[63],"link":[64],"well-formedness,":[66],"structure,":[67],"meaning)":[69],"has":[70],"largely":[73],"domain-unspecific":[74],"applications":[75],"LMs,":[77,129],"do":[79],"not":[80,183],"take":[81],"into":[82],"account":[83],"underlying":[85,148],"structure":[86],"sequences":[90,124],"studied.":[91],"A":[92],"formalization,":[94],"on":[95],"hand,":[98],"establishes":[99],"linguistically-informed":[100],"thus":[102],"domain-adapted":[103],"components":[104],"for":[105,133,187,200],"LM":[106],"applications.":[107],"It":[108],"facilitate":[110],"better":[112],"understanding":[113],"how":[115],"differences":[116],"similarities":[118],"influence":[125],"quality":[127],"is":[131,160],"crucial":[132,161],"design":[135],"interpretable":[137],"with":[139],"extractable":[140],"sequence-functions":[141],"relationship":[142],"rules,":[143],"ones":[147],"specificity":[151,159,208],"prediction":[152],"problem.":[153],"Deciphering":[154],"accelerating":[163],"rational":[164],"silico":[167],"biotherapeutic":[168],"drug":[169],"design.":[170],"Here,":[171],"we":[172],"formalize":[173],"properties":[175],"thereby":[181],"establish":[182],"only":[184],"foundation":[186],"tools":[192],"adaptive":[194],"immune":[195,206],"receptor":[196,207],"but":[198],"also":[199],"systematic":[202],"immunolinguistic":[203],"studies":[204],"general.":[210]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2026-02-09T09:26:11.010843","created_date":"2025-10-10T00:00:00"}