{"id":"https://openalex.org/W3168935962","doi":"https://doi.org/10.18653/v1/2021.findings-acl.311","title":"Biomedical Interpretable Entity Representations","display_name":"Biomedical Interpretable Entity Representations","publication_year":2021,"publication_date":"2021-01-01","ids":{"openalex":"https://openalex.org/W3168935962","doi":"https://doi.org/10.18653/v1/2021.findings-acl.311","mag":"3168935962"},"language":"en","primary_location":{"id":"doi:10.18653/v1/2021.findings-acl.311","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2021.findings-acl.311","pdf_url":"https://aclanthology.org/2021.findings-acl.311.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Findings of the Association for Computational Linguistics: ACL-IJCNLP 2021","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://aclanthology.org/2021.findings-acl.311.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061696723","display_name":"Diego Garc\u00eda-Olano","orcid":null},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Diego Garcia-Olano","raw_affiliation_strings":["IBM Research,","University of Texas at Austin,","The University of Texas at Austin, Austin, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM Research,","institution_ids":[]},{"raw_affiliation_string":"University of Texas at Austin,","institution_ids":["https://openalex.org/I86519309"]},{"raw_affiliation_string":"The University of Texas at Austin, Austin, United States","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001707231","display_name":"Yasumasa Onoe","orcid":null},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yasumasa Onoe","raw_affiliation_strings":["University of Texas at Austin,","University of Texas at Austin"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Texas at Austin,","institution_ids":["https://openalex.org/I86519309"]},{"raw_affiliation_string":"University of Texas at Austin","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073341059","display_name":"Ioana Baldini","orcid":"https://orcid.org/0000-0002-8257-9866"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ioana Baldini","raw_affiliation_strings":["IBM Research,","IBM"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM Research,","institution_ids":[]},{"raw_affiliation_string":"IBM","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103071668","display_name":"Joydeep Ghosh","orcid":"https://orcid.org/0000-0002-7366-3548"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joydeep Ghosh","raw_affiliation_strings":["University of Texas at Austin,","University of Texas at Austin"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Texas at Austin,","institution_ids":["https://openalex.org/I86519309"]},{"raw_affiliation_string":"University of Texas at Austin","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036790226","display_name":"Byron Wallace","orcid":"https://orcid.org/0000-0003-2409-7735"},"institutions":[{"id":"https://openalex.org/I87182695","display_name":"Universidad del Noreste","ror":"https://ror.org/02ahky613","country_code":"MX","type":"education","lineage":["https://openalex.org/I87182695"]}],"countries":["MX"],"is_corresponding":false,"raw_author_name":"Byron Wallace","raw_affiliation_strings":["Northeastern University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northeastern University","institution_ids":["https://openalex.org/I87182695"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015286159","display_name":"Kush R. Varshney","orcid":"https://orcid.org/0000-0002-7376-5536"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kush Varshney","raw_affiliation_strings":["IBM Research,","IBM"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBM Research,","institution_ids":[]},{"raw_affiliation_string":"IBM","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.05948788,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"3547","last_page":"3561"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9998000264167786,"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/T10028","display_name":"Topic Modeling","score":0.9998000264167786,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9979000091552734,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9926999807357788,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.8504836559295654},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7913087606430054},{"id":"https://openalex.org/keywords/biomedicine","display_name":"Biomedicine","score":0.7434995174407959},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.6242483258247375},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6037039160728455},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5914835929870605},{"id":"https://openalex.org/keywords/debugging","display_name":"Debugging","score":0.5889004468917847},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5886244773864746},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.5664516091346741},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.533449649810791},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4895366132259369},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.44037526845932007},{"id":"https://openalex.org/keywords/type","display_name":"Type (biology)","score":0.4316040873527527},{"id":"https://openalex.org/keywords/entity-linking","display_name":"Entity linking","score":0.4283071756362915},{"id":"https://openalex.org/keywords/knowledge-base","display_name":"Knowledge base","score":0.19366437196731567},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12913498282432556},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.08300581574440002}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.8504836559295654},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7913087606430054},{"id":"https://openalex.org/C66782513","wikidata":"https://www.wikidata.org/wiki/Q864601","display_name":"Biomedicine","level":2,"score":0.7434995174407959},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.6242483258247375},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6037039160728455},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5914835929870605},{"id":"https://openalex.org/C168065819","wikidata":"https://www.wikidata.org/wiki/Q845566","display_name":"Debugging","level":2,"score":0.5889004468917847},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5886244773864746},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.5664516091346741},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.533449649810791},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4895366132259369},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.44037526845932007},{"id":"https://openalex.org/C2777299769","wikidata":"https://www.wikidata.org/wiki/Q3707858","display_name":"Type (biology)","level":2,"score":0.4316040873527527},{"id":"https://openalex.org/C96711827","wikidata":"https://www.wikidata.org/wiki/Q17012245","display_name":"Entity linking","level":3,"score":0.4283071756362915},{"id":"https://openalex.org/C4554734","wikidata":"https://www.wikidata.org/wiki/Q593744","display_name":"Knowledge base","level":2,"score":0.19366437196731567},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12913498282432556},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.08300581574440002},{"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/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","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},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.18653/v1/2021.findings-acl.311","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2021.findings-acl.311","pdf_url":"https://aclanthology.org/2021.findings-acl.311.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Findings of the Association for Computational Linguistics: ACL-IJCNLP 2021","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:2106.09502","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2106.09502","pdf_url":"https://arxiv.org/pdf/2106.09502","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":null,"raw_type":"text"},{"id":"mag:3168935962","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/2106.09502.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.2106.09502","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2106.09502","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"Preprint"}],"best_oa_location":{"id":"doi:10.18653/v1/2021.findings-acl.311","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2021.findings-acl.311","pdf_url":"https://aclanthology.org/2021.findings-acl.311.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Findings of the Association for Computational Linguistics: ACL-IJCNLP 2021","raw_type":"proceedings-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.6100000143051147,"display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G2414053288","display_name":"RI: Medium: Learning Disentangled Representations for Text to Aid Interpretability and Transfer","funder_award_id":"1901117","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3272463826","display_name":"CAREER: Structured Scientific Evidence Extraction: Models and Corpora","funder_award_id":"1750978","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4353487559","display_name":null,"funder_award_id":"ONR-N00014","funder_id":"https://openalex.org/F4320337345","funder_display_name":"Office of Naval Research"},{"id":"https://openalex.org/G4504108201","display_name":null,"funder_award_id":"N00014-17-1","funder_id":"https://openalex.org/F4320337345","funder_display_name":"Office of Naval Research"},{"id":"https://openalex.org/G8876996369","display_name":null,"funder_award_id":"N00014","funder_id":"https://openalex.org/F4320337345","funder_display_name":"Office of Naval Research"},{"id":"https://openalex.org/G8929337198","display_name":null,"funder_award_id":"N00014-17","funder_id":"https://openalex.org/F4320337345","funder_display_name":"Office of Naval Research"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320337345","display_name":"Office of Naval Research","ror":"https://ror.org/00rk2pe57"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3168935962.pdf","grobid_xml":"https://content.openalex.org/works/W3168935962.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1830777114","https://openalex.org/W2140610559","https://openalex.org/W2250750514","https://openalex.org/W2525778437","https://openalex.org/W2593864460","https://openalex.org/W2766841988","https://openalex.org/W2793165286","https://openalex.org/W2797078590","https://openalex.org/W2798442412","https://openalex.org/W2911489562","https://openalex.org/W2917650994","https://openalex.org/W2945878859","https://openalex.org/W2946359678","https://openalex.org/W2946690328","https://openalex.org/W2962739339","https://openalex.org/W2962891712","https://openalex.org/W2963341956","https://openalex.org/W2963403868","https://openalex.org/W2964027067","https://openalex.org/W2964075320","https://openalex.org/W2970069267","https://openalex.org/W2970771982","https://openalex.org/W2970862333","https://openalex.org/W2971869958","https://openalex.org/W2983915252","https://openalex.org/W2989227969","https://openalex.org/W3021352513","https://openalex.org/W3034229721","https://openalex.org/W3094258447","https://openalex.org/W3102659883","https://openalex.org/W3105057865","https://openalex.org/W3105801792","https://openalex.org/W3106224367","https://openalex.org/W3114677412","https://openalex.org/W3117138190"],"related_works":["https://openalex.org/W3173595688","https://openalex.org/W2250214321","https://openalex.org/W2963925965","https://openalex.org/W2346952692","https://openalex.org/W2803609569","https://openalex.org/W2963866108","https://openalex.org/W3052690463","https://openalex.org/W2153476384","https://openalex.org/W3099170115","https://openalex.org/W3089876042","https://openalex.org/W3124933699","https://openalex.org/W2783378231","https://openalex.org/W2952826391","https://openalex.org/W2987352513","https://openalex.org/W3032558086","https://openalex.org/W2963750238","https://openalex.org/W2963695529","https://openalex.org/W1771625187","https://openalex.org/W3102600955","https://openalex.org/W2795378892"],"abstract_inverted_index":{"Pre-trained":[0],"language":[1],"models":[2,212],"induce":[3],"dense":[4,148],"entity":[5,71,120,130,154,169,172],"representations":[6,17,53,149],"that":[7,127,141,159],"offer":[8],"strong":[9,162],"performance":[10,163],"on":[11,41],"entity-centric":[12],"NLP":[13],"tasks,":[14],"but":[15,50],"such":[16,33],"are":[18,101,124],"not":[19,55],"immediately":[20],"interpretable.":[21],"This":[22],"can":[23],"be":[24],"a":[25,69,78,90,128,138],"barrier":[26],"to":[27,58,87,96,118,150,180,209],"model":[28,152],"uptake":[29],"in":[30,89,114,164,188],"important":[31,60],"domains":[32],"as":[34],"biomedicine.":[35,63],"There":[36],"has":[37],"been":[38],"recent":[39],"work":[40],"general":[42],"interpretable":[43],"representation":[44],"learning":[45],"(Onoe":[46],"and":[47,74,93,122,146,153,171,175,213],"Durrett,":[48],"2020),":[49],"these":[51,95],"domain-agnostic":[52],"do":[54],"readily":[56],"transfer":[57],"the":[59,133,182,200],"domain":[61],"of":[62,81,132,184,205],"In":[64],"this":[65,105],"paper,":[66],"we":[67,107,176,192],"create":[68],"new":[70],"type":[72,155,198],"system":[73],"training":[75],"set":[76],"from":[77,94],"large":[79],"corpus":[80],"biomedical":[82,165,197],"texts":[83],"by":[84],"mapping":[85,106],"entities":[86],"concepts":[88],"medical":[91],"ontology,":[92],"Wikipedia":[97],"pages":[98],"whose":[99],"categories":[100],"our":[102,194,214],"types.":[103],"From":[104],"derive":[108],"Biomedical":[109],"Interpretable":[110],"Entity":[111],"Representations":[112],"(BIERs),":[113],"which":[115],"dimensions":[116],"correspond":[117],"fine-grained":[119],"types,":[121],"values":[123],"predicted":[125],"probabilities":[126],"given":[129],"is":[131],"corresponding":[134,201],"type.":[135],"We":[136,157],"propose":[137],"novel":[139],"method":[140],"exploits":[142],"BIER's":[143],"final":[144],"sparse":[145],"intermediate":[147],"facilitate":[151],"debugging.":[156],"show":[158],"BIERs":[160],"achieve":[161],"tasks":[166],"including":[167],"named":[168],"disambiguation":[170],"label":[173],"classification,":[174],"provide":[177,193],"error":[178],"analysis":[179],"highlight":[181],"utility":[183],"their":[185],"interpretability,":[186],"particularly":[187],"low-supervision":[189],"settings.":[190],"Finally,":[191],"induced":[195],"68K":[196],"system,":[199],"37":[202],"million":[203],"triples":[204],"derived":[206],"data":[207],"used":[208],"train":[210],"BIER":[211],"best":[215],"performing":[216],"model.":[217]},"counts_by_year":[],"updated_date":"2026-08-11T07:18:39.950985","created_date":"2025-10-10T00:00:00"}
