{"id":"https://openalex.org/W4396673725","doi":"https://doi.org/10.1093/jamia/ocae095","title":"RT: a Retrieving and Chain-of-Thought framework for few-shot medical named entity recognition","display_name":"RT: a Retrieving and Chain-of-Thought framework for few-shot medical named entity recognition","publication_year":2024,"publication_date":"2024-05-06","ids":{"openalex":"https://openalex.org/W4396673725","doi":"https://doi.org/10.1093/jamia/ocae095","pmid":"https://pubmed.ncbi.nlm.nih.gov/38708849"},"language":"en","primary_location":{"id":"doi:10.1093/jamia/ocae095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocae095","pdf_url":null,"source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1093/jamia/ocae095","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101907703","display_name":"Mingchen Li","orcid":"https://orcid.org/0000-0001-5181-8193"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mingchen Li","raw_affiliation_strings":["Division of Computational Health Sciences, Department of Surgery, University of Minnesota , Minneapolis, MN 55455, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Computational Health Sciences, Department of Surgery, University of Minnesota , Minneapolis, MN 55455, United States","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026404757","display_name":"Huixue Zhou","orcid":"https://orcid.org/0000-0002-6524-5506"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Huixue Zhou","raw_affiliation_strings":["Division of Computational Health Sciences, Department of Surgery, University of Minnesota , Minneapolis, MN 55455, United States","Institute for Health Informatics, University of Minnesota , Minneapolis, MN 55455, United States"],"raw_orcid":"https://orcid.org/0000-0002-6524-5506","affiliations":[{"raw_affiliation_string":"Division of Computational Health Sciences, Department of Surgery, University of Minnesota , Minneapolis, MN 55455, United States","institution_ids":["https://openalex.org/I130238516"]},{"raw_affiliation_string":"Institute for Health Informatics, University of Minnesota , Minneapolis, MN 55455, United States","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101605012","display_name":"Han Yang","orcid":"https://orcid.org/0009-0000-4322-6753"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Han Yang","raw_affiliation_strings":["Division of Computational Health Sciences, Department of Surgery, University of Minnesota , Minneapolis, MN 55455, United States","Institute for Health Informatics, University of Minnesota , Minneapolis, MN 55455, United States"],"raw_orcid":"https://orcid.org/0009-0000-4322-6753","affiliations":[{"raw_affiliation_string":"Division of Computational Health Sciences, Department of Surgery, University of Minnesota , Minneapolis, MN 55455, United States","institution_ids":["https://openalex.org/I130238516"]},{"raw_affiliation_string":"Institute for Health Informatics, University of Minnesota , Minneapolis, MN 55455, United States","institution_ids":["https://openalex.org/I130238516"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100421963","display_name":"Rui Zhang","orcid":"https://orcid.org/0000-0001-8258-3585"},"institutions":[{"id":"https://openalex.org/I130238516","display_name":"University of Minnesota","ror":"https://ror.org/017zqws13","country_code":"US","type":"education","lineage":["https://openalex.org/I130238516"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rui Zhang","raw_affiliation_strings":["Division of Computational Health Sciences, Department of Surgery, University of Minnesota , Minneapolis, MN 55455, United States"],"raw_orcid":"https://orcid.org/0000-0001-8258-3585","affiliations":[{"raw_affiliation_string":"Division of Computational Health Sciences, Department of Surgery, University of Minnesota , Minneapolis, MN 55455, United States","institution_ids":["https://openalex.org/I130238516"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100421963"],"corresponding_institution_ids":["https://openalex.org/I130238516"],"apc_list":{"value":4549,"currency":"USD","value_usd":4549},"apc_paid":{"value":4549,"currency":"USD","value_usd":4549},"fwci":12.004,"has_fulltext":true,"cited_by_count":52,"citation_normalized_percentile":{"value":0.9886178,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"31","issue":"9","first_page":"1929","last_page":"1938"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.41839998960494995,"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":0.41839998960494995,"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":0.3885999917984009,"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/T11636","display_name":"Artificial Intelligence in Healthcare and Education","score":0.042399998754262924,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"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/computer-science","display_name":"Computer science","score":0.8332779407501221},{"id":"https://openalex.org/keywords/named-entity-recognition","display_name":"Named-entity recognition","score":0.7222890853881836},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.6712134480476379},{"id":"https://openalex.org/keywords/sentence","display_name":"Sentence","score":0.6464765667915344},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5969105362892151},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5484791398048401},{"id":"https://openalex.org/keywords/shot","display_name":"Shot (pellet)","score":0.5140761137008667},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4753384590148926},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.4392610490322113},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.06776195764541626}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8332779407501221},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.7222890853881836},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.6712134480476379},{"id":"https://openalex.org/C2777530160","wikidata":"https://www.wikidata.org/wiki/Q41796","display_name":"Sentence","level":2,"score":0.6464765667915344},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5969105362892151},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5484791398048401},{"id":"https://openalex.org/C2778344882","wikidata":"https://www.wikidata.org/wiki/Q278938","display_name":"Shot (pellet)","level":2,"score":0.5140761137008667},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4753384590148926},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4392610490322113},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.06776195764541626},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018875","descriptor_name":"Vocabulary, Controlled","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/jamia/ocae095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocae095","pdf_url":null,"source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},{"id":"pmid:38708849","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38708849","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the American Medical Informatics Association : JAMIA","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11339512","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11339512","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11339512/pdf/ocae095.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Am Med Inform Assoc","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/jamia/ocae095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/jamia/ocae095","pdf_url":null,"source":{"id":"https://openalex.org/S129839026","display_name":"Journal of the American Medical Informatics Association","issn_l":"1067-5027","issn":["1067-5027","1527-974X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of the American Medical Informatics Association","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.8299999833106995,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G2473746854","display_name":null,"funder_award_id":"R01 AG078154","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G2635792716","display_name":null,"funder_award_id":"R01AT009457","funder_id":"https://openalex.org/F4320337593","funder_display_name":"National Center for Complementary and Integrative Health"},{"id":"https://openalex.org/G5791301197","display_name":"A Translational Informatics Framework to Mine Efficacy and Safety of Dietary Supplements","funder_award_id":"5r01at009457-06","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6788124466","display_name":null,"funder_award_id":"R01 CA287413","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337593","display_name":"National Center for Complementary and Integrative Health","ror":"https://ror.org/00190t495"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W2169099542","https://openalex.org/W2190333735","https://openalex.org/W2346452181","https://openalex.org/W2601450892","https://openalex.org/W2911489562","https://openalex.org/W4206380771","https://openalex.org/W4310456519","https://openalex.org/W4312220150","https://openalex.org/W4320525813","https://openalex.org/W4388605937","https://openalex.org/W6735236233"],"related_works":["https://openalex.org/W2074502265","https://openalex.org/W4214877189","https://openalex.org/W3005759282","https://openalex.org/W3017222382","https://openalex.org/W3128216712","https://openalex.org/W3136915866","https://openalex.org/W4390279576","https://openalex.org/W2886890203","https://openalex.org/W4313535650","https://openalex.org/W2287770975"],"abstract_inverted_index":{"OBJECTIVES:":[0],"This":[1,208],"article":[2],"aims":[3],"to":[4,36,70,112,213,221,246],"enhance":[5,222],"the":[6,14,38,48,87,104,141,204,210,223,235,240,248,251],"performance":[7,224,275],"of":[8,121,143,168,194,203,239,259],"larger":[9],"language":[10,53,60],"models":[11,128],"(LLMs)":[12],"on":[13,133,151,172,276],"few-shot":[15,130,162,227,277],"biomedical":[16,226],"named":[17],"entity":[18,249],"recognition":[19],"(NER)":[20],"task":[21],"by":[22],"developing":[23],"a":[24,65,108,117,195,200,215,256],"simple":[25],"and":[26,31,35,55,83,135,148,170,174,184,218],"effective":[27],"method":[28],"called":[29],"Retrieving":[30],"Chain-of-Thought":[32,56,84,105,187,219],"(RT)":[33],"framework":[34,68,124,157,269],"evaluate":[37],"improvement":[39],"after":[40],"applying":[41],"RT":[42,67,75,90,123,156,268],"framework.":[43],"MATERIALS":[44],"AND":[45],"METHODS:":[46],"Given":[47],"remarkable":[49],"advancements":[50],"in":[51,225,233,250],"retrieval-based":[52,216,230],"model":[54,205],"across":[57],"various":[58],"natural":[59],"processing":[61],"tasks,":[62],"we":[63,139],"propose":[64],"pioneering":[66],"designed":[69],"amalgamate":[71],"both":[72,182],"approaches.":[73],"The":[74,229,267],"approach":[76],"encompasses":[77],"dedicated":[78],"modules":[79],"for":[80,99,129,161],"information":[81],"retrieval":[82,88],"processes.":[85],"In":[86],"module,":[89],"discerns":[91],"pertinent":[92],"examples":[93,238],"from":[94],"demonstrations":[95],"during":[96],"instructional":[97],"tuning":[98],"each":[100],"input":[101,241],"sentence.":[102,252],"Subsequently,":[103],"module":[106],"employs":[107],"systematic":[109],"reasoning":[110],"process":[111],"identify":[113],"entities.":[114],"We":[115,178,253],"conducted":[116,255],"comprehensive":[118],"comparative":[119],"analysis":[120],"our":[122,260],"against":[125],"16":[126],"other":[127,159],"NER":[131,163,278],"tasks":[132,164],"BC5CDR":[134,173],"NCBI":[136,175],"corpora.":[137],"Additionally,":[138,192],"explored":[140],"impacts":[142],"negative":[144,185],"samples,":[145,186],"output":[146],"formats,":[147],"missing":[149],"data":[150],"performance.":[152,206],"RESULTS:":[153],"Our":[154],"proposed":[155],"outperforms":[158],"LMs":[160],"with":[165,270],"micro-F1":[166],"scores":[167],"93.50":[169],"91.76":[171],"corpora,":[176],"respectively.":[177],"found":[179],"that":[180],"using":[181],"positive":[183],"(vs":[188],"Tree-of-Thought)":[189],"performed":[190],"better.":[191],"utilization":[193],"partially":[196],"annotated":[197],"dataset":[198],"has":[199,272],"marginal":[201],"effect":[202],"DISCUSSION:":[207],"is":[209],"first":[211],"investigation":[212],"combine":[214],"LLM":[217,231,271],"methodology":[220],"NER.":[228],"aids":[232],"retrieving":[234],"most":[236],"relevant":[237],"sentence,":[242],"offering":[243],"crucial":[244],"knowledge":[245],"predict":[247],"also":[254],"meticulous":[257],"examination":[258],"methodology,":[261],"incorporating":[262],"an":[263],"ablation":[264],"study.":[265],"CONCLUSION:":[266],"demonstrated":[273],"state-of-the-art":[274],"tasks.":[279]},"counts_by_year":[{"year":2026,"cited_by_count":13},{"year":2025,"cited_by_count":32},{"year":2024,"cited_by_count":7}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}
