{"id":"https://openalex.org/W4406271225","doi":"https://doi.org/10.1109/bibm62325.2024.10822556","title":"An Improved Method for Phenotype Concept Recognition Using Rich HPO Information","display_name":"An Improved Method for Phenotype Concept Recognition Using Rich HPO Information","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406271225","doi":"https://doi.org/10.1109/bibm62325.2024.10822556"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822556","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822556","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/A5114198374","display_name":"Jiewei Qi","orcid":null},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiewei Qi","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100619435","display_name":"Ling Luo","orcid":"https://orcid.org/0000-0002-5141-0259"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ling Luo","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051597671","display_name":"Zhihao Yang","orcid":"https://orcid.org/0000-0001-6186-2024"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhihao Yang","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100370493","display_name":"Jian Wang","orcid":"https://orcid.org/0000-0002-8116-7691"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Wang","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047668953","display_name":"Huiwei Zhou","orcid":"https://orcid.org/0000-0002-7766-4177"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huiwei Zhou","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5109284752","display_name":"Hongfei Lin","orcid":"https://orcid.org/0000-0002-7191-2280"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongfei Lin","raw_affiliation_strings":["Dalian University of Technology,College of Computer Science and Technology,Dalian,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dalian University of Technology,College of Computer Science and Technology,Dalian,China","institution_ids":["https://openalex.org/I27357992"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I27357992"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1135","last_page":"1140"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12647","display_name":"Traditional Chinese Medicine Studies","score":0.6693000197410583,"subfield":{"id":"https://openalex.org/subfields/2707","display_name":"Complementary and alternative medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T12647","display_name":"Traditional Chinese Medicine Studies","score":0.6693000197410583,"subfield":{"id":"https://openalex.org/subfields/2707","display_name":"Complementary and alternative medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.5763000249862671,"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/computer-science","display_name":"Computer science","score":0.698175311088562},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.47078222036361694},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45280128717422485},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.35913538932800293},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.11940532922744751},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.06418618559837341}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.698175311088562},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.47078222036361694},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45280128717422485},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.35913538932800293},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.11940532922744751},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06418618559837341},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822556","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822556","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":[{"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2","score":0.6700000166893005}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W2081580037","https://openalex.org/W2119613819","https://openalex.org/W2136410628","https://openalex.org/W2137724373","https://openalex.org/W2137854030","https://openalex.org/W2184957013","https://openalex.org/W2728059831","https://openalex.org/W2767470330","https://openalex.org/W2911489562","https://openalex.org/W2928818852","https://openalex.org/W3046375318","https://openalex.org/W3087028093","https://openalex.org/W3106811464","https://openalex.org/W3121524366","https://openalex.org/W4212919921","https://openalex.org/W4224997359","https://openalex.org/W4385245566","https://openalex.org/W4388488609","https://openalex.org/W4389520065","https://openalex.org/W4391387740","https://openalex.org/W4392282268","https://openalex.org/W4399941107","https://openalex.org/W6604181502","https://openalex.org/W6678830454","https://openalex.org/W6747741389","https://openalex.org/W6763185011","https://openalex.org/W6809646742","https://openalex.org/W6849437824","https://openalex.org/W6851895266","https://openalex.org/W6855198122","https://openalex.org/W6929686471"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2033914206","https://openalex.org/W2042327336"],"abstract_inverted_index":{"Automatically":[0],"identifying":[1],"human":[2],"phenotype":[3,18,46,86],"ontology":[4,37,84],"(HPO)":[5],"concepts":[6],"from":[7,29],"text":[8],"is":[9],"important":[10],"for":[11,17,74],"disease":[12],"analysis.":[13],"Existing":[14],"ontology-driven":[15],"methods":[16,137],"concept":[19,24,47,87],"recognition":[20,48,109],"mainly":[21],"rely":[22],"on":[23,122],"names":[25],"and":[26,62,114,126,138,149],"synonym":[27,72],"information":[28,61],"the":[30,35,93,107],"ontology,":[31],"without":[32],"fully":[33],"exploiting":[34],"rich":[36,52],"information.":[38,54],"In":[39],"this":[40],"paper,":[41],"we":[42,100],"present":[43],"an":[44,83],"improved":[45],"method":[49,132],"by":[50],"incorporating":[51],"HPO":[53,60],"We":[55,80],"first":[56],"design":[57],"prompts":[58],"with":[59],"use":[63],"a":[64,116,140],"cutting-edge":[65],"large":[66],"language":[67],"model":[68,89],"GPT-4":[69],"to":[70,90,105,135],"generate":[71],"augmentation":[73,104],"expanding":[75],"distant":[76],"supervised":[77],"training":[78],"data.":[79],"then":[81],"propose":[82],"vector-enhanced":[85],"classification":[88],"efficiently":[91],"integrate":[92],"taxonomic":[94],"hierarchical":[95],"structure":[96],"of":[97],"HPO.":[98],"Additionally,":[99],"employ":[101],"noisy":[102,112,144],"data":[103,150],"improve":[106],"model\u2019s":[108],"ability":[110],"in":[111,143],"texts":[113],"implement":[115],"negation":[117],"detection":[118],"function.":[119],"Experimental":[120],"results":[121],"three":[123],"standard":[124],"corpora":[125,129],"two":[127],"typo":[128],"show":[130],"our":[131],"compares":[133],"favorably":[134],"previous":[136],"achieves":[139],"significant":[141],"improvement":[142],"texts.":[145],"The":[146],"source":[147],"code":[148],"are":[151],"freely":[152],"available":[153],"at":[154],"https://github.com/DUTIR-BioNLP/PhenoTagger-Updates.":[155]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}