{"id":"https://openalex.org/W4413916431","doi":"https://doi.org/10.1016/j.engappai.2025.112001","title":"A two-stage model for unified sentence- and document-level biomedical event extraction","display_name":"A two-stage model for unified sentence- and document-level biomedical event extraction","publication_year":2025,"publication_date":"2025-09-02","ids":{"openalex":"https://openalex.org/W4413916431","doi":"https://doi.org/10.1016/j.engappai.2025.112001"},"language":"en","primary_location":{"id":"doi:10.1016/j.engappai.2025.112001","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.engappai.2025.112001","pdf_url":null,"source":{"id":"https://openalex.org/S900972176","display_name":"Engineering Applications of Artificial Intelligence","issn_l":"0952-1976","issn":["0952-1976","1873-6769"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Engineering Applications of Artificial Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1016/j.engappai.2025.112001","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101912322","display_name":"Fangfang Su","orcid":"https://orcid.org/0000-0002-6234-8227"},"institutions":[{"id":"https://openalex.org/I50760025","display_name":"Hangzhou Dianzi University","ror":"https://ror.org/0576gt767","country_code":"CN","type":"education","lineage":["https://openalex.org/I50760025"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fangfang Su","raw_affiliation_strings":["School of Cyberspace, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China"],"raw_orcid":"https://orcid.org/0000-0002-6234-8227","affiliations":[{"raw_affiliation_string":"School of Cyberspace, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China","institution_ids":["https://openalex.org/I50760025"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100333729","display_name":"Yue Zhang","orcid":"https://orcid.org/0000-0002-5214-2268"},"institutions":[{"id":"https://openalex.org/I3133055985","display_name":"Westlake University","ror":"https://ror.org/05hfa4n20","country_code":"CN","type":"education","lineage":["https://openalex.org/I3133055985"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yue Zhang","raw_affiliation_strings":["School of Engineering, Westlake University, Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, 310030, Zhejiang, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Engineering, Westlake University, Institute of Advanced Technology, Westlake Institute for Advanced Study, Hangzhou, 310030, Zhejiang, China","institution_ids":["https://openalex.org/I3133055985"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005761664","display_name":"Pengfei Jiao","orcid":"https://orcid.org/0000-0003-1049-1002"},"institutions":[{"id":"https://openalex.org/I50760025","display_name":"Hangzhou Dianzi University","ror":"https://ror.org/0576gt767","country_code":"CN","type":"education","lineage":["https://openalex.org/I50760025"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengfei Jiao","raw_affiliation_strings":["School of Cyberspace, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Cyberspace, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China","institution_ids":["https://openalex.org/I50760025"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070218627","display_name":"Zhidong Zhao","orcid":"https://orcid.org/0000-0001-6659-3732"},"institutions":[{"id":"https://openalex.org/I50760025","display_name":"Hangzhou Dianzi University","ror":"https://ror.org/0576gt767","country_code":"CN","type":"education","lineage":["https://openalex.org/I50760025"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhidong Zhao","raw_affiliation_strings":["School of Cyberspace, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Cyberspace, Hangzhou Dianzi University, Hangzhou, 310018, Zhejiang, China","institution_ids":["https://openalex.org/I50760025"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101922939","display_name":"Bobo Li","orcid":"https://orcid.org/0000-0002-0513-5540"},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bobo Li","raw_affiliation_strings":["Key Laboratory of Aerospace Information Security and Trusted Computing, Ministry of Education, School of Cyber Science and Engineering, Wuhan University, Wuhan, 430072, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Aerospace Information Security and Trusted Computing, Ministry of Education, School of Cyber Science and Engineering, Wuhan University, Wuhan, 430072, Hubei, China","institution_ids":["https://openalex.org/I37461747"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100325881","display_name":"Fei Li","orcid":"https://orcid.org/0000-0003-1816-1761"},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fei Li","raw_affiliation_strings":["Key Laboratory of Aerospace Information Security and Trusted Computing, Ministry of Education, School of Cyber Science and Engineering, Wuhan University, Wuhan, 430072, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Aerospace Information Security and Trusted Computing, Ministry of Education, School of Cyber Science and Engineering, Wuhan University, Wuhan, 430072, Hubei, China","institution_ids":["https://openalex.org/I37461747"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101801149","display_name":"Donghong Ji","orcid":"https://orcid.org/0000-0003-4020-983X"},"institutions":[{"id":"https://openalex.org/I37461747","display_name":"Wuhan University","ror":"https://ror.org/033vjfk17","country_code":"CN","type":"education","lineage":["https://openalex.org/I37461747"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Donghong Ji","raw_affiliation_strings":["Key Laboratory of Aerospace Information Security and Trusted Computing, Ministry of Education, School of Cyber Science and Engineering, Wuhan University, Wuhan, 430072, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Aerospace Information Security and Trusted Computing, Ministry of Education, School of Cyber Science and Engineering, Wuhan University, Wuhan, 430072, Hubei, China","institution_ids":["https://openalex.org/I37461747"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100333729"],"corresponding_institution_ids":["https://openalex.org/I3133055985"],"apc_list":{"value":3200,"currency":"USD","value_usd":3200},"apc_paid":{"value":3200,"currency":"USD","value_usd":3200},"fwci":1.1245,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.84542546,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"161","issue":null,"first_page":"112001","last_page":"112001"},"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9997000098228455,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9983000159263611,"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/computer-science","display_name":"Computer science","score":0.9196759462356567},{"id":"https://openalex.org/keywords/event","display_name":"Event (particle physics)","score":0.597976565361023},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.5815848112106323},{"id":"https://openalex.org/keywords/sentence","display_name":"Sentence","score":0.5442890524864197},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4587427079677582},{"id":"https://openalex.org/keywords/extraction","display_name":"Extraction (chemistry)","score":0.4459819197654724},{"id":"https://openalex.org/keywords/stage","display_name":"Stage (stratigraphy)","score":0.43580162525177},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.423062264919281}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.9196759462356567},{"id":"https://openalex.org/C2779662365","wikidata":"https://www.wikidata.org/wiki/Q5416694","display_name":"Event (particle physics)","level":2,"score":0.597976565361023},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.5815848112106323},{"id":"https://openalex.org/C2777530160","wikidata":"https://www.wikidata.org/wiki/Q41796","display_name":"Sentence","level":2,"score":0.5442890524864197},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4587427079677582},{"id":"https://openalex.org/C4725764","wikidata":"https://www.wikidata.org/wiki/Q844704","display_name":"Extraction (chemistry)","level":2,"score":0.4459819197654724},{"id":"https://openalex.org/C146357865","wikidata":"https://www.wikidata.org/wiki/Q1123245","display_name":"Stage (stratigraphy)","level":2,"score":0.43580162525177},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.423062264919281},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1016/j.engappai.2025.112001","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.engappai.2025.112001","pdf_url":null,"source":{"id":"https://openalex.org/S900972176","display_name":"Engineering Applications of Artificial Intelligence","issn_l":"0952-1976","issn":["0952-1976","1873-6769"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Engineering Applications of Artificial Intelligence","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1016/j.engappai.2025.112001","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.engappai.2025.112001","pdf_url":null,"source":{"id":"https://openalex.org/S900972176","display_name":"Engineering Applications of Artificial Intelligence","issn_l":"0952-1976","issn":["0952-1976","1873-6769"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Engineering Applications of Artificial Intelligence","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1453686608","display_name":null,"funder_award_id":"62176187","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7421578584","display_name":"\u8ba4\u77e5\u9a71\u52a8\u7684\u8de8\u6a21\u6001\u77e5\u8bc6\u56fe\u8c31\u57fa\u7840\u7406\u8bba\u4e0e\u667a\u80fd\u7b97\u6cd5","funder_award_id":"LDT23F01012F01","funder_id":"https://openalex.org/F4320338464","funder_display_name":"Natural Science Foundation of Zhejiang Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320338464","display_name":"Natural Science Foundation of Zhejiang Province","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":55,"referenced_works":["https://openalex.org/W169539560","https://openalex.org/W1531333757","https://openalex.org/W1677182931","https://openalex.org/W1940872118","https://openalex.org/W2008652694","https://openalex.org/W2032566933","https://openalex.org/W2064675550","https://openalex.org/W2075655036","https://openalex.org/W2095705004","https://openalex.org/W2100276951","https://openalex.org/W2106921868","https://openalex.org/W2108706252","https://openalex.org/W2110408238","https://openalex.org/W2144499799","https://openalex.org/W2147880316","https://openalex.org/W2167342631","https://openalex.org/W2251644265","https://openalex.org/W2292896937","https://openalex.org/W2296283641","https://openalex.org/W2414674322","https://openalex.org/W2574495026","https://openalex.org/W2778973872","https://openalex.org/W2885911173","https://openalex.org/W2945453987","https://openalex.org/W2945465038","https://openalex.org/W2952230511","https://openalex.org/W2963625095","https://openalex.org/W2970771982","https://openalex.org/W2979826702","https://openalex.org/W3034999214","https://openalex.org/W3036559261","https://openalex.org/W3093811011","https://openalex.org/W3099548761","https://openalex.org/W3100192071","https://openalex.org/W3104390324","https://openalex.org/W3116427155","https://openalex.org/W3126031088","https://openalex.org/W3167136668","https://openalex.org/W3173691187","https://openalex.org/W3175225269","https://openalex.org/W4206065942","https://openalex.org/W4220849614","https://openalex.org/W4221140922","https://openalex.org/W4224303302","https://openalex.org/W4281770772","https://openalex.org/W4286562652","https://openalex.org/W4300166660","https://openalex.org/W4320077685","https://openalex.org/W4362510680","https://openalex.org/W4388571633","https://openalex.org/W4390596320","https://openalex.org/W4390690464","https://openalex.org/W4394600506","https://openalex.org/W4396822718","https://openalex.org/W4403390197"],"related_works":["https://openalex.org/W2329386257","https://openalex.org/W2503350049","https://openalex.org/W2375873920","https://openalex.org/W2146114872","https://openalex.org/W2392060890","https://openalex.org/W2392760275","https://openalex.org/W2397616145","https://openalex.org/W2083530853","https://openalex.org/W2397320258","https://openalex.org/W4412054803"],"abstract_inverted_index":{"Biomedical":[0],"event":[1,41,70,85,96,121,148],"extraction,":[2,7,42,97,122],"a":[3,20],"cornerstone":[4],"of":[5,58,69,95,107],"information":[6],"has":[8],"increasingly":[9],"attracted":[10],"attention":[11],"within":[12],"the":[13,37,67,93,99,104,146,152,156,165],"biomedical":[14,40],"research":[15,38],"community.":[16],"Moreover,":[17],"it":[18],"is":[19],"highly":[21],"complex":[22],"task,":[23],"which":[24,123],"not":[25,124],"only":[26,125],"deals":[27],"with":[28],"many":[29],"sub-tasks":[30,106],"but":[31,129],"also":[32,130],"involves":[33],"nested":[34],"events.":[35],"Currently,":[36],"on":[39,78,155,164],"whether":[43],"pipelined":[44],"model":[45,150],"or":[46],"joint":[47],"method,":[48],"needs":[49],"to":[50,66],"be":[51],"processed":[52],"for":[53],"each":[54,60],"sub-task.":[55,115],"The":[56],"process":[57,94],"processing":[59,100],"sub-task":[61],"one":[62,64,114],"by":[63],"lead":[65],"degradation":[68],"extraction":[71,109,149],"performance.":[72],"In":[73,116],"addition,":[74,117],"most":[75],"studies":[76],"focus":[77],"extracting":[79],"sentence-level":[80],"events":[81,128],"and":[82,102,110,160],"ignore":[83],"cross-sentence":[84,127],"information.":[86,134],"To":[87],"solve":[88],"these":[89],"problems,":[90],"we":[91,118],"simplify":[92],"reduce":[98],"steps,":[101],"combine":[103],"two":[105],"relation":[108],"argument":[111],"combination":[112],"as":[113],"consider":[119],"document-level":[120,147],"extracts":[126],"considers":[131],"broader":[132],"context":[133],"Experimental":[135],"results":[136],"indicate":[137],"that":[138],"our":[139],"novel":[140],"approach":[141],"outperforms":[142],"prior":[143],"studies.":[144],"Additionally,":[145],"attains":[151],"top":[153],"performance":[154,163],"BioNLP\u201911":[157],"test":[158,167],"data":[159],"achieves":[161],"near-leading":[162],"BioNLP\u201913":[166],"data.":[168]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}
