{"id":"https://openalex.org/W4391164245","doi":"https://doi.org/10.1109/jbhi.2024.3358169","title":"LoGo-GR: A Local to Global Graphical Reasoning Framework for Extracting Structured Information From Biomedical Literature","display_name":"LoGo-GR: A Local to Global Graphical Reasoning Framework for Extracting Structured Information From Biomedical Literature","publication_year":2024,"publication_date":"2024-01-24","ids":{"openalex":"https://openalex.org/W4391164245","doi":"https://doi.org/10.1109/jbhi.2024.3358169","pmid":"https://pubmed.ncbi.nlm.nih.gov/38265897"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2024.3358169","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3358169","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5102935690","display_name":"Xueyang Zhou","orcid":"https://orcid.org/0009-0009-0374-878X"},"institutions":[{"id":"https://openalex.org/I308837","display_name":"Suzhou University of Science and Technology","ror":"https://ror.org/04en8wb91","country_code":"CN","type":"education","lineage":["https://openalex.org/I308837"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xueyang Zhou","raw_affiliation_strings":["School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, China","School of Electronic and Information Engineering and also with Jiangsu Province Key Laboratory of Intelligent Building Energy Efficiency, Suzhou University of Science and Technology, Suzhou, Jiangsu, China"],"affiliations":[{"raw_affiliation_string":"School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, China","institution_ids":["https://openalex.org/I308837"]},{"raw_affiliation_string":"School of Electronic and Information Engineering and also with Jiangsu Province Key Laboratory of Intelligent Building Energy Efficiency, Suzhou University of Science and Technology, Suzhou, Jiangsu, China","institution_ids":["https://openalex.org/I308837"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087429872","display_name":"Qiming Fu","orcid":"https://orcid.org/0000-0001-9757-4323"},"institutions":[{"id":"https://openalex.org/I308837","display_name":"Suzhou University of Science and Technology","ror":"https://ror.org/04en8wb91","country_code":"CN","type":"education","lineage":["https://openalex.org/I308837"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiming Fu","raw_affiliation_strings":["School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, China","School of Electronic and Information Engineering and also with Jiangsu Province Key Laboratory of Intelligent Building Energy Efficiency, Suzhou University of Science and Technology, Suzhou, Jiangsu, China"],"affiliations":[{"raw_affiliation_string":"School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, China","institution_ids":["https://openalex.org/I308837"]},{"raw_affiliation_string":"School of Electronic and Information Engineering and also with Jiangsu Province Key Laboratory of Intelligent Building Energy Efficiency, Suzhou University of Science and Technology, Suzhou, Jiangsu, China","institution_ids":["https://openalex.org/I308837"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101717171","display_name":"Youbing Xia","orcid":"https://orcid.org/0000-0002-0408-2045"},"institutions":[{"id":"https://openalex.org/I177388780","display_name":"Xuzhou Medical College","ror":"https://ror.org/04fe7hy80","country_code":"CN","type":"education","lineage":["https://openalex.org/I177388780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Youbing Xia","raw_affiliation_strings":["School of Medical Informatics, Xuzhou Medical University, Xuzhou, China","School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, China"],"affiliations":[{"raw_affiliation_string":"School of Medical Informatics, Xuzhou Medical University, Xuzhou, China","institution_ids":["https://openalex.org/I177388780"]},{"raw_affiliation_string":"School of Medical Informatics, Xuzhou Medical University, Xuzhou, Jiangsu, China","institution_ids":["https://openalex.org/I177388780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102956206","display_name":"Yunzhe Wang","orcid":"https://orcid.org/0000-0002-1755-6430"},"institutions":[{"id":"https://openalex.org/I308837","display_name":"Suzhou University of Science and Technology","ror":"https://ror.org/04en8wb91","country_code":"CN","type":"education","lineage":["https://openalex.org/I308837"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yunzhe Wang","raw_affiliation_strings":["School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, China","School of Electronic and Information Engineering and also with Jiangsu Province Key Laboratory of Intelligent Building Energy Efficiency, Suzhou University of Science and Technology, Suzhou, Jiangsu, China"],"affiliations":[{"raw_affiliation_string":"School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, China","institution_ids":["https://openalex.org/I308837"]},{"raw_affiliation_string":"School of Electronic and Information Engineering and also with Jiangsu Province Key Laboratory of Intelligent Building Energy Efficiency, Suzhou University of Science and Technology, Suzhou, Jiangsu, China","institution_ids":["https://openalex.org/I308837"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009920251","display_name":"You Lu","orcid":"https://orcid.org/0000-0002-0930-2764"},"institutions":[{"id":"https://openalex.org/I308837","display_name":"Suzhou University of Science and Technology","ror":"https://ror.org/04en8wb91","country_code":"CN","type":"education","lineage":["https://openalex.org/I308837"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"You Lu","raw_affiliation_strings":["School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, China","School of Electronic and Information Engineering and also with Jiangsu Province Key Laboratory of Intelligent Building Energy Efficiency, Suzhou University of Science and Technology, Suzhou, Jiangsu, China"],"affiliations":[{"raw_affiliation_string":"School of Electronic and Information Engineering, Suzhou University of Science and Technology, Suzhou, China","institution_ids":["https://openalex.org/I308837"]},{"raw_affiliation_string":"School of Electronic and Information Engineering and also with Jiangsu Province Key Laboratory of Intelligent Building Energy Efficiency, Suzhou University of Science and Technology, Suzhou, Jiangsu, China","institution_ids":["https://openalex.org/I308837"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100733225","display_name":"Yanming Chen","orcid":"https://orcid.org/0000-0001-9194-0580"},"institutions":[{"id":"https://openalex.org/I3923682","display_name":"Soochow University","ror":"https://ror.org/05t8y2r12","country_code":"CN","type":"education","lineage":["https://openalex.org/I3923682"]},{"id":"https://openalex.org/I4210124971","display_name":"Second Affiliated Hospital of Soochow University","ror":"https://ror.org/02xjrkt08","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210124971"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanming Chen","raw_affiliation_strings":["Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, China","Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China"],"affiliations":[{"raw_affiliation_string":"Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, China","institution_ids":["https://openalex.org/I3923682","https://openalex.org/I4210124971"]},{"raw_affiliation_string":"Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China","institution_ids":["https://openalex.org/I3923682","https://openalex.org/I4210124971"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100437534","display_name":"Jianping Chen","orcid":"https://orcid.org/0000-0002-2109-5761"},"institutions":[{"id":"https://openalex.org/I308837","display_name":"Suzhou University of Science and Technology","ror":"https://ror.org/04en8wb91","country_code":"CN","type":"education","lineage":["https://openalex.org/I308837"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianping Chen","raw_affiliation_strings":["School of Architecture and Urban Planning, Jiangsu Province Key Laboratory of Intelligent Building Energy Efficiency, Suzhou University of Science and Technology, Suzhou, China","School of Architecture and Urban Planning, Jiangsu Province Key laboratory of Intelligent Building Energy Efficiency, Suzhou University of Science and Technology, Suzhou, Jiangsu, China","Chongqing Industrial Big Data Innovation Center Co., Ltd., Chongqing, China"],"affiliations":[{"raw_affiliation_string":"School of Architecture and Urban Planning, Jiangsu Province Key Laboratory of Intelligent Building Energy Efficiency, Suzhou University of Science and Technology, Suzhou, China","institution_ids":["https://openalex.org/I308837"]},{"raw_affiliation_string":"School of Architecture and Urban Planning, Jiangsu Province Key laboratory of Intelligent Building Energy Efficiency, Suzhou University of Science and Technology, Suzhou, Jiangsu, China","institution_ids":["https://openalex.org/I308837"]},{"raw_affiliation_string":"Chongqing Industrial Big Data Innovation Center Co., Ltd., Chongqing, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5102935690"],"corresponding_institution_ids":["https://openalex.org/I308837"],"apc_list":null,"apc_paid":null,"fwci":0.9396,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.72218348,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"28","issue":"4","first_page":"2314","last_page":"2325"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994000196456909,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9994000196456909,"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/T10028","display_name":"Topic Modeling","score":0.996999979019165,"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":0.9818000197410583,"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":0.6902873516082764},{"id":"https://openalex.org/keywords/logo","display_name":"Logo (programming language)","score":0.4818671643733978},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4269223213195801},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.40357789397239685},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1157262921333313}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6902873516082764},{"id":"https://openalex.org/C2778720087","wikidata":"https://www.wikidata.org/wiki/Q201436","display_name":"Logo (programming language)","level":2,"score":0.4818671643733978},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4269223213195801},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.40357789397239685},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1157262921333313}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2024.3358169","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3358169","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:38265897","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38265897","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":"IEEE journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.5,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G1214954270","display_name":null,"funder_award_id":"62072324","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2353941024","display_name":null,"funder_award_id":"62102278","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5280656057","display_name":null,"funder_award_id":"62372318","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6618082628","display_name":null,"funder_award_id":"BE2020026","funder_id":"https://openalex.org/F4320327777","funder_display_name":"Jiangsu Provincial Key Research and Development Program"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320327777","display_name":"Jiangsu Provincial Key Research and Development Program","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W2064675550","https://openalex.org/W2346452181","https://openalex.org/W2801058001","https://openalex.org/W2883362973","https://openalex.org/W2889224519","https://openalex.org/W2892094955","https://openalex.org/W2896457183","https://openalex.org/W2911489562","https://openalex.org/W2920198243","https://openalex.org/W2952179106","https://openalex.org/W2952768212","https://openalex.org/W2963014179","https://openalex.org/W2963020213","https://openalex.org/W2965373594","https://openalex.org/W2970771982","https://openalex.org/W2971221499","https://openalex.org/W2971258845","https://openalex.org/W2975998869","https://openalex.org/W3017131202","https://openalex.org/W3035053871","https://openalex.org/W3044619194","https://openalex.org/W3093891978","https://openalex.org/W3101327207","https://openalex.org/W3101748173","https://openalex.org/W3102663935","https://openalex.org/W3103836967","https://openalex.org/W3113440918","https://openalex.org/W3116122129","https://openalex.org/W3120223152","https://openalex.org/W3134422801","https://openalex.org/W3173229273","https://openalex.org/W3174111043","https://openalex.org/W3202973654","https://openalex.org/W3213998394","https://openalex.org/W4214673031","https://openalex.org/W4223491992","https://openalex.org/W4225508536","https://openalex.org/W4280590868","https://openalex.org/W4281939536","https://openalex.org/W4285818444","https://openalex.org/W4289306518","https://openalex.org/W4292119927","https://openalex.org/W4297253404","https://openalex.org/W4297733535","https://openalex.org/W4309360743","https://openalex.org/W6729856301","https://openalex.org/W6745537798","https://openalex.org/W6756275492","https://openalex.org/W6766673545","https://openalex.org/W6842258392"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W4382895929","https://openalex.org/W2164977745","https://openalex.org/W4247466689","https://openalex.org/W2156726901","https://openalex.org/W2940416500","https://openalex.org/W2734681527","https://openalex.org/W654884026","https://openalex.org/W1577150342"],"abstract_inverted_index":{"In":[0,84,143,222],"the":[1,16,58,150],"biomedical":[2,32,174],"literature,":[3],"entities":[4,47,78,139],"are":[5],"often":[6],"distributed":[7],"within":[8],"multiple":[9],"sentences":[10],"and":[11,30,72,111,122,127,131,183,190,213,218,243],"exhibit":[12],"complex":[13,49,136],"interactions.":[14],"As":[15],"volume":[17],"of":[18,113],"literature":[19],"has":[20,24,188],"increased":[21],"dramatically,":[22],"it":[23,239],"become":[25],"impractical":[26],"to":[27,64,91,134,159,194],"manually":[28],"extract":[29],"maintain":[31],"knowledge,":[33],"which":[34,236],"would":[35],"entail":[36],"enormous":[37],"costs.":[38],"Fortunately,":[39],"document-level":[40,141,175,231,245],"relation":[41,115,232,246],"extraction":[42,233,247],"can":[43],"capture":[44,74,135],"associations":[45],"between":[46,77,138],"from":[48,57,70,118,140],"text,":[50],"helping":[51],"researchers":[52],"efficiently":[53],"mine":[54],"structured":[55],"knowledge":[56],"vast":[59],"medical":[60],"literature.":[61],"However,":[62],"how":[63],"effectively":[65],"synthesize":[66],"rich":[67],"global":[68,108,130],"information":[69,112,162],"context":[71,109],"accurately":[73],"local":[75,114,132],"dependencies":[76,117,148],"is":[79,240],"still":[80],"a":[81,89,99],"great":[82],"challenge.":[83],"this":[85],"paper,":[86],"we":[87],"propose":[88],"Local":[90],"Global":[92],"Graphical":[93],"Reasoning":[94],"framework":[95],"(LoGo-GR)":[96],"based":[97],"on":[98,171,205,216,229],"novel":[100],"Biased":[101],"Graph":[102],"Attention":[103],"mechanism":[104,154],"(B-GAT).":[105],"It":[106],"learns":[107],"feature":[110],"path":[116,124],"mention-level":[119],"interaction":[120],"graph":[121,125,152],"entity-level":[123],"respectively,":[126],"collaborates":[128],"with":[129,202,210],"reasoning":[133],"interactions":[137],"text.":[142],"particular,":[144],"B-GAT":[145],"integrates":[146],"structural":[147],"into":[149],"standard":[151],"attention":[153,157],"(GAT)":[155],"as":[156],"biases":[158],"adaptively":[160],"guide":[161],"aggregation":[163],"in":[164],"graphical":[165],"reasoning.":[166],"We":[167],"evaluate":[168],"our":[169],"method":[170],"three":[172],"publicly":[173],"datasets:":[176],"Drug-Mutation":[177],"Interaction":[178],"(DV),":[179],"Chemical-induced":[180],"Disease":[181],"(CDR),":[182],"Gene-Disease":[184],"Association":[185],"(GDA).":[186],"LoGo-GR":[187,224],"advanced":[189,208,227],"stable":[191],"performance":[192,201,209,228],"compared":[193],"other":[195],"state-of-the-art":[196,200],"methods":[197],"(it":[198],"achieves":[199],"96.14%-97.39%":[203],"F1":[204,212,215],"DV":[206],"dataset,":[207,234],"68.89%":[211],"84.22%":[214],"CDR":[217],"GDA":[219],"datasets,":[220],"respectively).":[221],"addition,":[223],"also":[225],"shows":[226],"general-domain":[230],"DocRED,":[235],"proves":[237],"that":[238],"an":[241],"effective":[242],"robust":[244],"framework.":[248]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-10-10T00:00:00"}
