{"id":"https://openalex.org/W4385488671","doi":"https://doi.org/10.1109/ijcnn54540.2023.10191706","title":"Enhancing Embedding Representations of Biomedical Data using Logic Knowledge","display_name":"Enhancing Embedding Representations of Biomedical Data using Logic Knowledge","publication_year":2023,"publication_date":"2023-06-18","ids":{"openalex":"https://openalex.org/W4385488671","doi":"https://doi.org/10.1109/ijcnn54540.2023.10191706"},"language":"en","primary_location":{"id":"doi:10.1109/ijcnn54540.2023.10191706","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ijcnn54540.2023.10191706","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 International Joint Conference on Neural Networks (IJCNN)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://lirias.kuleuven.be/retrieve/eafee4d7-fb2b-45fa-bfeb-a25b1a6a86d7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5109267259","display_name":"Michelangelo Diligenti","orcid":null},"institutions":[{"id":"https://openalex.org/I102064193","display_name":"University of Siena","ror":"https://ror.org/01tevnk56","country_code":"IT","type":"education","lineage":["https://openalex.org/I102064193"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Michelangelo Diligenti","raw_affiliation_strings":["University of Siena,DIISM,Siena,Italy","DIISM, University of Siena, Siena, Italy"],"affiliations":[{"raw_affiliation_string":"University of Siena,DIISM,Siena,Italy","institution_ids":["https://openalex.org/I102064193"]},{"raw_affiliation_string":"DIISM, University of Siena, Siena, Italy","institution_ids":["https://openalex.org/I102064193"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058772124","display_name":"Francesco Giannini","orcid":"https://orcid.org/0000-0001-8492-8110"},"institutions":[{"id":"https://openalex.org/I102064193","display_name":"University of Siena","ror":"https://ror.org/01tevnk56","country_code":"IT","type":"education","lineage":["https://openalex.org/I102064193"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Francesco Giannini","raw_affiliation_strings":["University of Siena,DIISM,Siena,Italy","DIISM, University of Siena, Siena, Italy"],"affiliations":[{"raw_affiliation_string":"University of Siena,DIISM,Siena,Italy","institution_ids":["https://openalex.org/I102064193"]},{"raw_affiliation_string":"DIISM, University of Siena, Siena, Italy","institution_ids":["https://openalex.org/I102064193"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091214145","display_name":"Stefano Fioravanti","orcid":"https://orcid.org/0000-0001-6918-1805"},"institutions":[{"id":"https://openalex.org/I102064193","display_name":"University of Siena","ror":"https://ror.org/01tevnk56","country_code":"IT","type":"education","lineage":["https://openalex.org/I102064193"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Stefano Fioravanti","raw_affiliation_strings":["University of Siena,DIISM,Siena,Italy","DIISM, University of Siena, Siena, Italy"],"affiliations":[{"raw_affiliation_string":"University of Siena,DIISM,Siena,Italy","institution_ids":["https://openalex.org/I102064193"]},{"raw_affiliation_string":"DIISM, University of Siena, Siena, Italy","institution_ids":["https://openalex.org/I102064193"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017471987","display_name":"Caterina Graziani","orcid":"https://orcid.org/0000-0002-7606-9405"},"institutions":[{"id":"https://openalex.org/I102064193","display_name":"University of Siena","ror":"https://ror.org/01tevnk56","country_code":"IT","type":"education","lineage":["https://openalex.org/I102064193"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Caterina Graziani","raw_affiliation_strings":["University of Siena,DIISM,Siena,Italy","DIISM, University of Siena, Siena, Italy"],"affiliations":[{"raw_affiliation_string":"University of Siena,DIISM,Siena,Italy","institution_ids":["https://openalex.org/I102064193"]},{"raw_affiliation_string":"DIISM, University of Siena, Siena, Italy","institution_ids":["https://openalex.org/I102064193"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053216941","display_name":"Moreno Falaschi","orcid":"https://orcid.org/0000-0002-6659-3828"},"institutions":[{"id":"https://openalex.org/I102064193","display_name":"University of Siena","ror":"https://ror.org/01tevnk56","country_code":"IT","type":"education","lineage":["https://openalex.org/I102064193"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Moreno Falaschi","raw_affiliation_strings":["University of Siena,DIISM,Siena,Italy","DIISM, University of Siena, Siena, Italy"],"affiliations":[{"raw_affiliation_string":"University of Siena,DIISM,Siena,Italy","institution_ids":["https://openalex.org/I102064193"]},{"raw_affiliation_string":"DIISM, University of Siena, Siena, Italy","institution_ids":["https://openalex.org/I102064193"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005466305","display_name":"Giuseppe Marra","orcid":"https://orcid.org/0000-0001-5940-9562"},"institutions":[{"id":"https://openalex.org/I4210115377","display_name":"VIB-KU Leuven Center for Microbiology","ror":"https://ror.org/02bpp8r91","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I4210115377","https://openalex.org/I99464096"]},{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Giuseppe Marra","raw_affiliation_strings":["KULeuven,DCS,Leuven,Belgium","DCS, KULeuven, Leuven, Belgium"],"affiliations":[{"raw_affiliation_string":"KULeuven,DCS,Leuven,Belgium","institution_ids":["https://openalex.org/I99464096","https://openalex.org/I4210115377"]},{"raw_affiliation_string":"DCS, KULeuven, Leuven, Belgium","institution_ids":["https://openalex.org/I99464096"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5109267259"],"corresponding_institution_ids":["https://openalex.org/I102064193"],"apc_list":null,"apc_paid":null,"fwci":0.5392,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.71491855,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11273","display_name":"Advanced Graph Neural Networks","score":0.9988999962806702,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.9988999962806702,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9979000091552734,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9965000152587891,"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":0.7080492973327637},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6382865309715271},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.5632111430168152},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.5357282757759094},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.5167790651321411},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4720785617828369},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.46458345651626587},{"id":"https://openalex.org/keywords/statistical-relational-learning","display_name":"Statistical relational learning","score":0.46131062507629395},{"id":"https://openalex.org/keywords/knowledge-graph","display_name":"Knowledge graph","score":0.4408300817012787},{"id":"https://openalex.org/keywords/domain-knowledge","display_name":"Domain knowledge","score":0.43244674801826477},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4094204902648926},{"id":"https://openalex.org/keywords/relational-database","display_name":"Relational database","score":0.3804873824119568},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3682486116886139}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7080492973327637},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6382865309715271},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.5632111430168152},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.5357282757759094},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.5167790651321411},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4720785617828369},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.46458345651626587},{"id":"https://openalex.org/C177877439","wikidata":"https://www.wikidata.org/wiki/Q7604413","display_name":"Statistical relational learning","level":3,"score":0.46131062507629395},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.4408300817012787},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.43244674801826477},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4094204902648926},{"id":"https://openalex.org/C5655090","wikidata":"https://www.wikidata.org/wiki/Q192588","display_name":"Relational database","level":2,"score":0.3804873824119568},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3682486116886139},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1109/ijcnn54540.2023.10191706","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ijcnn54540.2023.10191706","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 International Joint Conference on Neural Networks (IJCNN)","raw_type":"proceedings-article"},{"id":"pmh:oai:lirias2repo.kuleuven.be:20.500.12942/731597","is_oa":true,"landing_page_url":"https://lirias.kuleuven.be/handle/20.500.12942/731597","pdf_url":"https://lirias.kuleuven.be/retrieve/eafee4d7-fb2b-45fa-bfeb-a25b1a6a86d7","source":{"id":"https://openalex.org/S4306401954","display_name":"Lirias (KU Leuven)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99464096","host_organization_name":"KU Leuven","host_organization_lineage":["https://openalex.org/I99464096"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"International Joint Conference on Neural Networks (IJCNN), AUSTRALIA, Broadbeach, 18-23 June 2023","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:arpi.unipi.it:11568/1347004","is_oa":false,"landing_page_url":"https://hdl.handle.net/11568/1347004","pdf_url":null,"source":{"id":"https://openalex.org/S4377196265","display_name":"CINECA IRIS Institutial research information system (University of Pisa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I108290504","host_organization_name":"University of Pisa","host_organization_lineage":["https://openalex.org/I108290504"],"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":"info:eu-repo/semantics/conferenceObject"},{"id":"pmh:oai:arpi.unipi.it:11568/1347010","is_oa":false,"landing_page_url":"https://hdl.handle.net/11568/1347010","pdf_url":null,"source":{"id":"https://openalex.org/S4377196265","display_name":"CINECA IRIS Institutial research information system (University of Pisa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I108290504","host_organization_name":"University of Pisa","host_organization_lineage":["https://openalex.org/I108290504"],"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":"info:eu-repo/semantics/conferenceObject"},{"id":"pmh:oai:ricerca.sns.it:11384/150587","is_oa":false,"landing_page_url":"https://hdl.handle.net/11384/150587","pdf_url":null,"source":{"id":"https://openalex.org/S7407050981","display_name":"Scuola Normale Superiore di Pisa","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"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":"info:eu-repo/semantics/conferenceObject"},{"id":"pmh:oai:usiena-air.unisi.it:11365/1247694","is_oa":false,"landing_page_url":"https://hdl.handle.net/11365/1247694","pdf_url":null,"source":{"id":"https://openalex.org/S4377196319","display_name":"Use Siena air (University of Siena)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I102064193","host_organization_name":"University of Siena","host_organization_lineage":["https://openalex.org/I102064193"],"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":"info:eu-repo/semantics/conferenceObject"}],"best_oa_location":{"id":"pmh:oai:lirias2repo.kuleuven.be:20.500.12942/731597","is_oa":true,"landing_page_url":"https://lirias.kuleuven.be/handle/20.500.12942/731597","pdf_url":"https://lirias.kuleuven.be/retrieve/eafee4d7-fb2b-45fa-bfeb-a25b1a6a86d7","source":{"id":"https://openalex.org/S4306401954","display_name":"Lirias (KU Leuven)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99464096","host_organization_name":"KU Leuven","host_organization_lineage":["https://openalex.org/I99464096"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"International Joint Conference on Neural Networks (IJCNN), AUSTRALIA, Broadbeach, 18-23 June 2023","raw_type":"info:eu-repo/semantics/publishedVersion"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4385488671.pdf"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W205829674","https://openalex.org/W1508045687","https://openalex.org/W1533230146","https://openalex.org/W1977970897","https://openalex.org/W1994127362","https://openalex.org/W2009086942","https://openalex.org/W2009313526","https://openalex.org/W2097286355","https://openalex.org/W2127069089","https://openalex.org/W2127426251","https://openalex.org/W2127795553","https://openalex.org/W2130276068","https://openalex.org/W2150859678","https://openalex.org/W2151502664","https://openalex.org/W2165428180","https://openalex.org/W2184957013","https://openalex.org/W2296268288","https://openalex.org/W2432356473","https://openalex.org/W2563063592","https://openalex.org/W2604314403","https://openalex.org/W2728059831","https://openalex.org/W2759136286","https://openalex.org/W2766208765","https://openalex.org/W2774837955","https://openalex.org/W2916047525","https://openalex.org/W2948922044","https://openalex.org/W2962869320","https://openalex.org/W2963359213","https://openalex.org/W2970583209","https://openalex.org/W3000670742","https://openalex.org/W3003760334","https://openalex.org/W3021393704","https://openalex.org/W3021815340","https://openalex.org/W3093988619","https://openalex.org/W3116099552","https://openalex.org/W3157651462","https://openalex.org/W3211651881","https://openalex.org/W4300602297","https://openalex.org/W4318718450","https://openalex.org/W6608344535","https://openalex.org/W6631964550","https://openalex.org/W6674949343","https://openalex.org/W6678830454","https://openalex.org/W6678846912","https://openalex.org/W6679601859","https://openalex.org/W6718112784","https://openalex.org/W6735632219","https://openalex.org/W6747094798","https://openalex.org/W6763230164","https://openalex.org/W6764644601","https://openalex.org/W6772377222","https://openalex.org/W6849360865"],"related_works":["https://openalex.org/W3181676408","https://openalex.org/W1549959306","https://openalex.org/W320292658","https://openalex.org/W4292070284","https://openalex.org/W2186138942","https://openalex.org/W2806326686","https://openalex.org/W4386298164","https://openalex.org/W4312933959","https://openalex.org/W2001007279","https://openalex.org/W2079674650"],"abstract_inverted_index":{"Knowledge":[0],"Graph":[1],"Embeddings":[2],"(KGE)":[3],"have":[4],"become":[5],"a":[6,34,155,177],"quite":[7,49],"popular":[8],"class":[9],"of":[10,77,87,89,140,217,220,231],"models":[11],"specifically":[12],"devised":[13],"to":[14,51,101,135,175,196,212,223],"deal":[15,52],"with":[16,53,85],"ontologies":[17],"and":[18,31,62,95,227],"graph":[19,82,165],"structure":[20],"data,":[21],"as":[22,75],"they":[23,106],"can":[24,99],"implicitly":[25],"encode":[26],"statistical":[27],"dependencies":[28,114],"between":[29,60,92,115],"entities":[30],"relations":[32],"in":[33,66,124],"latent":[35,184],"space.":[36],"KGE":[37,183],"techniques":[38],"are":[39],"particularly":[40],"effective":[41],"for":[42],"the":[43,67,69,78,137,143,171,187,199,203,215,229],"biomedical":[44,83],"domain,":[45],"where":[46],"it":[47],"is":[48,194],"common":[50],"large":[54,103],"knowledge":[55,81,164],"graphs":[56],"underlying":[57],"complex":[58,112,125],"interactions":[59],"biological":[61],"chemical":[63],"objects.":[64],"Recently":[65],"literature,":[68],"PharmKG":[70,144,204],"dataset":[71],"has":[72],"been":[73],"proposed":[74,157],"one":[76],"most":[79],"challenging":[80],"benchmark,":[84],"hundreds":[86],"thousands":[88],"relational":[90,104,113],"facts":[91],"genes,":[93],"diseases":[94],"chemicals.":[96],"Despite":[97],"KGEs":[98,141],"scale":[100],"very":[102],"domains,":[105],"generally":[107],"fail":[108],"at":[109],"representing":[110],"more":[111],"facts,":[116],"like":[117],"logic":[118,133,173],"rules,":[119],"which":[120],"may":[121],"be":[122],"fundamental":[123],"experimental":[126],"settings.":[127],"In":[128,186],"this":[129,147],"paper,":[130],"we":[131,149,189,207],"exploit":[132],"rules":[134,174,221],"enhance":[136],"embedding":[138],"representations":[139],"on":[142,163,202],"dataset.":[145,205],"To":[146],"end,":[148],"adopt":[150],"Relational":[151],"Reasoning":[152],"Network":[153],"(R2N),":[154],"recently":[156],"neural-symbolic":[158],"approach":[159,193],"showing":[160],"promising":[161],"results":[162],"completion":[166],"tasks.":[167],"An":[168],"R2N":[169],"uses":[170],"available":[172],"build":[176],"neural":[178],"architecture":[179],"that":[180,191],"reasons":[181],"over":[182],"representations.":[185],"experiments,":[188],"show":[190],"our":[192],"able":[195],"significantly":[197],"improve":[198],"current":[200],"state-of-the-art":[201],"Finally,":[206],"provide":[208],"an":[209],"ablation":[210],"study":[211],"experimentally":[213],"compare":[214],"effect":[216],"alternative":[218],"sets":[219],"according":[222],"different":[224],"selection":[225],"criteria":[226],"varying":[228],"number":[230],"considered":[232],"rules.":[233]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-03-11T14:59:36.786465","created_date":"2025-10-10T00:00:00"}
