{"id":"https://openalex.org/W4405488853","doi":"https://doi.org/10.1109/embc53108.2024.10782639","title":"NamE: Capturing Biological Context in KGEs via Contextual Named Graph Embeddings","display_name":"NamE: Capturing Biological Context in KGEs via Contextual Named Graph Embeddings","publication_year":2024,"publication_date":"2024-07-15","ids":{"openalex":"https://openalex.org/W4405488853","doi":"https://doi.org/10.1109/embc53108.2024.10782639","pmid":"https://pubmed.ncbi.nlm.nih.gov/40039531"},"language":"en","primary_location":{"id":"doi:10.1109/embc53108.2024.10782639","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc53108.2024.10782639","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)","raw_type":"proceedings-article"},"type":"conference-paper","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/A5051084370","display_name":"Jeffrey Sardina","orcid":"https://orcid.org/0000-0003-0654-2938"},"institutions":[{"id":"https://openalex.org/I4210093804","display_name":"Accenture (Ireland)","ror":"https://ror.org/00hmyb194","country_code":"IE","type":"company","lineage":["https://openalex.org/I4210093804"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Jeffrey Sardina","raw_affiliation_strings":["Accenture,BioInnovation Labs,Dublin,Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Accenture,BioInnovation Labs,Dublin,Ireland","institution_ids":["https://openalex.org/I4210093804"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042660358","display_name":"Luca Costabello","orcid":"https://orcid.org/0000-0002-0720-9347"},"institutions":[{"id":"https://openalex.org/I4210093804","display_name":"Accenture (Ireland)","ror":"https://ror.org/00hmyb194","country_code":"IE","type":"company","lineage":["https://openalex.org/I4210093804"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Luca Costabello","raw_affiliation_strings":["Accenture,BioInnovation Labs,Dublin,Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Accenture,BioInnovation Labs,Dublin,Ireland","institution_ids":["https://openalex.org/I4210093804"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080169752","display_name":"Gu\u00e9ret Christophe","orcid":null},"institutions":[{"id":"https://openalex.org/I4210093804","display_name":"Accenture (Ireland)","ror":"https://ror.org/00hmyb194","country_code":"IE","type":"company","lineage":["https://openalex.org/I4210093804"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Christophe Gu\u00e9ret","raw_affiliation_strings":["Accenture,BioInnovation Labs,Dublin,Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Accenture,BioInnovation Labs,Dublin,Ireland","institution_ids":["https://openalex.org/I4210093804"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043270245","display_name":"Hossein Abbasian Mohammadi","orcid":"https://orcid.org/0000-0002-6836-4850"},"institutions":[{"id":"https://openalex.org/I19648265","display_name":"Wright State University","ror":"https://ror.org/04qk6pt94","country_code":"US","type":"education","lineage":["https://openalex.org/I19648265"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Hossein Mohammadi","raw_affiliation_strings":["Wright State University,Ohio,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Wright State University,Ohio,USA","institution_ids":["https://openalex.org/I19648265"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.3556,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.59879695,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"2024","issue":null,"first_page":"1","last_page":"4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11273","display_name":"Advanced Graph Neural Networks","score":0.9994000196456909,"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":0.9994000196456909,"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/T10028","display_name":"Topic Modeling","score":0.9990000128746033,"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":0.9958999752998352,"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":0.7412195205688477},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5034956336021423},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4940076470375061},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.35514041781425476},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3272087872028351},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.32571426033973694},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11109992861747742}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7412195205688477},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5034956336021423},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4940076470375061},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.35514041781425476},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3272087872028351},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.32571426033973694},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11109992861747742},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/embc53108.2024.10782639","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc53108.2024.10782639","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 46th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)","raw_type":"proceedings-article"},{"id":"pmid:40039531","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40039531","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":"Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":14,"referenced_works":["https://openalex.org/W1529533208","https://openalex.org/W2759136286","https://openalex.org/W2963450615","https://openalex.org/W2965653989","https://openalex.org/W3010336026","https://openalex.org/W3100807776","https://openalex.org/W3165706714","https://openalex.org/W3175609241","https://openalex.org/W3208785685","https://openalex.org/W3212341243","https://openalex.org/W4318983406","https://openalex.org/W6684133116","https://openalex.org/W6779490673","https://openalex.org/W6800546666"],"related_works":["https://openalex.org/W3188962172","https://openalex.org/W2772917594","https://openalex.org/W4312825515","https://openalex.org/W4306742369","https://openalex.org/W4303457083","https://openalex.org/W2131146434","https://openalex.org/W2951359407","https://openalex.org/W4376623224","https://openalex.org/W4387849428","https://openalex.org/W3204019825"],"abstract_inverted_index":{"Large":[0],"biological":[1,111],"databases":[2],"have":[3],"become":[4],"standard":[5],"in":[6,30,36,93,132],"many":[7],"fields":[8],"of":[9,14,71,96,149,159],"biology,":[10],"particularly":[11],"biomedicine.":[12],"Much":[13],"this":[15,66,89,113,125],"data":[16,67,81],"(such":[17,39,53],"as":[18,40,46,54,172],"that":[19,64,88,123,153],"from":[20],"DrugBank,":[21],"PharmKG,":[22],"PrimeKG,":[23],"BIOSNAP,":[24],"and":[25,42,48,78,145,169],"others)":[26],"is":[27],"now":[28],"expressed":[29],"a":[31,94,117],"Knowledge":[32,72],"Graph":[33,73],"(KG)":[34],"format":[35],"which":[37],"concepts":[38],"drugs":[41],"diseases)":[43],"are":[44,58],"represented":[45,59],"nodes":[47],"the":[49,80,157],"relationships":[50],"between":[51],"then":[52],"clinical":[55,147],"drug":[56],"indications)":[57],"by":[60,104,127,165],"edges.":[61],"Bioinformatics":[62],"pipelines":[63],"leverage":[65],"commonly":[68],"make":[69,162],"use":[70],"Embeddings":[74],"(KGEs)":[75],"to":[76,107,161,167,174],"learn":[77],"analyse":[79],"at":[82],"hand.":[83],"While":[84],"existing":[85,99],"work":[86],"demonstrates":[87],"can":[90],"effectively":[91],"assist":[92],"variety":[95],"biomedical":[97],"tasks,":[98],"KGE":[100,119,133,176],"approaches":[101],"remain":[102],"limited":[103],"their":[105],"inability":[106],"account":[108],"for":[109,130],"relevant":[110],"context.In":[112],"paper,":[114],"we":[115,151],"present":[116],"novel":[118],"framework,":[120],"called":[121],"NamE,":[122],"solves":[124],"problem":[126],"explicitly":[128],"modelling":[129],"context":[131],"systems.":[134],"In":[135],"experiments":[136],"on":[137],"two":[138],"applied":[139],"bioinformatics":[140],"use-cases,":[141],"predicting":[142,146],"drug-drug":[143],"interactions":[144],"indications":[148],"drugs,":[150],"show":[152],"NamE":[154],"substantially":[155],"improves":[156],"ability":[158],"KGEs":[160],"accurate":[163],"predictions":[164],"up":[166],"72.2%":[168],"90.9%":[170],"respectively":[171],"compared":[173],"conventional":[175],"methods.":[177]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
