{"id":"https://openalex.org/W4408158766","doi":"https://doi.org/10.3389/frma.2025.1509502","title":"Predicting implicit concept embeddings for singular relationship discovery replication of closed literature-based discovery","display_name":"Predicting implicit concept embeddings for singular relationship discovery replication of closed literature-based discovery","publication_year":2025,"publication_date":"2025-03-05","ids":{"openalex":"https://openalex.org/W4408158766","doi":"https://doi.org/10.3389/frma.2025.1509502","pmid":"https://pubmed.ncbi.nlm.nih.gov/40110121"},"language":"en","primary_location":{"id":"doi:10.3389/frma.2025.1509502","is_oa":true,"landing_page_url":"https://doi.org/10.3389/frma.2025.1509502","pdf_url":null,"source":{"id":"https://openalex.org/S2596295431","display_name":"Frontiers in Research Metrics and Analytics","issn_l":"2504-0537","issn":["2504-0537"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Research Metrics and Analytics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.3389/frma.2025.1509502","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052360583","display_name":"Clint Cuffy","orcid":null},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Clint Cuffy","raw_affiliation_strings":["Natural Language Processing Lab, Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Natural Language Processing Lab, Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States","institution_ids":["https://openalex.org/I184840846"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083901654","display_name":"Bridget T. McInnes","orcid":"https://orcid.org/0000-0003-2297-6672"},"institutions":[{"id":"https://openalex.org/I184840846","display_name":"Virginia Commonwealth University","ror":"https://ror.org/02nkdxk79","country_code":"US","type":"education","lineage":["https://openalex.org/I184840846"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bridget T. McInnes","raw_affiliation_strings":["Natural Language Processing Lab, Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Natural Language Processing Lab, Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States","institution_ids":["https://openalex.org/I184840846"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5052360583"],"corresponding_institution_ids":["https://openalex.org/I184840846"],"apc_list":{"value":950,"currency":"USD","value_usd":950},"apc_paid":{"value":950,"currency":"USD","value_usd":950},"fwci":0.6802,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.66626604,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"10","issue":null,"first_page":"1509502","last_page":"1509502"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.5885000228881836,"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":0.5885000228881836,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.19629999995231628,"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":0.03750000149011612,"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/replication","display_name":"Replication (statistics)","score":0.7624005675315857},{"id":"https://openalex.org/keywords/false-discovery-rate","display_name":"False discovery rate","score":0.4333057403564453},{"id":"https://openalex.org/keywords/econometrics","display_name":"Econometrics","score":0.399222731590271},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3974573314189911},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3665611743927002},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.358160138130188},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33229199051856995},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.2652699947357178},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17338359355926514}],"concepts":[{"id":"https://openalex.org/C12590798","wikidata":"https://www.wikidata.org/wiki/Q3933199","display_name":"Replication (statistics)","level":2,"score":0.7624005675315857},{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.4333057403564453},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.399222731590271},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3974573314189911},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3665611743927002},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.358160138130188},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33229199051856995},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2652699947357178},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17338359355926514},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3389/frma.2025.1509502","is_oa":true,"landing_page_url":"https://doi.org/10.3389/frma.2025.1509502","pdf_url":null,"source":{"id":"https://openalex.org/S2596295431","display_name":"Frontiers in Research Metrics and Analytics","issn_l":"2504-0537","issn":["2504-0537"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Research Metrics and Analytics","raw_type":"journal-article"},{"id":"pmid:40110121","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40110121","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":"Frontiers in research metrics and analytics","raw_type":null},{"id":"pmh:oai:doaj.org/article:d9acca5fc717470384072877b3e4c8a4","is_oa":true,"landing_page_url":"https://doaj.org/article/d9acca5fc717470384072877b3e4c8a4","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Research Metrics and Analytics, Vol 10 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11920161","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11920161","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Front Res Metr Anal","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/frma.2025.1509502","is_oa":true,"landing_page_url":"https://doi.org/10.3389/frma.2025.1509502","pdf_url":null,"source":{"id":"https://openalex.org/S2596295431","display_name":"Frontiers in Research Metrics and Analytics","issn_l":"2504-0537","issn":["2504-0537"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Research Metrics and Analytics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":61,"referenced_works":["https://openalex.org/W90362830","https://openalex.org/W1964670939","https://openalex.org/W1992724001","https://openalex.org/W2011726136","https://openalex.org/W2016944307","https://openalex.org/W2022188162","https://openalex.org/W2033377040","https://openalex.org/W2053186076","https://openalex.org/W2067096102","https://openalex.org/W2090891622","https://openalex.org/W2095161681","https://openalex.org/W2100822723","https://openalex.org/W2117446654","https://openalex.org/W2118002992","https://openalex.org/W2130190939","https://openalex.org/W2142678031","https://openalex.org/W2152091759","https://openalex.org/W2154851992","https://openalex.org/W2159583324","https://openalex.org/W2170788078","https://openalex.org/W2251330086","https://openalex.org/W2301454168","https://openalex.org/W2344432445","https://openalex.org/W2393319904","https://openalex.org/W2424491960","https://openalex.org/W2518194013","https://openalex.org/W2524209183","https://openalex.org/W2560674852","https://openalex.org/W2612090342","https://openalex.org/W2805208465","https://openalex.org/W2805549855","https://openalex.org/W2885931112","https://openalex.org/W2896730986","https://openalex.org/W2905315292","https://openalex.org/W2908070408","https://openalex.org/W2933827798","https://openalex.org/W2939566318","https://openalex.org/W2962756421","https://openalex.org/W2997546679","https://openalex.org/W3025908968","https://openalex.org/W3041537557","https://openalex.org/W3093150592","https://openalex.org/W3104097132","https://openalex.org/W3156292534","https://openalex.org/W3162328503","https://openalex.org/W3164831918","https://openalex.org/W3206536909","https://openalex.org/W4206419686","https://openalex.org/W4213060373","https://openalex.org/W4234188104","https://openalex.org/W4285236424","https://openalex.org/W4367840539","https://openalex.org/W4406262333","https://openalex.org/W6603694148","https://openalex.org/W6608344535","https://openalex.org/W6637242042","https://openalex.org/W6648834952","https://openalex.org/W6730125093","https://openalex.org/W6754395950","https://openalex.org/W6758745058","https://openalex.org/W6936242187"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2389124870","https://openalex.org/W1921844237","https://openalex.org/W2168149717","https://openalex.org/W200978175","https://openalex.org/W2178204436","https://openalex.org/W2113356685","https://openalex.org/W4300887971","https://openalex.org/W1979597421","https://openalex.org/W4293336298"],"abstract_inverted_index":{"Objective:":[0],"Literature-based":[1],"Discovery":[2],"(LBD)":[3],"identifies":[4],"new":[5,33],"knowledge":[6,68,81,102,131],"by":[7,222],"leveraging":[8],"existing":[9,240],"literature.":[10],"It":[11,25],"exploits":[12],"interconnecting":[13,144],"implicit":[14,91,121,177],"relationships":[15],"to":[16,29,53,58,71,89,99,118,171,187,205,238,269,301],"build":[17],"bridges":[18],"between":[19,62,191,335],"isolated":[20],"sets":[21],"of":[22,142,175,230,281,305,332,338,349],"non-interacting":[23,63],"literatures.":[24,64],"has":[26],"been":[27],"used":[28],"facilitate":[30],"drug":[31,34],"repurposing,":[32],"discovery,":[35],"and":[36,86,128,159,198,209,234,251,261,284,345],"study":[37],"adverse":[38],"event":[39],"reactions.":[40],"Within":[41],"the":[42,97,124,130,136,140,148,169,173,194,228,289,303],"last":[43],"decade,":[44],"LBD":[45,78],"systems":[46,95],"have":[47,100],"transitioned":[48],"from":[49],"using":[50,154,263,297],"statistical":[51,298],"methods":[52],"exploring":[54],"deep":[55],"learning":[56,157,313],"(DL)":[57],"analyze":[59,294],"semantic":[60],"spaces":[61],"Recent":[65],"works":[66,76],"explore":[67,184,202],"graphs":[69],"(KG)":[70],"represent":[72,188],"explicit":[73],"relationships.":[74,92],"These":[75],"envision":[77],"as":[79,139],"a":[80,115,155,329,336],"graph":[82,170],"completion":[83],"(KGC)":[84],"task":[85,138,141],"use":[87],"DL":[88],"generate":[90],"However,":[93],"these":[94],"require":[96],"researcher":[98,343],"domain-expert":[101],"when":[103,255],"submitting":[104],"relevant":[105],"queries":[106],"for":[107,319],"novel":[108,116],"hypothesis":[109],"discovery.":[110],"Methods:":[111],"Our":[112,242,325],"method":[113,221,237,268,275,326],"explores":[114],"approach":[117,204,341],"identify":[119],"all":[120,165],"hypotheses":[122],"given":[123],"researcher's":[125],"search":[126],"query":[127],"expedites":[129],"discovery":[132,323],"process.":[133],"We":[134,150,182,218,292,309],"revise":[135],"KGC":[137],"predicting":[143],"vertex":[145,317],"embeddings":[146,318],"within":[147,168,193,227],"graph.":[149],"train":[151],"our":[152,161,220,236,258,267,274,295,306,311],"model":[153,211,252],"similarity":[156],"objective":[158,314],"compare":[160,235],"model's":[162],"predictions":[163],"against":[164],"known":[166,225],"vertices":[167,192,334],"determine":[172],"likelihood":[174],"an":[176,203],"relationship":[178,321],"(i.e.,":[179,213],"connecting":[180],"edge).":[181],"also":[183,327],"three":[185],"approaches":[186],"edge":[189],"connections":[190],"KG:":[195],"average,":[196],"concatenation,":[197],"Hadamard.":[199],"Lastly,":[200],"we":[201,272],"induce":[206],"inductive":[207],"biases":[208],"expedite":[210],"convergence":[212,253],"input":[214,259],"representation":[215],"scaling).":[216],"Results:":[217],"evaluate":[219],"replicating":[223],"five":[224,282],"discoveries":[226],"Hallmark":[229],"Cancer":[231],"(HOC)":[232],"datasets":[233,283],"two":[239,280],"works.":[241],"results":[243,296],"show":[244],"no":[245],"significant":[246],"difference":[247],"in":[248],"reported":[249],"ranks":[250],"rate":[254],"comparing":[256],"scaling":[257],"representations":[260],"not":[262],"this":[264],"method.":[265,307],"Comparing":[266],"previous":[270],"works,":[271],"found":[273,310],"achieves":[276,285],"optimal":[277],"performance":[278,287],"on":[279,288],"comparable":[286],"remaining":[290],"datasets.":[291],"further":[293,347],"significance":[299],"testing":[300],"demonstrate":[302],"efficacy":[304],"Conclusion:":[308],"similarity-based":[312],"predicts":[315],"linking":[316,333],"single":[320],"closed":[322],"replication.":[324],"provides":[328],"ranked":[330],"list":[331],"set":[337],"inputs.":[339],"This":[340],"reduces":[342],"burden":[344],"allows":[346],"exploration":[348],"generated":[350],"hypotheses.":[351]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}