{"id":"https://openalex.org/W3073354919","doi":"https://doi.org/10.1109/tkde.2020.3017687","title":"T-PAIR: Temporal Node-pair Embedding for Automatic Biomedical Hypothesis Generation","display_name":"T-PAIR: Temporal Node-pair Embedding for Automatic Biomedical Hypothesis Generation","publication_year":2020,"publication_date":"2020-01-01","ids":{"openalex":"https://openalex.org/W3073354919","doi":"https://doi.org/10.1109/tkde.2020.3017687","mag":"3073354919"},"language":"en","primary_location":{"id":"doi:10.1109/tkde.2020.3017687","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tkde.2020.3017687","pdf_url":null,"source":{"id":"https://openalex.org/S30698027","display_name":"IEEE Transactions on Knowledge and Data Engineering","issn_l":"1041-4347","issn":["1041-4347","1558-2191","2326-3865"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320439","host_organization_name":"IEEE Computer Society","host_organization_lineage":["https://openalex.org/P4310320439","https://openalex.org/P4310319808"],"host_organization_lineage_names":["IEEE Computer Society","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 Transactions on Knowledge and Data Engineering","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"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/A5010631591","display_name":"Uchenna Akujuobi","orcid":"https://orcid.org/0000-0002-7102-7994"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":true,"raw_author_name":"Uchenna Akujuobi","raw_affiliation_strings":["Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5071179999","display_name":"Michael Spranger","orcid":"https://orcid.org/0000-0001-9443-7008"},"institutions":[{"id":"https://openalex.org/I4210122684","display_name":"Sony Computer Science Laboratories","ror":"https://ror.org/02nc46417","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210122684"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Michael Spranger","raw_affiliation_strings":["Sony Computer Science Laboratories Inc., Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Sony Computer Science Laboratories Inc., Tokyo, Japan","institution_ids":["https://openalex.org/I4210122684"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070784871","display_name":"Sucheendra K. Palaniappan","orcid":"https://orcid.org/0000-0002-2829-2311"},"institutions":[{"id":"https://openalex.org/I4210118579","display_name":"Systems Biology Institute","ror":"https://ror.org/02c7akf81","country_code":"JP","type":"nonprofit","lineage":["https://openalex.org/I4210118579"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Sucheendra K Palaniappan","raw_affiliation_strings":["Systems Biology Institute, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Systems Biology Institute, Tokyo, Japan","institution_ids":["https://openalex.org/I4210118579"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000755750","display_name":"Xiangliang Zhang","orcid":"https://orcid.org/0000-0002-3574-5665"},"institutions":[{"id":"https://openalex.org/I71920554","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38","country_code":"SA","type":"education","lineage":["https://openalex.org/I71920554"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Xiangliang Zhang","raw_affiliation_strings":["Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia"],"affiliations":[{"raw_affiliation_string":"Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia","institution_ids":["https://openalex.org/I71920554"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5010631591"],"corresponding_institution_ids":["https://openalex.org/I71920554"],"apc_list":null,"apc_paid":null,"fwci":1.1599,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.77679694,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"1"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9993000030517578,"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":0.9993000030517578,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9970999956130981,"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":0.9955999851226807,"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":0.7314002513885498},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6691678762435913},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.623908281326294},{"id":"https://openalex.org/keywords/node","display_name":"Node (physics)","score":0.5835357308387756},{"id":"https://openalex.org/keywords/term","display_name":"Term (time)","score":0.5153026580810547},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4890959858894348},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3839029371738434},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3662490248680115},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3548475503921509},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0946902334690094}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7314002513885498},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6691678762435913},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.623908281326294},{"id":"https://openalex.org/C62611344","wikidata":"https://www.wikidata.org/wiki/Q1062658","display_name":"Node (physics)","level":2,"score":0.5835357308387756},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.5153026580810547},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4890959858894348},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3839029371738434},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3662490248680115},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3548475503921509},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0946902334690094},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","level":1,"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/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tkde.2020.3017687","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tkde.2020.3017687","pdf_url":null,"source":{"id":"https://openalex.org/S30698027","display_name":"IEEE Transactions on Knowledge and Data Engineering","issn_l":"1041-4347","issn":["1041-4347","1558-2191","2326-3865"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320439","host_organization_name":"IEEE Computer Society","host_organization_lineage":["https://openalex.org/P4310320439","https://openalex.org/P4310319808"],"host_organization_lineage_names":["IEEE Computer Society","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 Transactions on Knowledge and Data Engineering","raw_type":"journal-article"},{"id":"pmh:oai:repository.kaust.edu.sa:10754/664664","is_oa":false,"landing_page_url":"http://hdl.handle.net/10754/664664","pdf_url":null,"source":{"id":"https://openalex.org/S4306401596","display_name":"King Abdullah University of Science and Technology Repository (King Abdullah University of Science and Technology)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I71920554","host_organization_name":"King Abdullah University of Science and Technology","host_organization_lineage":["https://openalex.org/I71920554"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5050910958","display_name":null,"funder_award_id":"NSFC No. 61828302","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322320","display_name":"King Abdullah University of Science and Technology","ror":"https://ror.org/01q3tbs38"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":61,"referenced_works":["https://openalex.org/W340874798","https://openalex.org/W1023993098","https://openalex.org/W1562176487","https://openalex.org/W1580481679","https://openalex.org/W1583930768","https://openalex.org/W1981022368","https://openalex.org/W1983507216","https://openalex.org/W2010316443","https://openalex.org/W2011726136","https://openalex.org/W2015954361","https://openalex.org/W2024030746","https://openalex.org/W2038316408","https://openalex.org/W2052681001","https://openalex.org/W2054473834","https://openalex.org/W2057954853","https://openalex.org/W2060300932","https://openalex.org/W2067096102","https://openalex.org/W2089475299","https://openalex.org/W2119646114","https://openalex.org/W2130190939","https://openalex.org/W2136636278","https://openalex.org/W2142628731","https://openalex.org/W2149184178","https://openalex.org/W2154851992","https://openalex.org/W2184957013","https://openalex.org/W2259800810","https://openalex.org/W2283196293","https://openalex.org/W2413102523","https://openalex.org/W2427903045","https://openalex.org/W2433281745","https://openalex.org/W2466124480","https://openalex.org/W2556343638","https://openalex.org/W2565238637","https://openalex.org/W2591456992","https://openalex.org/W2624431344","https://openalex.org/W2732803752","https://openalex.org/W2748189976","https://openalex.org/W2774367863","https://openalex.org/W2787927827","https://openalex.org/W2797520986","https://openalex.org/W2887092413","https://openalex.org/W2890058722","https://openalex.org/W2906051537","https://openalex.org/W2922924332","https://openalex.org/W2951538941","https://openalex.org/W2954442758","https://openalex.org/W2954691982","https://openalex.org/W2962756421","https://openalex.org/W2963503534","https://openalex.org/W2964129543","https://openalex.org/W3101358844","https://openalex.org/W3104097132","https://openalex.org/W4249865584","https://openalex.org/W4251194840","https://openalex.org/W6634744552","https://openalex.org/W6635812994","https://openalex.org/W6678830454","https://openalex.org/W6692595061","https://openalex.org/W6738964360","https://openalex.org/W6748344800","https://openalex.org/W6750647964"],"related_works":["https://openalex.org/W2468279273","https://openalex.org/W2354198838","https://openalex.org/W1989130879","https://openalex.org/W2103419012","https://openalex.org/W2988126442","https://openalex.org/W1974414866","https://openalex.org/W2057568687","https://openalex.org/W2063982682","https://openalex.org/W2338543196","https://openalex.org/W2932872266"],"abstract_inverted_index":{"In":[0],"this":[1,43,129],"paper,":[2],"we":[3],"study":[4,250],"an":[5,156],"automatic":[6],"hypothesis":[7],"generation":[8],"(HG)":[9],"problem,":[10],"which":[11,190],"refers":[12],"to":[13,27,95,103,115,145,172],"the":[14,47,57,66,77,80,87,91,107,118,147,166,174,180,183,230,237,243,253,256],"discovery":[15],"of":[16,36,42,49,52,60,150,182,226,255],"meaningful":[17],"implicit":[18],"connections":[19,119],"between":[20,224],"scientific":[21,61,81],"terms,":[22,82],"including":[23],"but":[24],"not":[25,101],"limited":[26],"diseases,":[28],"chemicals,":[29],"drugs,":[30],"and":[31,54,169,210,248],"genes":[32],"extracted":[33],"from":[34,195],"databases":[35],"biomedical":[37],"publications.":[38],"Most":[39],"prior":[40],"studies":[41],"problem":[44,93,131],"focused":[45],"on":[46,86,186,219,236],"use":[48],"static":[50],"information":[51],"terms":[53,108,228,241],"largely":[55],"ignored":[56],"temporal":[58,148,175],"dynamics":[59,67],"term":[62],"relations.":[63,89,153],"Even":[64],"when":[65],"were":[68,217],"considered":[69],"in":[70,137,201],"a":[71,124,133,138],"few":[72],"recent":[73],"studies,":[74],"they":[75],"learned":[76],"representations":[78],"for":[79],"rather":[83],"than":[84],"focusing":[85],"term-pair":[88,97,222],"Since":[90],"HG":[92,130],"is":[94,100,112,144],"predict":[96],"connections,":[98],"it":[99,111],"enough":[102],"know":[104,116],"with":[105],"whom":[106],"are":[109,191],"connected,":[110],"more":[113],"important":[114],"how":[117],"have":[120],"been":[121],"formed":[122],"(in":[123,229,242],"dynamic":[125,139],"process).":[126],"We":[127,154,178],"formulate":[128],"as":[132,233,235],"future":[134,221],"connectivity":[135],"prediction":[136],"attributed":[140],"graph.":[141],"The":[142],"key":[143],"capture":[146],"evolution":[149],"node-pair":[151,176],"(term-pair)":[152],"propose":[155],"inductive":[157,244],"edge":[158],"(node-pair)":[159],"embedding":[160],"method":[161],"named":[162],"T-PAIR,":[163],"utilizing":[164],"both":[165],"graphical":[167],"structure":[168],"node":[170],"attribute":[171],"encode":[173],"relationship.":[177],"demonstrate":[179],"efficiency":[181],"proposed":[184,257],"model":[185],"three":[187,192],"real-world":[188],"datasets,":[189],"graphs":[193],"constructed":[194],"Pubmed":[196],"papers":[197],"published":[198],"until":[199],"2019":[200],"<italic":[202,206,211],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[203,207,212],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">Neurology</i>":[204],",":[205,209,214],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">Immunotherapy</i>":[208],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">Virology</i>":[213],"respectively.":[215],"Evaluations":[216],"conducted":[218],"predicting":[220],"relations":[223,238],"millions":[225],"seen":[227],"transductive":[231],"setting),":[232],"well":[234],"involving":[239],"unseen":[240],"setting).":[245],"Experiment":[246],"results":[247],"case":[249],"analyses":[251],"show":[252],"effectiveness":[254],"model.":[258]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":1}],"updated_date":"2026-02-27T16:54:17.756197","created_date":"2025-10-10T00:00:00"}
