{"id":"https://openalex.org/W3036658719","doi":"https://doi.org/10.1109/tcbb.2020.3003947","title":"A Scalable Embedding Based Neural Network Method for Discovering Knowledge From Biomedical Literature","display_name":"A Scalable Embedding Based Neural Network Method for Discovering Knowledge From Biomedical Literature","publication_year":2020,"publication_date":"2020-06-22","ids":{"openalex":"https://openalex.org/W3036658719","doi":"https://doi.org/10.1109/tcbb.2020.3003947","mag":"3036658719","pmid":"https://pubmed.ncbi.nlm.nih.gov/32750871"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2020.3003947","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.3003947","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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/ACM Transactions on Computational Biology and Bioinformatics","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/A5048043129","display_name":"Shengtian Sang","orcid":"https://orcid.org/0000-0003-0851-9520"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shengtian Sang","raw_affiliation_strings":["Department of Medicine, Stanford University, Stanford, CA, USA"],"affiliations":[{"raw_affiliation_string":"Department of Medicine, Stanford University, Stanford, CA, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100705977","display_name":"Xiaoxia Liu","orcid":"https://orcid.org/0009-0003-6662-9020"},"institutions":[{"id":"https://openalex.org/I43313876","display_name":"Dalian Maritime University","ror":"https://ror.org/002b7nr53","country_code":"CN","type":"education","lineage":["https://openalex.org/I43313876"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoxia Liu","raw_affiliation_strings":["Information Science and Technology College, Dalian Maritime University, Dalian, China"],"affiliations":[{"raw_affiliation_string":"Information Science and Technology College, Dalian Maritime University, Dalian, China","institution_ids":["https://openalex.org/I43313876"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100386506","display_name":"Xiaoyu Chen","orcid":"https://orcid.org/0000-0003-4009-8156"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoyu Chen","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017835678","display_name":"Di Zhao","orcid":"https://orcid.org/0000-0002-0876-5126"},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Di Zhao","raw_affiliation_strings":["College of Computer Science and Technology, Dalian University of Technology, Dalian, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5048043129"],"corresponding_institution_ids":["https://openalex.org/I97018004"],"apc_list":null,"apc_paid":null,"fwci":0.6628,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.66925554,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"19","issue":"3","first_page":"1294","last_page":"1301"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9998999834060669,"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":0.9998999834060669,"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/T13083","display_name":"Advanced Text Analysis Techniques","score":0.9681000113487244,"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/T10215","display_name":"Semantic Web and Ontologies","score":0.9598000049591064,"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":0.7514587044715881},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6626233458518982},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6390660405158997},{"id":"https://openalex.org/keywords/knowledge-graph","display_name":"Knowledge graph","score":0.6141357421875},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5236577391624451},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4961632192134857},{"id":"https://openalex.org/keywords/knowledge-extraction","display_name":"Knowledge extraction","score":0.4322742521762848},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.43022847175598145},{"id":"https://openalex.org/keywords/graph-embedding","display_name":"Graph embedding","score":0.4235851764678955},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.38873088359832764},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.38262027502059937},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3655654788017273}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7514587044715881},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6626233458518982},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6390660405158997},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.6141357421875},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5236577391624451},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4961632192134857},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.4322742521762848},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.43022847175598145},{"id":"https://openalex.org/C75564084","wikidata":"https://www.wikidata.org/wiki/Q5597085","display_name":"Graph embedding","level":3,"score":0.4235851764678955},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.38873088359832764},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.38262027502059937},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3655654788017273},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011642","descriptor_name":"Publications","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019359","descriptor_name":"Knowledge","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051188","descriptor_name":"Knowledge Bases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2020.3003947","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.3003947","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"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/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32750871","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32750871","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/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.699999988079071,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G7097813879","display_name":null,"funder_award_id":"3132019202","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"}],"funders":[{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W842045238","https://openalex.org/W1522301498","https://openalex.org/W1631679626","https://openalex.org/W1971106435","https://openalex.org/W1972694920","https://openalex.org/W1973058638","https://openalex.org/W1981229377","https://openalex.org/W2011726136","https://openalex.org/W2015604457","https://openalex.org/W2015954361","https://openalex.org/W2034537627","https://openalex.org/W2084395771","https://openalex.org/W2087035995","https://openalex.org/W2094405302","https://openalex.org/W2098201295","https://openalex.org/W2099668895","https://openalex.org/W2103427999","https://openalex.org/W2116296021","https://openalex.org/W2122402213","https://openalex.org/W2143448637","https://openalex.org/W2150355110","https://openalex.org/W2157632574","https://openalex.org/W2251469093","https://openalex.org/W2271312715","https://openalex.org/W2291868800","https://openalex.org/W2488922396","https://openalex.org/W2562110925","https://openalex.org/W2592742128","https://openalex.org/W2753199411","https://openalex.org/W2805208465","https://openalex.org/W4253608092","https://openalex.org/W6601241269","https://openalex.org/W6623651389","https://openalex.org/W6631190155","https://openalex.org/W6632766574","https://openalex.org/W6678830454","https://openalex.org/W7025199648"],"related_works":["https://openalex.org/W2604454537","https://openalex.org/W2808284704","https://openalex.org/W2897702399","https://openalex.org/W4206028705","https://openalex.org/W2757431232","https://openalex.org/W2954554213","https://openalex.org/W2251363251","https://openalex.org/W4206547516","https://openalex.org/W4293236197","https://openalex.org/W3036264823"],"abstract_inverted_index":{"Nowadays,":[0],"the":[1,20,73,115,138,146,151,171,176,181,212,233,241],"amount":[2],"of":[3,35,72,215],"biomedical":[4,68,102,118,123],"literatures":[5],"is":[6,16,48,130,167,184,227],"growing":[7],"at":[8],"an":[9,228],"explosive":[10],"speed,":[11],"and":[12,81,107,125,148,188,223],"much":[13],"useful":[14],"knowledge":[15,103,128,152,221],"yet":[17],"undiscovered":[18],"in":[19,54,90,150,240],"literature.":[21,56,92,242],"Classical":[22],"information":[23,30],"retrieval":[24],"techniques":[25],"allow":[26],"to":[27,41,76,86,144],"access":[28],"explicit":[29],"from":[31,122],"a":[32,98,127,155,160],"given":[33],"collection":[34],"information,":[36],"but":[37,209],"are":[38,78,120,142],"not":[39,79,83,201],"able":[40],"recognize":[42],"implicit":[43],"connections.":[44],"Literature-based":[45],"discovery":[46,191],"(LBD)":[47],"characterized":[49],"by":[50,63,132,175],"uncovering":[51],"hidden":[52,205,239],"associations":[53,89,173,206,236],"non-interacting":[55],"It":[57,217],"could":[58,200],"significantly":[59],"support":[60],"scientific":[61],"research":[62],"identifying":[64],"new":[65],"connections":[66],"between":[67,117,207,237],"entities.":[69],"However,":[70],"most":[71],"existing":[74],"approaches":[75],"LBD":[77],"scalable":[80],"may":[82],"be":[84],"sufficient":[85],"detect":[87],"complex":[88,235],"non-directly-connected":[91],"In":[93],"this":[94],"article,":[95],"we":[96],"present":[97],"model":[99,183],"which":[100],"incorporates":[101],"graph,":[104],"graph":[105,129,139,153,178,222],"embedding,":[106],"deep":[108,224],"learning":[109,225],"methods":[110,226],"for":[111,186,231],"literature-based":[112,190],"discovery.":[113],"First,":[114],"relations":[116,149],"entities":[119,147,238],"extracted":[121],"abstracts":[124],"then":[126],"constructed":[131],"using":[133],"these":[134],"obtained":[135],"relations.":[136],"Second,":[137],"embedding":[140],"technologies":[141],"applied":[143],"convert":[145],"into":[154],"low-dimensional":[156],"vector":[157],"space.":[158],"Third,":[159],"bidirectional":[161],"Long":[162],"Short-Term":[163],"Memory":[164],"(BLSTM)":[165],"network":[166],"trained":[168],"based":[169],"on":[170],"entity":[172],"represented":[174],"pre-trained":[177],"embeddings.":[179],"Finally,":[180],"learned":[182],"used":[185],"open":[187],"closed":[189],"tasks.":[192],"The":[193],"experimental":[194],"results":[195],"show":[196],"that":[197,219],"our":[198],"method":[199],"only":[202],"effectively":[203],"discover":[204],"entities,":[208],"also":[210],"reveal":[211],"corresponding":[213],"mechanism":[214],"interactions.":[216],"suggests":[218],"incorporating":[220],"effective":[229],"way":[230],"capturing":[232],"underlying":[234]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":3},{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
