{"id":"https://openalex.org/W2946028604","doi":"https://doi.org/10.3233/jifs-179026","title":"In the pursuit of semantic similarity for literature on microbial transcriptional regulation","display_name":"In the pursuit of semantic similarity for literature on microbial transcriptional regulation","publication_year":2019,"publication_date":"2019-05-14","ids":{"openalex":"https://openalex.org/W2946028604","doi":"https://doi.org/10.3233/jifs-179026","mag":"2946028604"},"language":"en","primary_location":{"id":"doi:10.3233/jifs-179026","is_oa":false,"landing_page_url":"https://doi.org/10.3233/jifs-179026","pdf_url":null,"source":{"id":"https://openalex.org/S179157397","display_name":"Journal of Intelligent & Fuzzy Systems","issn_l":"1064-1246","issn":["1064-1246","1875-8967"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Intelligent &amp; Fuzzy Systems","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/A5074701315","display_name":"Oscar Lithgow-Serrano","orcid":"https://orcid.org/0000-0003-1995-1669"},"institutions":[{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX"],"is_corresponding":true,"raw_author_name":"Oscar Lithgow-Serrano","raw_affiliation_strings":["Computational Genomics, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM), Morelos, M\u00e9xico","Instituto de Investigaciones en Matem\u00e1ticas Aplicadas y en Sistemas (IIMAS), Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM), Ciudad de M\u00e9xico, M\u00e9xico"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Genomics, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM), Morelos, M\u00e9xico","institution_ids":["https://openalex.org/I8961855"]},{"raw_affiliation_string":"Instituto de Investigaciones en Matem\u00e1ticas Aplicadas y en Sistemas (IIMAS), Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM), Ciudad de M\u00e9xico, M\u00e9xico","institution_ids":["https://openalex.org/I8961855"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079232768","display_name":"Julio Collado\u2010Vides","orcid":"https://orcid.org/0000-0001-8780-7664"},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]},{"id":"https://openalex.org/I8961855","display_name":"Universidad Nacional Aut\u00f3noma de M\u00e9xico","ror":"https://ror.org/01tmp8f25","country_code":"MX","type":"education","lineage":["https://openalex.org/I8961855"]}],"countries":["MX","US"],"is_corresponding":false,"raw_author_name":"Julio Collado-Vides","raw_affiliation_strings":["Computational Genomics, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM), Morelos, M\u00e9xico","Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Genomics, Centro de Ciencias Gen\u00f3micas, Universidad Nacional Aut\u00f3noma de M\u00e9xico (UNAM), Morelos, M\u00e9xico","institution_ids":["https://openalex.org/I8961855"]},{"raw_affiliation_string":"Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA","institution_ids":["https://openalex.org/I111088046"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5074701315"],"corresponding_institution_ids":["https://openalex.org/I8961855"],"apc_list":null,"apc_paid":null,"fwci":0.2486,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.54495316,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"36","issue":"5","first_page":"4777","last_page":"4786"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9957000017166138,"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":0.9957000017166138,"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":0.9944000244140625,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9940000176429749,"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":0.7784827947616577},{"id":"https://openalex.org/keywords/automatic-summarization","display_name":"Automatic summarization","score":0.6957292556762695},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6551748514175415},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.6383380889892578},{"id":"https://openalex.org/keywords/semantic-similarity","display_name":"Semantic similarity","score":0.6360973119735718},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.6085790395736694},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6049052476882935},{"id":"https://openalex.org/keywords/vocabulary","display_name":"Vocabulary","score":0.561956524848938},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.5096931457519531},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.48639681935310364},{"id":"https://openalex.org/keywords/syntax","display_name":"Syntax","score":0.4723842144012451},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.47039517760276794},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.4555034637451172},{"id":"https://openalex.org/keywords/meaning","display_name":"Meaning (existential)","score":0.4542555809020996},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.36249327659606934},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.21980425715446472}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7784827947616577},{"id":"https://openalex.org/C170858558","wikidata":"https://www.wikidata.org/wiki/Q1394144","display_name":"Automatic summarization","level":2,"score":0.6957292556762695},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6551748514175415},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.6383380889892578},{"id":"https://openalex.org/C130318100","wikidata":"https://www.wikidata.org/wiki/Q2268914","display_name":"Semantic similarity","level":2,"score":0.6360973119735718},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.6085790395736694},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6049052476882935},{"id":"https://openalex.org/C2777601683","wikidata":"https://www.wikidata.org/wiki/Q6499736","display_name":"Vocabulary","level":2,"score":0.561956524848938},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5096931457519531},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.48639681935310364},{"id":"https://openalex.org/C60048249","wikidata":"https://www.wikidata.org/wiki/Q37437","display_name":"Syntax","level":2,"score":0.4723842144012451},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.47039517760276794},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.4555034637451172},{"id":"https://openalex.org/C2780876879","wikidata":"https://www.wikidata.org/wiki/Q3054749","display_name":"Meaning (existential)","level":2,"score":0.4542555809020996},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.36249327659606934},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.21980425715446472},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C542102704","wikidata":"https://www.wikidata.org/wiki/Q183257","display_name":"Psychotherapist","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.3233/jifs-179026","is_oa":false,"landing_page_url":"https://doi.org/10.3233/jifs-179026","pdf_url":null,"source":{"id":"https://openalex.org/S179157397","display_name":"Journal of Intelligent & Fuzzy Systems","issn_l":"1064-1246","issn":["1064-1246","1875-8967"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Intelligent &amp; Fuzzy Systems","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320308943","display_name":"Microsoft Research","ror":"https://ror.org/00d0nc645"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W131533222","https://openalex.org/W1531237901","https://openalex.org/W1958547877","https://openalex.org/W1984052055","https://openalex.org/W1996445490","https://openalex.org/W2052477699","https://openalex.org/W2064587498","https://openalex.org/W2081580037","https://openalex.org/W2082815071","https://openalex.org/W2108530510","https://openalex.org/W2123442489","https://openalex.org/W2133458109","https://openalex.org/W2153579005","https://openalex.org/W2163993443","https://openalex.org/W2167609405","https://openalex.org/W2200913422","https://openalex.org/W2250539671","https://openalex.org/W2251939518","https://openalex.org/W2270234620","https://openalex.org/W2317261134","https://openalex.org/W2516222713","https://openalex.org/W2736149021","https://openalex.org/W2768371542","https://openalex.org/W2769306608","https://openalex.org/W2882319491","https://openalex.org/W2892666819","https://openalex.org/W2950824039","https://openalex.org/W2963949413","https://openalex.org/W3149550307","https://openalex.org/W4285719527","https://openalex.org/W4294170691","https://openalex.org/W6699346704"],"related_works":["https://openalex.org/W2366403280","https://openalex.org/W1495108544","https://openalex.org/W3148229873","https://openalex.org/W4242223894","https://openalex.org/W2091301346","https://openalex.org/W2150160875","https://openalex.org/W1517524280","https://openalex.org/W4306886878","https://openalex.org/W2090814745","https://openalex.org/W2154994723"],"abstract_inverted_index":{"The":[0,28,194],"constant":[1],"increase":[2],"in":[3,25,80,93,101,188,220],"the":[4,22,45,48,81,115,132,136,141,150,176,201,221,227],"production":[5],"of":[6,30,50,84,118,152,164,178,223],"scientific":[7],"literature":[8],"is":[9,35,62,76,91,121,126,214],"making":[10],"it":[11,75,125],"very":[12,198],"difficult":[13],"for":[14,65,218],"experts":[15],"to":[16,19,40,88,112,128,135,160,174,206,233],"keep":[17],"up":[18],"date":[20],"with":[21],"state-of-the-art":[23],"knowledge":[24],"their":[26],"fields.":[27],"use":[29,161],"Natural":[31],"Language":[32],"Processing":[33],"(NLP)":[34],"becoming":[36],"a":[37,58,63,77,189,208,237],"necessary":[38],"aid":[39],"tackle":[41],"this":[42],"challenge.":[43],"In":[44,139],"NLP":[46],"field,":[47],"task":[49,195],"measuring":[51],"semantic":[52],"similarity":[53,165,190],"between":[54],"two":[55],"sentences":[56],"plays":[57],"vital":[59],"role.":[60],"It":[61],"cornerstone":[64],"tasks":[66],"like":[67],"Q&amp;A,":[68],"Information":[69],"Retrieval,":[70],"Automatic":[71],"Summarization,":[72],"etc.,":[73],"and":[74,124,144,170,173,184,200],"crucial":[78],"element":[79],"ultimate":[82],"goal":[83],"computers":[85],"being":[86],"able":[87],"decode":[89],"what":[90],"conveyed":[92],"human":[94,228],"language":[95],"expression.":[96],"Measuring":[97],"Semantic":[98],"Similarity":[99],"(SS)":[100],"short":[102],"texts":[103],"has":[104,158,196,204],"specific":[105,143],"challenges.":[106],"Because":[107],"there":[108,213],"are":[109],"fewer":[110],"words":[111],"be":[113,207],"compared,":[114],"meaning":[116],"contribution":[117,134],"each":[119],"word":[120],"more":[122],"relevant,":[123],"important":[127],"take":[129],"into":[130],"account":[131],"syntax\u2019s":[133],"composed":[137],"meaning.":[138],"addition,":[140],"highly":[142],"specialized":[145],"vocabulary":[146],"\u2014":[147],"Microbial":[148],"Transcriptional-Regulation\u2014implies":[149],"lack":[151],"massive":[153],"training":[154],"resources.":[155],"Our":[156],"approach":[157],"been":[159],"an":[162],"ensemble":[163,202],"metrics":[166],"including":[167],"string,":[168],"distributional,":[169],"knowledge-based":[171],"metric":[172],"combine":[175],"results":[177],"such":[179],"analyses.":[180],"We":[181],"have":[182,231],"trained":[183],"tested":[185],"these":[186],"methods":[187,225],"corpus":[191],"developed":[192],"in-house.":[193],"proved":[197,205],"challenging,":[199],"strategy":[203],"good":[209],"approach.":[210],"Even":[211],"though":[212],"still":[215],"much":[216],"room":[217],"improvement":[219],"precision":[222],"our":[224],"concerning":[226],"evaluation,":[229],"we":[230],"managed":[232],"improve":[234],"them":[235],"reaching":[236],"strong":[238],"correlation":[239],"(":[240],"\u03c1":[241],"=":[242],"0.700).":[243]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
