{"id":"https://openalex.org/W3004541267","doi":"https://doi.org/10.1109/bibm47256.2019.8983294","title":"When the How Outweighs the What: the Pivotal Importance of Context","display_name":"When the How Outweighs the What: the Pivotal Importance of Context","publication_year":2019,"publication_date":"2019-11-01","ids":{"openalex":"https://openalex.org/W3004541267","doi":"https://doi.org/10.1109/bibm47256.2019.8983294","mag":"3004541267"},"language":"en","primary_location":{"id":"doi:10.1109/bibm47256.2019.8983294","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983294","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-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/A5052915205","display_name":"Cole A. Lyman","orcid":"https://orcid.org/0000-0001-7921-165X"},"institutions":[{"id":"https://openalex.org/I4210111757","display_name":"Rochester General Hospital","ror":"https://ror.org/01jk6xr82","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210111757"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Cole A. Lyman","raw_affiliation_strings":["Center for Clinical Systems Biology,Rochester General Hospital,Rochester,NY,USA","Rochester General Hospital, Center for Clinical Systems Biology, Rochester, NY, USA"],"affiliations":[{"raw_affiliation_string":"Center for Clinical Systems Biology,Rochester General Hospital,Rochester,NY,USA","institution_ids":["https://openalex.org/I4210111757"]},{"raw_affiliation_string":"Rochester General Hospital, Center for Clinical Systems Biology, Rochester, NY, USA","institution_ids":["https://openalex.org/I4210111757"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067822307","display_name":"Connor Anderson","orcid":null},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Connor Anderson","raw_affiliation_strings":["Brigham Young University,Computer Science Dept.,Provo,UT,USA","Computer Science Dept., Brigham Young University, Provo, UT, USA"],"affiliations":[{"raw_affiliation_string":"Brigham Young University,Computer Science Dept.,Provo,UT,USA","institution_ids":["https://openalex.org/I100005738"]},{"raw_affiliation_string":"Computer Science Dept., Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040059357","display_name":"Matt Morris","orcid":null},"institutions":[{"id":"https://openalex.org/I4210111757","display_name":"Rochester General Hospital","ror":"https://ror.org/01jk6xr82","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210111757"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matt Morris","raw_affiliation_strings":["Center for Clinical Systems Biology,Rochester General Hospital,Rochester,NY,USA","Rochester General Hospital, Center for Clinical Systems Biology, Rochester, NY, USA"],"affiliations":[{"raw_affiliation_string":"Center for Clinical Systems Biology,Rochester General Hospital,Rochester,NY,USA","institution_ids":["https://openalex.org/I4210111757"]},{"raw_affiliation_string":"Rochester General Hospital, Center for Clinical Systems Biology, Rochester, NY, USA","institution_ids":["https://openalex.org/I4210111757"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007761661","display_name":"Umesh K. Nandal","orcid":null},"institutions":[{"id":"https://openalex.org/I1318003438","display_name":"RELX Group (Netherlands)","ror":"https://ror.org/02scfj030","country_code":"NL","type":"company","lineage":["https://openalex.org/I1318003438","https://openalex.org/I4210160603"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Umesh K. Nandal","raw_affiliation_strings":["Content Transformations, Life Sciences Elsevier,Amsterdam,Netherlands","Content Transformations, Life Sciences Elsevier, Amsterdam, Netherlands"],"affiliations":[{"raw_affiliation_string":"Content Transformations, Life Sciences Elsevier,Amsterdam,Netherlands","institution_ids":["https://openalex.org/I1318003438"]},{"raw_affiliation_string":"Content Transformations, Life Sciences Elsevier, Amsterdam, Netherlands","institution_ids":["https://openalex.org/I1318003438"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109498098","display_name":"Marianna J. Martindale","orcid":null},"institutions":[{"id":"https://openalex.org/I66946132","display_name":"University of Maryland, College Park","ror":"https://ror.org/047s2c258","country_code":"US","type":"education","lineage":["https://openalex.org/I66946132"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marianna J. Martindale","raw_affiliation_strings":["iSchool, University of Maryland,College Park,MD,USA","iSchool, University of Maryland, College Park, MD, USA"],"affiliations":[{"raw_affiliation_string":"iSchool, University of Maryland,College Park,MD,USA","institution_ids":["https://openalex.org/I66946132"]},{"raw_affiliation_string":"iSchool, University of Maryland, College Park, MD, USA","institution_ids":["https://openalex.org/I66946132"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058435710","display_name":"Mark Clement","orcid":"https://orcid.org/0000-0003-4902-3521"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark Clement","raw_affiliation_strings":["Brigham Young University,Computer Science Dept.,Provo,UT,USA","Computer Science Dept., Brigham Young University, Provo, UT, USA"],"affiliations":[{"raw_affiliation_string":"Brigham Young University,Computer Science Dept.,Provo,UT,USA","institution_ids":["https://openalex.org/I100005738"]},{"raw_affiliation_string":"Computer Science Dept., Brigham Young University, Provo, UT, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015262975","display_name":"Gordon Broderick","orcid":"https://orcid.org/0000-0002-3588-8252"},"institutions":[{"id":"https://openalex.org/I155173764","display_name":"Rochester Institute of Technology","ror":"https://ror.org/00v4yb702","country_code":"US","type":"education","lineage":["https://openalex.org/I155173764"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gordon Broderick","raw_affiliation_strings":["Rochester Institute of Technology,Dept. of Biomedical Engineering,Rochester,NY,USA","Dept. of Biomedical Engineering, Rochester Institute of Technology, Rochester, NY, USA"],"affiliations":[{"raw_affiliation_string":"Rochester Institute of Technology,Dept. of Biomedical Engineering,Rochester,NY,USA","institution_ids":["https://openalex.org/I155173764"]},{"raw_affiliation_string":"Dept. of Biomedical Engineering, Rochester Institute of Technology, Rochester, NY, USA","institution_ids":["https://openalex.org/I155173764"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5052915205"],"corresponding_institution_ids":["https://openalex.org/I4210111757"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.2236675,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"2149","last_page":"2156"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9797000288963318,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9797000288963318,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9725000262260437,"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":0.9696000218391418,"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":0.733597993850708},{"id":"https://openalex.org/keywords/leverage","display_name":"Leverage (statistics)","score":0.7302587032318115},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6634230613708496},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.6146788597106934},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5546938180923462},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.49451300501823425},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.47912856936454773},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.45715802907943726},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.4367710053920746},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4105871021747589},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12464490532875061}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.733597993850708},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.7302587032318115},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6634230613708496},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.6146788597106934},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5546938180923462},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.49451300501823425},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.47912856936454773},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.45715802907943726},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.4367710053920746},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4105871021747589},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12464490532875061},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","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/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm47256.2019.8983294","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm47256.2019.8983294","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":35,"referenced_works":["https://openalex.org/W1964525882","https://openalex.org/W1975387345","https://openalex.org/W1983242089","https://openalex.org/W1993453733","https://openalex.org/W2021748243","https://openalex.org/W2030932194","https://openalex.org/W2031067020","https://openalex.org/W2035524614","https://openalex.org/W2050034605","https://openalex.org/W2095705004","https://openalex.org/W2097553584","https://openalex.org/W2101109022","https://openalex.org/W2101234009","https://openalex.org/W2115959705","https://openalex.org/W2119821739","https://openalex.org/W2140601463","https://openalex.org/W2152143870","https://openalex.org/W2163480486","https://openalex.org/W2187089797","https://openalex.org/W2493916176","https://openalex.org/W2593919854","https://openalex.org/W2896457183","https://openalex.org/W2911489562","https://openalex.org/W2930542186","https://openalex.org/W2962784628","https://openalex.org/W2963341956","https://openalex.org/W2963403868","https://openalex.org/W2979826702","https://openalex.org/W4239510810","https://openalex.org/W4247817218","https://openalex.org/W4385245566","https://openalex.org/W6674330103","https://openalex.org/W6675354045","https://openalex.org/W6732900196","https://openalex.org/W6739901393"],"related_works":["https://openalex.org/W2090763504","https://openalex.org/W4390516098","https://openalex.org/W2181948922","https://openalex.org/W148178222","https://openalex.org/W2384362569","https://openalex.org/W2104657898","https://openalex.org/W1948992892","https://openalex.org/W2142795561","https://openalex.org/W1886884218","https://openalex.org/W1910826599"],"abstract_inverted_index":{"A":[0],"growing":[1],"body":[2],"of":[3,10,29,72,88,112,135,146,147,193,215],"knowledge":[4,25],"about":[5],"biological":[6,11,90,226],"mechanisms":[7],"and":[8,97,109,153,208,218],"interaction":[9,47],"components":[12],"is":[13,50,56],"contained":[14],"in":[15,44,52,58,83,132,142,176,189,201],"the":[16,27,39,42,46,63,70,84,94,113,171,194,213],"peer-reviewed":[17],"scientific":[18],"literature.":[19],"In":[20,99],"order":[21],"to":[22,125,184],"leverage":[23],"this":[24],"towards":[26],"development":[28],"predictive":[30],"models,":[31],"one":[32],"must":[33],"first":[34],"extract":[35],"these":[36],"relationships":[37],"from":[38,118,128],"text.":[40],"However,":[41],"context":[43],"which":[45],"was":[48],"reported":[49],"critical":[51],"ensuring":[53],"that":[54,205],"it":[55],"used":[57,188,200],"a":[59,79,89,104,133,143],"manner":[60],"consistent":[61],"with":[62,161],"model's":[64],"intended":[65],"application.":[66],"Here":[67],"we":[68],"assess":[69],"applicability":[71],"two":[73,110],"generic":[74],"automated":[75],"methods":[76],"for":[77],"leveraging":[78],"broader":[80],"contextual":[81],"structure":[82],"more":[85],"specific":[86],"domain":[87],"experiment":[91],"using":[92],"only":[93,167],"paper's":[95],"title":[96],"abstract.":[98],"an":[100],"example":[101],"use":[102],"case,":[103],"Support":[105],"Vector":[106],"Machine":[107],"(SVM)":[108],"variants":[111],"broadly-used":[114],"Bidirectional":[115],"Encoder":[116],"Representations":[117],"Transformers":[119],"(BERT)":[120],"neural":[121,163],"network":[122,164],"model,":[123],"serve":[124],"distinguish":[126],"mouse":[127,207],"human":[129,209],"subject":[130],"experiments":[131],"corpus":[134],"over":[136],"12,000":[137],"papers":[138],"documenting":[139],"mechanistic":[140],"interactions":[141],"regulatory":[144],"model":[145],"mucosal":[148],"immune":[149],"signaling.":[150],"The":[151],"BERT":[152],"domain-specific":[154],"BioBERT":[155],"yielded":[156],"essentially":[157],"equivalent":[158],"classification":[159],"accuracy":[160],"both":[162],"models":[165],"performing":[166],"marginally":[168],"better":[169],"than":[170,222],"SVM.":[172],"Words":[173],"occurring":[174],"frequently":[175],"abstracts":[177,211],"were":[178,187,199],"largely":[179],"non-specific,":[180],"whereas":[181],"words":[182,198],"unique":[183],"each":[185],"class":[186],"4%":[190],"or":[191,224],"less":[192],"abstracts.":[195],"These":[196],"high-specificity":[197],"very":[202],"similar":[203],"contexts":[204],"separated":[206],"study":[210,216],"on":[212],"basis":[214],"design":[217],"experimental":[219],"procedure":[220],"rather":[221],"species":[223],"basic":[225],"markers.":[227]},"counts_by_year":[{"year":2023,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}