{"id":"https://openalex.org/W2962860563","doi":"https://doi.org/10.1109/tcbb.2019.2913855","title":"On the Unreported-Profile-is-Negative Assumption for Predictive Cheminformatics","display_name":"On the Unreported-Profile-is-Negative Assumption for Predictive Cheminformatics","publication_year":2019,"publication_date":"2019-04-30","ids":{"openalex":"https://openalex.org/W2962860563","doi":"https://doi.org/10.1109/tcbb.2019.2913855","mag":"2962860563","pmid":"https://pubmed.ncbi.nlm.nih.gov/31056508"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2019.2913855","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2913855","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/A5023655697","display_name":"Chao Lan","orcid":"https://orcid.org/0000-0003-2526-7206"},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chao Lan","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS, USA"],"raw_orcid":"https://orcid.org/0000-0003-2526-7206","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS, USA","institution_ids":["https://openalex.org/I146416000"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061826551","display_name":"Sai Nivedita Chandrasekaran","orcid":null},"institutions":[{"id":"https://openalex.org/I4210124444","display_name":"Sears Holdings (United States)","ror":"https://ror.org/02sx1y706","country_code":"US","type":"company","lineage":["https://openalex.org/I4210124444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sai Nivedita Chandrasekaran","raw_affiliation_strings":["CEO's Office, Sears Holdings Corporation, Bay Harbor Islands, FL"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CEO's Office, Sears Holdings Corporation, Bay Harbor Islands, FL","institution_ids":["https://openalex.org/I4210124444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5105352906","display_name":"Jun Huan","orcid":"https://orcid.org/0000-0003-4929-2617"},"institutions":[{"id":"https://openalex.org/I146416000","display_name":"University of Kansas","ror":"https://ror.org/001tmjg57","country_code":"US","type":"education","lineage":["https://openalex.org/I146416000"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jun Huan","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, University of Kansas, Lawrence, KS, USA","institution_ids":["https://openalex.org/I146416000"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5023655697"],"corresponding_institution_ids":["https://openalex.org/I146416000"],"apc_list":null,"apc_paid":null,"fwci":0.1445,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.57323045,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"17","issue":"4","first_page":"1352","last_page":"1363"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12535","display_name":"Machine Learning and Data Classification","score":0.9972000122070312,"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"}},"topics":[{"id":"https://openalex.org/T12535","display_name":"Machine Learning and Data Classification","score":0.9972000122070312,"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/T11652","display_name":"Imbalanced Data Classification Techniques","score":0.9890999794006348,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9865000247955322,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.9417312145233154},{"id":"https://openalex.org/keywords/perspective","display_name":"Perspective (graphical)","score":0.7234817743301392},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6897116899490356},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6349806785583496},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6229544878005981},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.578446090221405},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3994181156158447},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.10431835055351257}],"concepts":[{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.9417312145233154},{"id":"https://openalex.org/C12713177","wikidata":"https://www.wikidata.org/wiki/Q1900281","display_name":"Perspective (graphical)","level":2,"score":0.7234817743301392},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6897116899490356},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6349806785583496},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6229544878005981},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.578446090221405},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3994181156158447},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.10431835055351257},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000080911","descriptor_name":"Cheminformatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000080911","descriptor_name":"Cheminformatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000080911","descriptor_name":"Cheminformatics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D062313","descriptor_name":"Databases, Pharmaceutical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2019.2913855","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2019.2913855","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:31056508","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31056508","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":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":116,"referenced_works":["https://openalex.org/W3035862","https://openalex.org/W9155011","https://openalex.org/W14576171","https://openalex.org/W22461475","https://openalex.org/W120250592","https://openalex.org/W153313452","https://openalex.org/W159036455","https://openalex.org/W265767496","https://openalex.org/W1497303847","https://openalex.org/W1518712659","https://openalex.org/W1530558387","https://openalex.org/W1538189649","https://openalex.org/W1556081409","https://openalex.org/W1559054844","https://openalex.org/W1587644773","https://openalex.org/W1593505700","https://openalex.org/W1703735685","https://openalex.org/W1747861911","https://openalex.org/W1766968125","https://openalex.org/W1825821140","https://openalex.org/W1829340448","https://openalex.org/W1861993554","https://openalex.org/W1965887320","https://openalex.org/W1966716922","https://openalex.org/W1967292583","https://openalex.org/W1968329810","https://openalex.org/W1969387993","https://openalex.org/W1978033244","https://openalex.org/W1984014392","https://openalex.org/W1984084871","https://openalex.org/W1987034590","https://openalex.org/W1987431925","https://openalex.org/W1992380306","https://openalex.org/W1994176837","https://openalex.org/W1999031685","https://openalex.org/W2012914116","https://openalex.org/W2016210016","https://openalex.org/W2023603028","https://openalex.org/W2024523156","https://openalex.org/W2027829212","https://openalex.org/W2029348196","https://openalex.org/W2038307235","https://openalex.org/W2038553416","https://openalex.org/W2044758663","https://openalex.org/W2045673749","https://openalex.org/W2050871273","https://openalex.org/W2052171434","https://openalex.org/W2054141820","https://openalex.org/W2056234582","https://openalex.org/W2059733647","https://openalex.org/W2090679992","https://openalex.org/W2097532544","https://openalex.org/W2098573517","https://openalex.org/W2100294832","https://openalex.org/W2101409192","https://openalex.org/W2104052971","https://openalex.org/W2104520867","https://openalex.org/W2106029302","https://openalex.org/W2108740562","https://openalex.org/W2113310024","https://openalex.org/W2123958887","https://openalex.org/W2124187902","https://openalex.org/W2130652100","https://openalex.org/W2131159579","https://openalex.org/W2131904035","https://openalex.org/W2132442585","https://openalex.org/W2132870739","https://openalex.org/W2133227149","https://openalex.org/W2134435539","https://openalex.org/W2134510195","https://openalex.org/W2135790056","https://openalex.org/W2137233422","https://openalex.org/W2140310134","https://openalex.org/W2153477625","https://openalex.org/W2158295392","https://openalex.org/W2161607603","https://openalex.org/W2170283814","https://openalex.org/W2237874459","https://openalex.org/W2248044446","https://openalex.org/W2248525918","https://openalex.org/W2251470557","https://openalex.org/W2270414365","https://openalex.org/W2286085333","https://openalex.org/W2294273376","https://openalex.org/W2325923789","https://openalex.org/W2399976582","https://openalex.org/W2403190083","https://openalex.org/W2463645429","https://openalex.org/W2592839484","https://openalex.org/W2598600156","https://openalex.org/W2950921101","https://openalex.org/W2963863756","https://openalex.org/W2994844380","https://openalex.org/W4243150419","https://openalex.org/W6600122749","https://openalex.org/W6600386379","https://openalex.org/W6600959050","https://openalex.org/W6606214242","https://openalex.org/W6609875705","https://openalex.org/W6630897461","https://openalex.org/W6631896747","https://openalex.org/W6637474009","https://openalex.org/W6637870237","https://openalex.org/W6639315830","https://openalex.org/W6675354903","https://openalex.org/W6679539681","https://openalex.org/W6679740073","https://openalex.org/W6680830989","https://openalex.org/W6680838405","https://openalex.org/W6682894622","https://openalex.org/W6690035613","https://openalex.org/W6691596220","https://openalex.org/W6696048895","https://openalex.org/W6697009023","https://openalex.org/W6719292619","https://openalex.org/W7033836176"],"related_works":["https://openalex.org/W1573015311","https://openalex.org/W2889938001","https://openalex.org/W4386509167","https://openalex.org/W3165034028","https://openalex.org/W1570419641","https://openalex.org/W4293771607","https://openalex.org/W2296499206","https://openalex.org/W3210319767","https://openalex.org/W132037564","https://openalex.org/W4246770172"],"abstract_inverted_index":{"In":[0,32,96],"cheminformatics,":[1],"compound-target":[2],"binding":[3,66],"profiles":[4,28,67,92,105],"has":[5],"been":[6],"a":[7,22,54,63,100,134],"main":[8],"source":[9],"of":[10,50,90],"data":[11,15],"for":[12,44],"research.":[13],"For":[14],"repositories":[16],"that":[17,26,102],"only":[18,121],"provide":[19],"positive":[20],"profiles,":[21,130],"popular":[23],"assumption":[24,43,84],"is":[25,60],"unreported":[27,91,129],"are":[29,68],"all":[30],"negative.":[31],"this":[33,42],"paper,":[34],"we":[35,76,98,140],"caution":[36],"the":[37,83],"audience":[38],"not":[39,120],"to":[40,72,127],"take":[41],"granted,":[45],"and":[46,86,106,110,145],"present":[47],"empirical":[48],"evidence":[49],"its":[51],"ineffectiveness":[52],"from":[53],"machine":[55],"learning":[56],"perspective.":[57],"Our":[58],"examination":[59],"based":[61],"on":[62],"setting":[64],"where":[65],"used":[69],"as":[70],"features":[71],"train":[73],"predictive":[74,108],"models;":[75],"show":[77,111],"(1)":[78],"prediction":[79,94],"performance":[80,115],"degrades":[81],"when":[82],"fails":[85],"(2)":[87],"explicit":[88],"recovery":[89,125],"improves":[93],"performance.":[95],"particular,":[97],"propose":[99],"framework":[101],"jointly":[103],"recovers":[104],"learns":[107],"model,":[109],"it":[112],"achieves":[113],"further":[114],"improvement.":[116],"The":[117],"presented":[118],"study":[119],"suggests":[122],"applying":[123],"matrix":[124],"methods":[126],"recover":[128],"but":[131],"also":[132],"initiates":[133],"new":[135],"missing":[136],"feature":[137],"problem":[138],"which":[139],"called":[141],"Learning":[142],"with":[143],"Positive":[144],"Unknown":[146],"Features.":[147]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
