{"id":"https://openalex.org/W3016065264","doi":"https://doi.org/10.1021/acs.jcim.9b01075","title":"Ranking Molecules with Vanishing Kernels and a Single Parameter: Active Applicability Domain<i>Included</i>","display_name":"Ranking Molecules with Vanishing Kernels and a Single Parameter: Active Applicability Domain<i>Included</i>","publication_year":2020,"publication_date":"2020-04-13","ids":{"openalex":"https://openalex.org/W3016065264","doi":"https://doi.org/10.1021/acs.jcim.9b01075","mag":"3016065264","pmid":"https://pubmed.ncbi.nlm.nih.gov/32281797"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.9b01075","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b01075","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","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/A5071115328","display_name":"Francois Berenger","orcid":"https://orcid.org/0000-0003-1377-944X"},"institutions":[{"id":"https://openalex.org/I207014233","display_name":"Kyushu Institute of Technology","ror":"https://ror.org/02278tr80","country_code":"JP","type":"education","lineage":["https://openalex.org/I207014233"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Francois Berenger","raw_affiliation_strings":["Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Kawazu, 680-4 Iizuka, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Kawazu, 680-4 Iizuka, Japan","institution_ids":["https://openalex.org/I207014233"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035394108","display_name":"Yoshihiro Yamanishi","orcid":"https://orcid.org/0000-0003-2279-8773"},"institutions":[{"id":"https://openalex.org/I207014233","display_name":"Kyushu Institute of Technology","ror":"https://ror.org/02278tr80","country_code":"JP","type":"education","lineage":["https://openalex.org/I207014233"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yoshihiro Yamanishi","raw_affiliation_strings":["Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Kawazu, 680-4 Iizuka, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, Kawazu, 680-4 Iizuka, Japan","institution_ids":["https://openalex.org/I207014233"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5071115328"],"corresponding_institution_ids":["https://openalex.org/I207014233"],"apc_list":null,"apc_paid":null,"fwci":0.433,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.67789874,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"60","issue":"9","first_page":"4376","last_page":"4387"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"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":1.0,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials 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":0.978600025177002,"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":0.7365153431892395},{"id":"https://openalex.org/keywords/ranking","display_name":"Ranking (information retrieval)","score":0.6899605989456177},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.6181473731994629},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5541375279426575},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.5114420652389526},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4848383665084839},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.48420193791389465},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4610084891319275},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4604094922542572},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.43801456689834595},{"id":"https://openalex.org/keywords/simple","display_name":"Simple (philosophy)","score":0.42452242970466614},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4203983545303345},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3585912585258484},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.32615238428115845},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2415362000465393},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13775524497032166},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.11740610003471375},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.10912156105041504}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7365153431892395},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.6899605989456177},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.6181473731994629},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5541375279426575},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.5114420652389526},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4848383665084839},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.48420193791389465},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4610084891319275},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4604094922542572},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.43801456689834595},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.42452242970466614},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4203983545303345},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3585912585258484},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.32615238428115845},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2415362000465393},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13775524497032166},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.11740610003471375},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.10912156105041504},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"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/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008024","descriptor_name":"Ligands","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.9b01075","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.9b01075","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:32281797","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32281797","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":"Journal of chemical information and modeling","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G568067577","display_name":null,"funder_award_id":"JPMJCR18Y5","funder_id":"https://openalex.org/F4320334789","funder_display_name":"Japan Science and Technology Agency"},{"id":"https://openalex.org/G8556906096","display_name":null,"funder_award_id":"18H03334","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320334789","display_name":"Japan Science and Technology Agency","ror":"https://ror.org/00097mb19"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":79,"referenced_works":["https://openalex.org/W56921542","https://openalex.org/W164290786","https://openalex.org/W1505823450","https://openalex.org/W1526146785","https://openalex.org/W1538131130","https://openalex.org/W1757990252","https://openalex.org/W1983775902","https://openalex.org/W1983989471","https://openalex.org/W1984994707","https://openalex.org/W1996327711","https://openalex.org/W1996975182","https://openalex.org/W1999798000","https://openalex.org/W2000050698","https://openalex.org/W2006262236","https://openalex.org/W2008572210","https://openalex.org/W2015861736","https://openalex.org/W2019044526","https://openalex.org/W2020756525","https://openalex.org/W2021083597","https://openalex.org/W2021748110","https://openalex.org/W2033757486","https://openalex.org/W2040870580","https://openalex.org/W2042110087","https://openalex.org/W2042613327","https://openalex.org/W2049644877","https://openalex.org/W2053080554","https://openalex.org/W2054886599","https://openalex.org/W2055431029","https://openalex.org/W2057802165","https://openalex.org/W2058557545","https://openalex.org/W2062450879","https://openalex.org/W2065160746","https://openalex.org/W2081301924","https://openalex.org/W2084306359","https://openalex.org/W2087347434","https://openalex.org/W2091967195","https://openalex.org/W2094125466","https://openalex.org/W2095705004","https://openalex.org/W2109553965","https://openalex.org/W2114704115","https://openalex.org/W2118585731","https://openalex.org/W2118865162","https://openalex.org/W2134552503","https://openalex.org/W2155653793","https://openalex.org/W2163967463","https://openalex.org/W2170464542","https://openalex.org/W2177317049","https://openalex.org/W2213735563","https://openalex.org/W2254686952","https://openalex.org/W2276859037","https://openalex.org/W2290847742","https://openalex.org/W2418371935","https://openalex.org/W2549144853","https://openalex.org/W2558999090","https://openalex.org/W2559997609","https://openalex.org/W2585439946","https://openalex.org/W2594183968","https://openalex.org/W2734982589","https://openalex.org/W2740946158","https://openalex.org/W2751756351","https://openalex.org/W2784270883","https://openalex.org/W2809395091","https://openalex.org/W2889555425","https://openalex.org/W2906627336","https://openalex.org/W2909055772","https://openalex.org/W2913059114","https://openalex.org/W2913092285","https://openalex.org/W2917906087","https://openalex.org/W2919818934","https://openalex.org/W2936578763","https://openalex.org/W2937935913","https://openalex.org/W2956131382","https://openalex.org/W2972499938","https://openalex.org/W2990650678","https://openalex.org/W3100157108","https://openalex.org/W4237944733","https://openalex.org/W4239510810","https://openalex.org/W4251391716","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W3180887190","https://openalex.org/W2320211095","https://openalex.org/W2308164565","https://openalex.org/W2062768126","https://openalex.org/W3003855012","https://openalex.org/W2059230675","https://openalex.org/W2347569454","https://openalex.org/W4241018400","https://openalex.org/W4211208557","https://openalex.org/W2135835957"],"abstract_inverted_index":{"In":[0,42,56],"ligand-based":[1],"virtual":[2],"screening,":[3],"high-throughput":[4],"screening":[5,164],"(HTS)":[6],"data":[7],"sets":[8],"can":[9,18,121,160],"be":[10,19],"exploited":[11],"to":[12,21,37,64,138],"train":[13],"classification":[14],"models.":[15],"Such":[16],"models":[17],"used":[20],"prioritize":[22],"yet":[23],"untested":[24],"molecules,":[25],"from":[26],"the":[27,38,91,163],"most":[28],"likely":[29,40],"active":[30,155],"(against":[31],"a":[32,45,85,98,126,145,167],"protein":[33],"target":[34],"of":[35,166],"interest)":[36],"least":[39],"active.":[41],"this":[43,158],"study,":[44],"single-parameter":[46],"ranking":[47],"method":[48],"with":[49,84,125],"an":[50,71,154],"Applicability":[51],"Domain":[52],"(AD)":[53],"is":[54,104,117],"proposed.":[55],"effect,":[57],"Kernel":[58],"Density":[59],"Estimates":[60],"(KDE)":[61],"are":[62,75,133],"revisited":[63],"improve":[65],"their":[66],"computational":[67],"efficiency":[68],"and":[69,88,136,175],"incorporate":[70],"AD.":[72,156],"Two":[73],"modifications":[74],"proposed:":[76],"(i)":[77],"using":[78,90],"vanishing":[79],"kernels":[80],"(i.e.,":[81],"kernel":[82],"functions":[83],"finite":[86],"support)":[87],"(ii)":[89],"Tanimoto":[92],"distance":[93],"between":[94],"molecular":[95],"fingerprints":[96],"as":[97],"radial":[99],"basis":[100],"function.":[101],"This":[102],"construction":[103],"termed":[105],"\"Vanishing":[106],"Ranking":[107],"Kernels\"":[108],"(VRK).":[109],"Using":[110],"VRK":[111,120,132,150,168],"on":[112],"21":[113],"HTS":[114],"assays,":[115],"it":[116],"shown":[118],"that":[119],"compete":[122],"in":[123],"performance":[124],"graph":[127],"convolutional":[128],"deep":[129],"neural":[130],"network.":[131],"conceptually":[134],"simple":[135],"fast":[137],"train.":[139],"During":[140],"training,":[141],"they":[142],"require":[143],"optimizing":[144],"single":[146],"parameter.":[147],"A":[148],"trained":[149],"model":[151],"usually":[152],"defines":[153],"Exploiting":[157],"AD":[159],"significantly":[161],"increase":[162],"frequency":[165],"model.":[169],"Software:":[170],"https://github.com/UnixJunkie/rankers.":[171],"Data":[172],"sets:":[173],"https://zenodo.org/record/1320776":[174],"https://zenodo.org/record/3540423.":[176]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
