{"id":"https://openalex.org/W2621574814","doi":"https://doi.org/10.1186/s12859-017-1660-6","title":"Predicting anatomic therapeutic chemical classification codes using tiered learning","display_name":"Predicting anatomic therapeutic chemical classification codes using tiered learning","publication_year":2017,"publication_date":"2017-06-01","ids":{"openalex":"https://openalex.org/W2621574814","doi":"https://doi.org/10.1186/s12859-017-1660-6","mag":"2621574814","pmid":"https://pubmed.ncbi.nlm.nih.gov/28617230"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-017-1660-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1660-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1660-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1660-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090307707","display_name":"Thomas Olson","orcid":null},"institutions":[{"id":"https://openalex.org/I71838634","display_name":"San Francisco State University","ror":"https://ror.org/05ykr0121","country_code":"US","type":"education","lineage":["https://openalex.org/I71838634"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas Olson","raw_affiliation_strings":["Department of Computer Science, San Francisco State University, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, San Francisco State University, San Francisco, CA, USA","institution_ids":["https://openalex.org/I71838634"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073550054","display_name":"Rahul Singh","orcid":"https://orcid.org/0000-0003-3900-4298"},"institutions":[{"id":"https://openalex.org/I4210157321","display_name":"Center for Discovery","ror":"https://ror.org/04jna0a58","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210157321"]},{"id":"https://openalex.org/I71838634","display_name":"San Francisco State University","ror":"https://ror.org/05ykr0121","country_code":"US","type":"education","lineage":["https://openalex.org/I71838634"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rahul Singh","raw_affiliation_strings":["Center for Discovery and Innovation in Parasitic Diseases, University of California, San Diego, CA, USA. rahul@sfsu.edu","Department of Computer Science, San Francisco State University, San Francisco, CA, USA. rahul@sfsu.edu","Department of Computer Science, San Francisco State University, San Francisco, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Discovery and Innovation in Parasitic Diseases, University of California, San Diego, CA, USA. rahul@sfsu.edu","institution_ids":["https://openalex.org/I4210157321"]},{"raw_affiliation_string":"Department of Computer Science, San Francisco State University, San Francisco, CA, USA. rahul@sfsu.edu","institution_ids":["https://openalex.org/I71838634"]},{"raw_affiliation_string":"Department of Computer Science, San Francisco State University, San Francisco, CA, USA","institution_ids":["https://openalex.org/I71838634"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5073550054"],"corresponding_institution_ids":["https://openalex.org/I4210157321","https://openalex.org/I71838634"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.9572,"has_fulltext":true,"cited_by_count":21,"citation_normalized_percentile":{"value":0.77425278,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"18","issue":"S8","first_page":"266","last_page":"266"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.8129000067710876,"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":0.8129000067710876,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.07270000129938126,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.029100000858306885,"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/generalizability-theory","display_name":"Generalizability theory","score":0.7807093858718872},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7076424956321716},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6730899214744568},{"id":"https://openalex.org/keywords/initialization","display_name":"Initialization","score":0.6358051896095276},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6076958775520325},{"id":"https://openalex.org/keywords/chemical-space","display_name":"Chemical space","score":0.5209338068962097},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.47949057817459106},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4716495871543884},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39935243129730225},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.1903461515903473},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.135686993598938},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10565093159675598},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09985750913619995}],"concepts":[{"id":"https://openalex.org/C27158222","wikidata":"https://www.wikidata.org/wiki/Q5532422","display_name":"Generalizability theory","level":2,"score":0.7807093858718872},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7076424956321716},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6730899214744568},{"id":"https://openalex.org/C114466953","wikidata":"https://www.wikidata.org/wiki/Q6034165","display_name":"Initialization","level":2,"score":0.6358051896095276},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6076958775520325},{"id":"https://openalex.org/C99726746","wikidata":"https://www.wikidata.org/wiki/Q906396","display_name":"Chemical space","level":3,"score":0.5209338068962097},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.47949057817459106},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4716495871543884},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39935243129730225},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.1903461515903473},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.135686993598938},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10565093159675598},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09985750913619995},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D004353","descriptor_name":"Drug Evaluation, Preclinical","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-017-1660-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1660-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1660-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28617230","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28617230","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:c5a5fa0436194d66ad3e0af775a9a4d4","is_oa":false,"landing_page_url":"https://doaj.org/article/c5a5fa0436194d66ad3e0af775a9a4d4","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 18, Iss S8, Pp 1-13 (2017)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4323916","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC5471942","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:5471942","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5471942","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-017-1660-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1660-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1660-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320309305","display_name":"San Francisco State University","ror":"https://ror.org/05ykr0121"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2621574814.pdf","grobid_xml":"https://content.openalex.org/works/W2621574814.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W1976582164","https://openalex.org/W1979537657","https://openalex.org/W1988037271","https://openalex.org/W2027958923","https://openalex.org/W2033377040","https://openalex.org/W2062941476","https://openalex.org/W2084267598","https://openalex.org/W2087064593","https://openalex.org/W2096021562","https://openalex.org/W2096541451","https://openalex.org/W2101234009","https://openalex.org/W2112243395","https://openalex.org/W2121604817","https://openalex.org/W2125251256","https://openalex.org/W2131347449","https://openalex.org/W2131987814","https://openalex.org/W2135732933","https://openalex.org/W2138745145","https://openalex.org/W2143792284","https://openalex.org/W2144119837","https://openalex.org/W2145578524","https://openalex.org/W2147405665","https://openalex.org/W2169678694","https://openalex.org/W2294516783","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W2973074952","https://openalex.org/W2594328795","https://openalex.org/W3183930479","https://openalex.org/W4320732452","https://openalex.org/W135095951","https://openalex.org/W3199987505","https://openalex.org/W4385760073","https://openalex.org/W4286980196","https://openalex.org/W2600435468","https://openalex.org/W2324927567"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1,23,60,123,139,150,205],"low":[2],"success":[3],"rate":[4],"and":[5,49,79,136,147,295],"high":[6],"cost":[7],"of":[8,14,20,58,66,72,97,106,110,118,131,167,176,194,207,218,224,234,246],"drug":[9,77,84],"discovery":[10],"requires":[11],"the":[12,55,103,107,111,116,119,171,174,177,212,235,244,258,261,273,285,293],"development":[13],"new":[15],"paradigms":[16],"to":[17,42,62,114,159,187,200,242,271],"identify":[18],"molecules":[19],"therapeutic":[21],"value.":[22],"Anatomical":[24],"Therapeutic":[25],"Chemical":[26],"(ATC)":[27],"Code":[28],"System":[29],"is":[30],"a":[31,88,129,192,231,254,280],"World":[32],"Health":[33],"Organization":[34],"(WHO)":[35],"proposed":[36,124],"classification":[37,148],"that":[38,100,166,182,214,249],"assigns":[39],"multi-level":[40],"codes":[41,65,99,248,259,278],"compounds":[43,67,132],"based":[44,283],"on":[45,102,284],"their":[46,201],"therapeutic,":[47],"pharmacological":[48],"chemical":[50,74,143],"characteristics":[51],"as":[52,54,83],"well":[53],"in-vivo":[56],"sites(s)":[57],"activity.":[59],"ability":[61],"predict":[63],"ATC":[64,98,112,236,277,286],"can":[68,239,250],"assist":[69],"in":[70,80,133,181,211],"creation":[71],"high-quality":[73],"libraries":[75],"for":[76,95,191,276,297],"screening":[78],"applications":[81],"such":[82],"repositioning.":[85],"We":[86],"propose":[87],"machine":[89,195],"learning":[90,94,156,179,196,267,274],"architecture":[91],"called":[92],"tiered":[93,155,178],"prediction":[96,104,151,189,294],"relies":[101],"results":[105],"higher":[108,289],"levels":[109,263],"code":[113,287],"simplify":[115],"predictions":[117],"lower":[120],"levels.":[121,290],"RESULTS:":[122],"approach":[125,209],"was":[126,157,185],"validated":[127],"using":[128],"number":[130],"both":[134],"cross-validation":[135],"test":[137],"setting.":[138],"validation":[140],"experiments":[141,172],"compared":[142,199],"descriptors,":[144],"initialization":[145],"methods":[146],"algorithms.":[149],"accuracy":[152],"obtained":[153],"with":[154],"found":[158,186],"be":[160,240,251],"either":[161],"comparable":[162],"or":[163],"better":[164],"than":[165],"established":[168],"methods.":[169],"Additionally,":[170],"demonstrated":[173],"generalizability":[175],"architecture,":[180],"its":[183],"use":[184],"improve":[188],"rates":[190],"majority":[193],"algorithms":[197],"when":[198],"stand-alone":[202],"application.":[203],"CONCLUSION:":[204],"basis":[206],"our":[208],"lies":[210],"observation":[213,270],"anatomical-therapeutic":[215],"biological":[216],"activity":[217],"certain":[219],"types":[220],"typically":[221],"precludes":[222],"activities":[223],"many":[225],"other":[226],"types.":[227],"Thus,":[228],"there":[229],"exists":[230],"characteristic":[232],"distribution":[233],"codes,":[237],"which":[238],"leveraged":[241],"limit":[243],"search-space":[245],"possible":[247],"ascribed":[252],"at":[253,260,279,288],"particular":[255,281],"level":[256,282],"once":[257],"preceding":[262],"are":[264],"known.":[265],"Tiered":[266],"utilizes":[268],"this":[269],"constrain":[272],"space":[275],"This":[291],"simplifies":[292],"allows":[296],"improved":[298],"accuracy.":[299]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
