{"id":"https://openalex.org/W4285737626","doi":"https://doi.org/10.1093/bib/bbac237","title":"Best practice and reproducible science are required to advance artificial intelligence in real-world applications","display_name":"Best practice and reproducible science are required to advance artificial intelligence in real-world applications","publication_year":2022,"publication_date":"2022-06-27","ids":{"openalex":"https://openalex.org/W4285737626","doi":"https://doi.org/10.1093/bib/bbac237","pmid":"https://pubmed.ncbi.nlm.nih.gov/35848999"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac237","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac237","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","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/A5049377184","display_name":"Zhichao Liu","orcid":"https://orcid.org/0000-0002-5376-9003"},"institutions":[{"id":"https://openalex.org/I1304557061","display_name":"National Center for Toxicological Research","ror":"https://ror.org/05jmhh281","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1304557061","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zhichao Liu","raw_affiliation_strings":["National Center for Toxicological Research, US Food and Drug Administration , Jefferson, AR, USA"],"raw_orcid":"https://orcid.org/0000-0002-5376-9003","affiliations":[{"raw_affiliation_string":"National Center for Toxicological Research, US Food and Drug Administration , Jefferson, AR, USA","institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100416903","display_name":"Ting Li","orcid":"https://orcid.org/0000-0003-2280-8433"},"institutions":[{"id":"https://openalex.org/I1304557061","display_name":"National Center for Toxicological Research","ror":"https://ror.org/05jmhh281","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1304557061","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ting Li","raw_affiliation_strings":["National Center for Toxicological Research, US Food and Drug Administration , Jefferson, AR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Toxicological Research, US Food and Drug Administration , Jefferson, AR, USA","institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089604233","display_name":"Skylar Connor","orcid":"https://orcid.org/0000-0002-3347-9180"},"institutions":[{"id":"https://openalex.org/I1304557061","display_name":"National Center for Toxicological Research","ror":"https://ror.org/05jmhh281","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1304557061","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Skylar Connor","raw_affiliation_strings":["National Center for Toxicological Research, US Food and Drug Administration , Jefferson, AR, USA"],"raw_orcid":"https://orcid.org/0000-0002-3347-9180","affiliations":[{"raw_affiliation_string":"National Center for Toxicological Research, US Food and Drug Administration , Jefferson, AR, USA","institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070704034","display_name":"Shraddha Thakkar","orcid":"https://orcid.org/0000-0002-2920-7713"},"institutions":[{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1333606569","display_name":"Center for Drug Evaluation and Research","ror":"https://ror.org/00yf3tm42","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070","https://openalex.org/I1333606569"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shraddha Thakkar","raw_affiliation_strings":["Center for Drug Evaluation and Research, US FDA , Silver Spring, MD 20993, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Drug Evaluation and Research, US FDA , Silver Spring, MD 20993, USA","institution_ids":["https://openalex.org/I1333606569","https://openalex.org/I1320320070"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046722857","display_name":"Ruth Roberts","orcid":"https://orcid.org/0000-0002-7763-7558"},"institutions":[{"id":"https://openalex.org/I79619799","display_name":"University of Birmingham","ror":"https://ror.org/03angcq70","country_code":"GB","type":"education","lineage":["https://openalex.org/I79619799"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ruth Roberts","raw_affiliation_strings":["ApconiX Ltd, Alderley Park , Alderley Edge, SK10 4TG, UK","University of Birmingham , Edgbaston, Birmingham, B15 2TT, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ApconiX Ltd, Alderley Park , Alderley Edge, SK10 4TG, UK","institution_ids":[]},{"raw_affiliation_string":"University of Birmingham , Edgbaston, Birmingham, B15 2TT, UK","institution_ids":["https://openalex.org/I79619799"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5068886380","display_name":"Weida Tong","orcid":"https://orcid.org/0000-0003-3488-6148"},"institutions":[{"id":"https://openalex.org/I1304557061","display_name":"National Center for Toxicological Research","ror":"https://ror.org/05jmhh281","country_code":"US","type":"facility","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1304557061","https://openalex.org/I1320320070"]},{"id":"https://openalex.org/I1320320070","display_name":"United States Food and Drug Administration","ror":"https://ror.org/034xvzb47","country_code":"US","type":"government","lineage":["https://openalex.org/I1299022934","https://openalex.org/I1320320070"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Weida Tong","raw_affiliation_strings":["National Center for Toxicological Research, US Food and Drug Administration , Jefferson, AR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Center for Toxicological Research, US Food and Drug Administration , Jefferson, AR, USA","institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5049377184","https://openalex.org/A5068886380"],"corresponding_institution_ids":["https://openalex.org/I1304557061","https://openalex.org/I1320320070"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.6034,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.70315966,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"23","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9987999796867371,"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/T10375","display_name":"Pharmacogenetics and Drug Metabolism","score":0.9933000206947327,"subfield":{"id":"https://openalex.org/subfields/3004","display_name":"Pharmacology"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.8764139413833618},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6592226624488831},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5381252765655518},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.5249190926551819},{"id":"https://openalex.org/keywords/test-set","display_name":"Test set","score":0.5077365636825562},{"id":"https://openalex.org/keywords/test","display_name":"Test (biology)","score":0.4891074299812317},{"id":"https://openalex.org/keywords/recall","display_name":"Recall","score":0.46685510873794556},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4636809229850769},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.45696112513542175},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4296693801879883},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3734568953514099},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14084026217460632},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.12034004926681519}],"concepts":[{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.8764139413833618},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6592226624488831},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5381252765655518},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.5249190926551819},{"id":"https://openalex.org/C169903167","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Test set","level":2,"score":0.5077365636825562},{"id":"https://openalex.org/C2777267654","wikidata":"https://www.wikidata.org/wiki/Q3519023","display_name":"Test (biology)","level":2,"score":0.4891074299812317},{"id":"https://openalex.org/C100660578","wikidata":"https://www.wikidata.org/wiki/Q18733","display_name":"Recall","level":2,"score":0.46685510873794556},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4636809229850769},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.45696112513542175},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4296693801879883},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3734568953514099},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14084026217460632},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.12034004926681519},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"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/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C180747234","wikidata":"https://www.wikidata.org/wiki/Q23373","display_name":"Cognitive psychology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056486","descriptor_name":"Chemical and Drug Induced Liver Injury","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056486","descriptor_name":"Chemical and Drug Induced Liver Injury","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056486","descriptor_name":"Chemical and Drug Induced Liver Injury","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac237","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac237","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35848999","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35848999","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.5699999928474426}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W12748326","https://openalex.org/W151461617","https://openalex.org/W1565605888","https://openalex.org/W1990506447","https://openalex.org/W2000660841","https://openalex.org/W2289901683","https://openalex.org/W2406493898","https://openalex.org/W2570760970","https://openalex.org/W3023042104","https://openalex.org/W3172904256","https://openalex.org/W4200013827","https://openalex.org/W6606223794"],"related_works":["https://openalex.org/W2358294942","https://openalex.org/W2003657145","https://openalex.org/W4367460280","https://openalex.org/W1999699871","https://openalex.org/W4225124612","https://openalex.org/W2043806667","https://openalex.org/W2021633306","https://openalex.org/W2006801911","https://openalex.org/W2033669961","https://openalex.org/W1972167985"],"abstract_inverted_index":{"Drug-induced":[0],"liver":[1],"injury":[2],"(DILI)":[3],"is":[4,98],"one":[5],"of":[6,108,118,131],"the":[7,105,111,126],"most":[8],"significant":[9],"concerns":[10],"in":[11,24,26,29,90,119],"medical":[12],"practice":[13],"but":[14],"yet":[15],"it":[16],"still":[17],"cannot":[18],"be":[19],"fully":[20],"recapitulated":[21],"with":[22],"existing":[23],"vivo,":[25],"vitro":[27],"and":[28,68,76,88,110,113,139,142,144],"silico":[30,91,120],"approaches.":[31],"To":[32],"address":[33],"this":[34,116,123],"challenge,":[35],"Chen":[36],"et":[37],"al.":[38],"[":[39],"1]":[40],"developed":[41],"a":[42,80],"deep":[43],"learning-based":[44],"DILI":[45,92,109],"prediction":[46,60],"model":[47,56,96,137,145],"based":[48],"on":[49,79],"chemical":[50],"structure":[51],"information":[52],"alone.":[53],"The":[54],"reported":[55],"yielded":[57],"an":[58],"outstanding":[59],"performance":[61,97],"(i.e.":[62],"0.958,":[63],"0.976,":[64],"0.935,":[65],"0.947,":[66],"0.926":[67],"0.913":[69],"for":[70],"AUC,":[71],"accuracy,":[72],"recall,":[73],"precision,":[74],"F1-score":[75],"specificity,":[77],"respectively,":[78],"test":[81],"set),":[82],"far":[83],"outperforming":[84],"all":[85],"publicly":[86],"available":[87],"similar":[89],"models.":[93],"This":[94],"extraordinary":[95],"counter-intuitive":[99],"to":[100,125],"what":[101],"we":[102,128],"know":[103],"about":[104],"underlying":[106],"biology":[107],"principles":[112],"hypothesis":[114],"behind":[115],"type":[117],"approach.":[121],"In":[122],"Letter":[124],"Editor,":[127],"raise":[129],"awareness":[130],"several":[132],"issues":[133],"concerning":[134],"data":[135,143],"curation,":[136],"validation":[138],"comparison":[140],"practices,":[141],"reproducibility.":[146]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2023,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
