{"id":"https://openalex.org/W3203480730","doi":"https://doi.org/10.1093/bib/bbab393","title":"Representation of molecules for drug response prediction","display_name":"Representation of molecules for drug response prediction","publication_year":2021,"publication_date":"2021-09-08","ids":{"openalex":"https://openalex.org/W3203480730","doi":"https://doi.org/10.1093/bib/bbab393","mag":"3203480730","pmid":"https://pubmed.ncbi.nlm.nih.gov/34571534"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab393","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab393","pdf_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab393/42230501/bbab393.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab393/42230501/bbab393.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060352086","display_name":"Xin An","orcid":"https://orcid.org/0000-0003-0683-5511"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xin An","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100330043","display_name":"Xi Chen","orcid":"https://orcid.org/0000-0003-3459-4217"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xi Chen","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016691617","display_name":"Daiyao Yi","orcid":null},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daiyao Yi","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112506417","display_name":"Hongyang Li","orcid":null},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hongyang Li","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011032655","display_name":"Yuanfang Guan","orcid":"https://orcid.org/0000-0001-8275-2852"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuanfang Guan","raw_affiliation_strings":["Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, USA"],"raw_orcid":"https://orcid.org/0000-0001-8275-2852","affiliations":[{"raw_affiliation_string":"Department of Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, MI, USA","institution_ids":["https://openalex.org/I27837315"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5112506417"],"corresponding_institution_ids":["https://openalex.org/I27837315"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":4.3511,"has_fulltext":true,"cited_by_count":56,"citation_normalized_percentile":{"value":0.9497183,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"23","issue":"1","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":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":0.9976999759674072,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9972000122070312,"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/representation","display_name":"Representation (politics)","score":0.7174572944641113},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.6170397400856018},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5423899292945862},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4176425635814667},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4072178602218628},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.16343459486961365},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.16036471724510193},{"id":"https://openalex.org/keywords/political-science","display_name":"Political science","score":0.060450077056884766}],"concepts":[{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.7174572944641113},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.6170397400856018},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5423899292945862},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4176425635814667},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4072178602218628},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.16343459486961365},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.16036471724510193},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.060450077056884766},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","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":"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":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbab393","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab393","pdf_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab393/42230501/bbab393.pdf","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:34571534","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34571534","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},{"id":"pmh:oai:pubmedcentral.nih.gov:8769696","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8769696","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbab393","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab393","pdf_url":"https://academic.oup.com/bib/article-pdf/23/1/bbab393/42230501/bbab393.pdf","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"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.7099999785423279}],"awards":[{"id":"https://openalex.org/G1641753078","display_name":null,"funder_award_id":"R35GM133346","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5098683201","display_name":null,"funder_award_id":"R35GM133346-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8392768535","display_name":null,"funder_award_id":"R35 GM133346","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8979743913","display_name":null,"funder_award_id":"#1452656","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3203480730.pdf","grobid_xml":"https://content.openalex.org/works/W3203480730.grobid-xml"},"referenced_works_count":114,"referenced_works":["https://openalex.org/W1508604947","https://openalex.org/W1975875968","https://openalex.org/W1988037271","https://openalex.org/W2031372687","https://openalex.org/W2043398720","https://openalex.org/W2080635178","https://openalex.org/W2096541451","https://openalex.org/W2108933868","https://openalex.org/W2119512897","https://openalex.org/W2125789330","https://openalex.org/W2129860849","https://openalex.org/W2159940675","https://openalex.org/W2170973067","https://openalex.org/W2175970000","https://openalex.org/W2200017991","https://openalex.org/W2267040404","https://openalex.org/W2290847742","https://openalex.org/W2517536022","https://openalex.org/W2528161821","https://openalex.org/W2569335714","https://openalex.org/W2594183968","https://openalex.org/W2604272474","https://openalex.org/W2604296437","https://openalex.org/W2606780347","https://openalex.org/W2730223999","https://openalex.org/W2775061087","https://openalex.org/W2787055278","https://openalex.org/W2792791113","https://openalex.org/W2805399276","https://openalex.org/W2807021761","https://openalex.org/W2807463161","https://openalex.org/W2811201370","https://openalex.org/W2883248903","https://openalex.org/W2896457183","https://openalex.org/W2899057363","https://openalex.org/W2900516335","https://openalex.org/W2901246787","https://openalex.org/W2903198840","https://openalex.org/W2904147875","https://openalex.org/W2906092989","https://openalex.org/W2906797579","https://openalex.org/W2907492528","https://openalex.org/W2914721378","https://openalex.org/W2921591500","https://openalex.org/W2942173509","https://openalex.org/W2944974555","https://openalex.org/W2946099214","https://openalex.org/W2948035163","https://openalex.org/W2949159188","https://openalex.org/W2950182476","https://openalex.org/W2951449549","https://openalex.org/W2955385017","https://openalex.org/W2960677646","https://openalex.org/W2962711740","https://openalex.org/W2962764460","https://openalex.org/W2963028280","https://openalex.org/W2963046727","https://openalex.org/W2964015378","https://openalex.org/W2964113829","https://openalex.org/W2964677890","https://openalex.org/W2965750004","https://openalex.org/W2968734407","https://openalex.org/W2971933740","https://openalex.org/W2980264739","https://openalex.org/W2981742563","https://openalex.org/W2994958138","https://openalex.org/W2995175648","https://openalex.org/W2995884357","https://openalex.org/W3000373012","https://openalex.org/W3001022866","https://openalex.org/W3004984396","https://openalex.org/W3005505802","https://openalex.org/W3006302308","https://openalex.org/W3018302085","https://openalex.org/W3023204497","https://openalex.org/W3032089175","https://openalex.org/W3035302862","https://openalex.org/W3036576513","https://openalex.org/W3041266166","https://openalex.org/W3042826782","https://openalex.org/W3047749858","https://openalex.org/W3048965072","https://openalex.org/W3083874242","https://openalex.org/W3087318293","https://openalex.org/W3090947871","https://openalex.org/W3092034553","https://openalex.org/W3094540299","https://openalex.org/W3095329356","https://openalex.org/W3100157108","https://openalex.org/W3100537819","https://openalex.org/W3100848837","https://openalex.org/W3116202926","https://openalex.org/W3116278528","https://openalex.org/W3130891725","https://openalex.org/W3131450843","https://openalex.org/W3138781613","https://openalex.org/W3139532774","https://openalex.org/W3166272013","https://openalex.org/W4210257598","https://openalex.org/W4289436753","https://openalex.org/W6726873649","https://openalex.org/W6736161267","https://openalex.org/W6736685754","https://openalex.org/W6754929296","https://openalex.org/W6755207826","https://openalex.org/W6756216553","https://openalex.org/W6756950626","https://openalex.org/W6758930985","https://openalex.org/W6763653667","https://openalex.org/W6769353078","https://openalex.org/W6772452955","https://openalex.org/W6773640581","https://openalex.org/W6775553191","https://openalex.org/W6947950241"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W3204019825"],"abstract_inverted_index":{"The":[0],"rapid":[1],"development":[2],"of":[3,18,59,80,93,114,118],"machine":[4,29,60],"learning":[5,8,30,61],"and":[6,84,103],"deep":[7],"algorithms":[9],"in":[10,21,37,62],"the":[11,26,57,78,115],"recent":[12],"decade":[13],"has":[14,31],"spurred":[15],"an":[16],"outburst":[17],"their":[19,101],"applications":[20],"many":[22],"research":[23],"fields.":[24],"In":[25],"chemistry":[27],"domain,":[28],"been":[32],"widely":[33],"used":[34,95],"to":[35,56,77],"aid":[36],"drug":[38,40,63,81],"screening,":[39],"toxicity":[41],"prediction,":[42,46,50],"quantitative":[43],"structure-activity":[44],"relationship":[45],"anti-cancer":[47],"synergy":[48],"score":[49],"etc.":[51],"This":[52,106],"review":[53,107],"is":[54,73],"dedicated":[55],"application":[58,104],"response":[64,82],"prediction.":[65],"Specifically,":[66],"we":[67],"focus":[68],"on":[69],"molecular":[70,96,119],"representations,":[71],"which":[72],"a":[74,111],"crucial":[75],"element":[76],"success":[79],"prediction":[83,87],"other":[85],"chemistry-related":[86],"tasks.":[88],"We":[89],"introduce":[90],"three":[91],"types":[92],"commonly":[94],"representation":[97],"methods,":[98],"together":[99],"with":[100],"implementation":[102],"examples.":[105],"will":[108],"serve":[109],"as":[110],"brief":[112],"introduction":[113],"broad":[116],"field":[117],"representations.":[120]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":20},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
