{"id":"https://openalex.org/W4293372952","doi":"https://doi.org/10.1093/bib/bbac346","title":"Identifying the kind behind SMILES\u2014anatomical therapeutic chemical classification using structure-only representations","display_name":"Identifying the kind behind SMILES\u2014anatomical therapeutic chemical classification using structure-only representations","publication_year":2022,"publication_date":"2022-08-26","ids":{"openalex":"https://openalex.org/W4293372952","doi":"https://doi.org/10.1093/bib/bbac346","pmid":"https://pubmed.ncbi.nlm.nih.gov/36027578"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac346","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac346","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/A5020690901","display_name":"Yi Cao","orcid":"https://orcid.org/0000-0002-1279-5491"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi Cao","raw_affiliation_strings":["Department of Computer Science, Sichuan University , 610065, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Sichuan University , 610065, Chengdu, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110933223","display_name":"Zhen-Qun Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Zhen-Qun Yang","raw_affiliation_strings":["Department of Biomedical Engineering, Chinese University of Hong Kong , Street, Shatin, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Chinese University of Hong Kong , Street, Shatin, Hong Kong","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089910828","display_name":"Xu-Lu Zhang","orcid":"https://orcid.org/0000-0003-2473-460X"},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xu-Lu Zhang","raw_affiliation_strings":["Department of Computer Science, Sichuan University , 610065, Chengdu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Sichuan University , 610065, Chengdu, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043696243","display_name":"Wenqi Fan","orcid":"https://orcid.org/0000-0002-4049-1233"},"institutions":[{"id":"https://openalex.org/I14243506","display_name":"Hong Kong Polytechnic University","ror":"https://ror.org/0030zas98","country_code":"HK","type":"education","lineage":["https://openalex.org/I14243506"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Wenqi Fan","raw_affiliation_strings":["Department of Computing, Hong Kong Polytechnic University , Kowloon, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computing, Hong Kong Polytechnic University , Kowloon, Hong Kong","institution_ids":["https://openalex.org/I14243506"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100631214","display_name":"Yaowei Wang","orcid":"https://orcid.org/0000-0002-7853-1587"},"institutions":[{"id":"https://openalex.org/I4210136793","display_name":"Peng Cheng Laboratory","ror":"https://ror.org/03qdqbt06","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210136793"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yaowei Wang","raw_affiliation_strings":["Peng Cheng Laboratory , 518000, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Peng Cheng Laboratory , 518000, Shenzhen, China","institution_ids":["https://openalex.org/I4210136793"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033886406","display_name":"Jiajun Shen","orcid":"https://orcid.org/0000-0002-5042-0201"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jiajun Shen","raw_affiliation_strings":["TCL AI Research Institute , Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TCL AI Research Institute , Hong Kong","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041491902","display_name":"Dong\u2010Qing Wei","orcid":"https://orcid.org/0000-0003-4200-7502"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dong-Qing Wei","raw_affiliation_strings":["School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100404176","display_name":"Qing Li","orcid":"https://orcid.org/0000-0003-3370-471X"},"institutions":[{"id":"https://openalex.org/I14243506","display_name":"Hong Kong Polytechnic University","ror":"https://ror.org/0030zas98","country_code":"HK","type":"education","lineage":["https://openalex.org/I14243506"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Qing Li","raw_affiliation_strings":["Department of Computing, Hong Kong Polytechnic University , Kowloon, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computing, Hong Kong Polytechnic University , Kowloon, Hong Kong","institution_ids":["https://openalex.org/I14243506"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064374603","display_name":"Xiao-Yong Wei","orcid":"https://orcid.org/0000-0002-5706-5177"},"institutions":[{"id":"https://openalex.org/I14243506","display_name":"Hong Kong Polytechnic University","ror":"https://ror.org/0030zas98","country_code":"HK","type":"education","lineage":["https://openalex.org/I14243506"]},{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN","HK"],"is_corresponding":true,"raw_author_name":"Xiao-Yong Wei","raw_affiliation_strings":["Department of Computer Science, Sichuan University , 610065, Chengdu, China","Department of Computing, Hong Kong Polytechnic University , Kowloon, Hong Kong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Sichuan University , 610065, Chengdu, China","institution_ids":["https://openalex.org/I24185976"]},{"raw_affiliation_string":"Department of Computing, Hong Kong Polytechnic University , Kowloon, Hong Kong","institution_ids":["https://openalex.org/I14243506"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5064374603"],"corresponding_institution_ids":["https://openalex.org/I14243506","https://openalex.org/I24185976"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":1.37,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.83194597,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"23","issue":"5","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":0.9997000098228455,"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":0.9997000098228455,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9980000257492065,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9556000232696533,"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":0.8038195967674255},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.7572930455207825},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.6065307855606079},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.592682957649231},{"id":"https://openalex.org/keywords/pyramid","display_name":"Pyramid (geometry)","score":0.5421029925346375},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5381795763969421},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5287943482398987},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.46461570262908936},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.39999473094940186},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07714325189590454}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8038195967674255},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.7572930455207825},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.6065307855606079},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.592682957649231},{"id":"https://openalex.org/C142575187","wikidata":"https://www.wikidata.org/wiki/Q3358290","display_name":"Pyramid (geometry)","level":2,"score":0.5421029925346375},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5381795763969421},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5287943482398987},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.46461570262908936},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39999473094940186},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07714325189590454},{"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/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D010865","descriptor_name":"Pilot Projects","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010865","descriptor_name":"Pilot Projects","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010865","descriptor_name":"Pilot Projects","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":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbac346","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbac346","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:36027578","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36027578","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/16","display_name":"Peace, Justice and strong institutions","score":0.5699999928474426}],"awards":[{"id":"https://openalex.org/G450452401","display_name":null,"funder_award_id":"P0036200","funder_id":"https://openalex.org/F4320322598","funder_display_name":"Hong Kong Polytechnic University"},{"id":"https://openalex.org/G7891390100","display_name":null,"funder_award_id":"61872256","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322598","display_name":"Hong Kong Polytechnic University","ror":"https://ror.org/0030zas98"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1975147762","https://openalex.org/W1976582164","https://openalex.org/W1978394996","https://openalex.org/W2013196554","https://openalex.org/W2034070267","https://openalex.org/W2044834685","https://openalex.org/W2068632118","https://openalex.org/W2096021562","https://openalex.org/W2114850508","https://openalex.org/W2120026469","https://openalex.org/W2125251256","https://openalex.org/W2138745145","https://openalex.org/W2147405665","https://openalex.org/W2161621183","https://openalex.org/W2200017991","https://openalex.org/W2294516783","https://openalex.org/W2530181556","https://openalex.org/W2595626209","https://openalex.org/W2607357445","https://openalex.org/W2607532780","https://openalex.org/W2772308895","https://openalex.org/W2896506587","https://openalex.org/W2900713360","https://openalex.org/W2914757825","https://openalex.org/W2930957955","https://openalex.org/W2947423323","https://openalex.org/W2950955377","https://openalex.org/W2965979634","https://openalex.org/W2970764640","https://openalex.org/W2973114758","https://openalex.org/W2975087811","https://openalex.org/W2979645924","https://openalex.org/W2986232138","https://openalex.org/W2989615256","https://openalex.org/W2999143619","https://openalex.org/W3012446587","https://openalex.org/W3022199064","https://openalex.org/W3096828292","https://openalex.org/W3097145107","https://openalex.org/W3103092523","https://openalex.org/W3137198614","https://openalex.org/W3190923190","https://openalex.org/W3192945554","https://openalex.org/W3196214900","https://openalex.org/W4205241946","https://openalex.org/W4286908162","https://openalex.org/W4293508416","https://openalex.org/W4294170691","https://openalex.org/W6644458826","https://openalex.org/W6682691769","https://openalex.org/W6746779403","https://openalex.org/W6755619182","https://openalex.org/W6770131888","https://openalex.org/W6802795467"],"related_works":["https://openalex.org/W2366107444","https://openalex.org/W2378211422","https://openalex.org/W4388145910","https://openalex.org/W1976205134","https://openalex.org/W2381570729","https://openalex.org/W2745001401","https://openalex.org/W4248336175","https://openalex.org/W4321353415","https://openalex.org/W3009369890","https://openalex.org/W2031260042"],"abstract_inverted_index":{"Anatomical":[0],"Therapeutic":[1],"Chemical":[2],"(ATC)":[3],"classification":[4],"for":[5,77],"compounds/drugs":[6],"plays":[7],"an":[8],"important":[9],"role":[10],"in":[11,107,122,164,175,180],"drug":[12,73],"development":[13],"and":[14,80,135,138,142,177,191],"basic":[15],"research.":[16],"However,":[17],"previous":[18,108],"methods":[19,172],"depend":[20,31],"on":[21,32,51,62],"interactions":[22],"extracted":[23],"from":[24],"STITCH":[25],"dataset":[26],"which":[27,98],"may":[28],"make":[29,185],"it":[30,126,168],"lab":[33,65],"experiments.":[34],"We":[35,184],"present":[36],"a":[37,72,91,130,143,148],"pilot":[38],"study":[39],"to":[40,58,153,195],"explore":[41],"the":[42,46,52,60,63,69,83,104,123,165,170,186,197],"possibility":[43],"of":[44,71,95,129,150,182,199],"conducting":[45],"ATC":[47],"prediction":[48,112],"solely":[49],"based":[50],"molecular":[53],"structures.":[54],"The":[55,116],"motivation":[56],"is":[57,99,114,118,127],"eliminate":[59],"reliance":[61],"costly":[64],"experiments":[66,166],"so":[67],"that":[68,125,133],"characteristics":[70],"can":[74],"be":[75],"pre-assessed":[76],"better":[78,120],"decision-making":[79],"effort-saving":[81],"before":[82],"actual":[84],"development.":[85],"To":[86],"this":[87,200],"end,":[88],"we":[89],"construct":[90],"new":[92],"benchmark":[93,187],"consisting":[94],"4545":[96],"compounds":[97],"with":[100,119],"larger":[101],"scale":[102],"than":[103],"one":[105],"used":[106],"study.":[109,201],"A":[110],"light-weight":[111],"model":[113,117],"proposed.":[115],"explainability":[121],"sense":[124],"consists":[128],"straightforward":[131],"tokenization":[132],"extracts":[134],"embeds":[136],"statistically":[137],"physicochemically":[139],"meaningful":[140],"tokens,":[141],"deep":[144],"network":[145],"backed":[146],"by":[147,173,178],"set":[149],"pyramid":[151],"kernels":[152],"capture":[154],"multi-resolution":[155],"chemical":[156],"structural":[157],"characteristics.":[158],"Its":[159],"efficacy":[160],"has":[161],"been":[162],"validated":[163],"where":[167],"outperforms":[169],"state-of-the-art":[171],"15.53%":[174],"accuracy":[176],"69.66%":[179],"terms":[181],"efficiency.":[183],"dataset,":[188],"source":[189],"code":[190],"web":[192],"server":[193],"open":[194],"ease":[196],"reproduction":[198]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
