{"id":"https://openalex.org/W4365150514","doi":"https://doi.org/10.1186/s13321-023-00713-z","title":"Investigation of chemical structure recognition by encoder\u2013decoder models in learning progress","display_name":"Investigation of chemical structure recognition by encoder\u2013decoder models in learning progress","publication_year":2023,"publication_date":"2023-04-12","ids":{"openalex":"https://openalex.org/W4365150514","doi":"https://doi.org/10.1186/s13321-023-00713-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/37046349"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-023-00713-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00713-z","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00713-z","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00713-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079497729","display_name":"Shumpei Nemoto","orcid":null},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Shumpei Nemoto","raw_affiliation_strings":["Department of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002472002","display_name":"Tadahaya Mizuno","orcid":"https://orcid.org/0000-0002-1638-602X"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tadahaya Mizuno","raw_affiliation_strings":["Department of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan. tadahaya@gmail.com","Department of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan. tadahaya@gmail.com","institution_ids":[]},{"raw_affiliation_string":"Department of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061014418","display_name":"Hiroyuki Kusuhara","orcid":"https://orcid.org/0000-0002-3641-8746"},"institutions":[{"id":"https://openalex.org/I74801974","display_name":"The University of Tokyo","ror":"https://ror.org/057zh3y96","country_code":"JP","type":"education","lineage":["https://openalex.org/I74801974"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiroyuki Kusuhara","raw_affiliation_strings":["Department of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Pharmaceutical Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan","institution_ids":["https://openalex.org/I74801974"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5079497729"],"corresponding_institution_ids":["https://openalex.org/I74801974"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":1.9434,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.87991636,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"15","issue":"1","first_page":"45","last_page":"45"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9987999796867371,"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":0.9987999796867371,"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/T12327","display_name":"Various Chemistry Research Topics","score":0.949999988079071,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7697338461875916},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.6301403045654297},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45547983050346375},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3835148215293884},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3486230671405792},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3225703835487366},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.07694536447525024}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7697338461875916},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.6301403045654297},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45547983050346375},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3835148215293884},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3486230671405792},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3225703835487366},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.07694536447525024}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-023-00713-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00713-z","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00713-z","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:37046349","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37046349","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 cheminformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10100163","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10100163","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10100163/pdf/13321_2023_Article_713.pdf","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":"J Cheminform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:40d03cbe96f44c5390ad2d9f6c8dd4cf","is_oa":true,"landing_page_url":"https://doaj.org/article/40d03cbe96f44c5390ad2d9f6c8dd4cf","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 15, Iss 1, Pp 1-9 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13321-023-00713-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-023-00713-z","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-023-00713-z","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"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":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2966590335","display_name":null,"funder_award_id":"JP22mk0101250h","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G3236194794","display_name":null,"funder_award_id":"Grant-in-Aid","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G3519797222","display_name":null,"funder_award_id":"KAKENHI Grant-in-Aid for Scientific Research (C)","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G399425797","display_name":null,"funder_award_id":"21K06663","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4120323150","display_name":"\u52b4\u50cd\u707d\u5bb3\u306b\u95a2\u3059\u308b\u793e\u4f1a\u7d4c\u6e08\u5b66\u7684\u306a\u3089\u3073\u306b\u52b4\u50cd\u79d1\u5b66\u7684\u7814\u7a76(\u7d992\u5e74)","funder_award_id":"10125","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4220906510","display_name":null,"funder_award_id":"Scientific Research (C)","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G4330101750","display_name":null,"funder_award_id":"KAKENHI Grant-in-Aid for Scientific","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7167128334","display_name":null,"funder_award_id":"Grant-in-Aid for Scientific Researc","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7337825077","display_name":null,"funder_award_id":"Grant-in-Aid for Sc","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G8109125745","display_name":null,"funder_award_id":"Grant-in-Aid for Scientific Research (C)","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G8759943101","display_name":null,"funder_award_id":"rant-in-Aid for Scientific Research","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G975188225","display_name":null,"funder_award_id":"KAKENHI","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"}],"funders":[{"id":"https://openalex.org/F4320311405","display_name":"Japan Agency for Medical Research and Development","ror":"https://ror.org/004rtk039"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4365150514.pdf"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1757990252","https://openalex.org/W1988037271","https://openalex.org/W2016589492","https://openalex.org/W2039183761","https://openalex.org/W2121604817","https://openalex.org/W2177317049","https://openalex.org/W2200017991","https://openalex.org/W2295598076","https://openalex.org/W2323328911","https://openalex.org/W2529996553","https://openalex.org/W2765224015","https://openalex.org/W2777416523","https://openalex.org/W2795631711","https://openalex.org/W2805002767","https://openalex.org/W2889326414","https://openalex.org/W2901476322","https://openalex.org/W2949676527","https://openalex.org/W2963223306","https://openalex.org/W2964199361","https://openalex.org/W2984339599","https://openalex.org/W2991736596","https://openalex.org/W2999309192","https://openalex.org/W3023204497","https://openalex.org/W3085821739","https://openalex.org/W3098254076","https://openalex.org/W3098269892","https://openalex.org/W3100358278","https://openalex.org/W3107551345","https://openalex.org/W3121462455","https://openalex.org/W3147675882","https://openalex.org/W3194368700","https://openalex.org/W3214740101","https://openalex.org/W4221062742","https://openalex.org/W4226159083","https://openalex.org/W4283586469","https://openalex.org/W6601517772"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W3046775127","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474"],"abstract_inverted_index":{"Descriptor":[0],"generation":[1,119],"methods":[2,95],"using":[3,87],"latent":[4],"representations":[5],"of":[6,17,20,41,51,80,100,112,141,157,180,192],"encoder-decoder":[7],"(ED)":[8],"models":[9,50,75,114],"with":[10,115],"SMILES":[11,116,181],"as":[12,117],"input":[13],"are":[14],"useful":[15],"because":[16],"the":[18,25,33,38,57,78,98,110,122,139,146,155,158,165,172,177],"continuity":[19],"descriptor":[21,118],"and":[22,55,62,83,132],"restorability":[23],"to":[24,108,138,175,185],"structure.":[26],"However,":[27],"it":[28],"is":[29,35,160,171],"not":[30,104],"clear":[31],"how":[32],"structure":[34,128,144,159],"recognized":[36],"in":[37,73,133],"learning":[39,53,63,136,178],"progress":[40,54,179],"ED":[42,49,74,113,183],"models.":[43],"In":[44],"this":[45,170],"work,":[46],"we":[47,125],"created":[48],"various":[52],"investigated":[56],"relationship":[58],"between":[59],"structural":[60],"information":[61],"progress.":[64],"We":[65],"showed":[66,126],"that":[67,92,127,153],"compound":[68],"substructures":[69],"were":[70],"learned":[71],"early":[72],"by":[76,182],"monitoring":[77],"accuracy":[79,99],"downstream":[81,101],"tasks":[82,102],"input-output":[84],"substructure":[85],"similarity":[86],"substructure-based":[88],"descriptors,":[89],"which":[90],"suggests":[91],"existing":[93],"evaluation":[94],"based":[96],"on":[97],"may":[103],"be":[105,151],"sensitive":[106],"enough":[107],"evaluate":[109],"performance":[111],"methods.":[120],"On":[121],"other":[123],"hand,":[124],"restoration":[129],"was":[130],"time-consuming,":[131],"particular,":[134],"insufficient":[135],"led":[137],"estimation":[140],"a":[142,161,189],"larger":[143],"than":[145],"actual":[147],"one.":[148],"It":[149],"can":[150],"inferred":[152],"determining":[154],"endpoint":[156],"difficult":[162],"task":[163],"for":[164,188],"model.":[166],"To":[167],"our":[168],"knowledge,":[169],"first":[173],"study":[174],"link":[176],"model":[184],"chemical":[186],"structures":[187],"wide":[190],"range":[191],"chemicals.":[193]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4}],"updated_date":"2026-04-22T08:38:42.863108","created_date":"2025-10-10T00:00:00"}
