{"id":"https://openalex.org/W4390205041","doi":"https://doi.org/10.26599/bdma.2023.9020009","title":"Molecular Generation and Optimization of Molecular Properties Using a Transformer Model","display_name":"Molecular Generation and Optimization of Molecular Properties Using a Transformer Model","publication_year":2023,"publication_date":"2023-12-25","ids":{"openalex":"https://openalex.org/W4390205041","doi":"https://doi.org/10.26599/bdma.2023.9020009"},"language":"en","primary_location":{"id":"doi:10.26599/bdma.2023.9020009","is_oa":true,"landing_page_url":"https://doi.org/10.26599/bdma.2023.9020009","pdf_url":"https://ieeexplore.ieee.org/ielx7/8254253/10372994/10373001.pdf","source":{"id":"https://openalex.org/S4210209060","display_name":"Big Data Mining and Analytics","issn_l":"2096-0654","issn":["2096-0654"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311901","host_organization_name":"Tsinghua University Press","host_organization_lineage":["https://openalex.org/P4310311901"],"host_organization_lineage_names":["Tsinghua University Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Big Data Mining and Analytics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://ieeexplore.ieee.org/ielx7/8254253/10372994/10373001.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102641220","display_name":"Zhongyin Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I88830068","display_name":"Shaanxi Normal University","ror":"https://ror.org/0170z8493","country_code":"CN","type":"education","lineage":["https://openalex.org/I88830068"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhongyin Xu","raw_affiliation_strings":["School of Computer Science, Shaanxi Normal University,Xi&#x0027;an,China,710119"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Shaanxi Normal University,Xi&#x0027;an,China,710119","institution_ids":["https://openalex.org/I88830068"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058768577","display_name":"Xiujuan Lei","orcid":"https://orcid.org/0000-0002-9901-1732"},"institutions":[{"id":"https://openalex.org/I88830068","display_name":"Shaanxi Normal University","ror":"https://ror.org/0170z8493","country_code":"CN","type":"education","lineage":["https://openalex.org/I88830068"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiujuan Lei","raw_affiliation_strings":["School of Computer Science, Shaanxi Normal University,Xi&#x0027;an,China,710119"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Shaanxi Normal University,Xi&#x0027;an,China,710119","institution_ids":["https://openalex.org/I88830068"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100544225","display_name":"Mei Ma","orcid":null},"institutions":[{"id":"https://openalex.org/I88830068","display_name":"Shaanxi Normal University","ror":"https://ror.org/0170z8493","country_code":"CN","type":"education","lineage":["https://openalex.org/I88830068"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mei Ma","raw_affiliation_strings":["School of Computer Science, Shaanxi Normal University,Xi&#x0027;an,China,710119"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Shaanxi Normal University,Xi&#x0027;an,China,710119","institution_ids":["https://openalex.org/I88830068"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101465265","display_name":"Yi Pan","orcid":"https://orcid.org/0000-0002-2766-3096"},"institutions":[{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi Pan","raw_affiliation_strings":["Shenzhen Institute of Advanced Technology,Faculty of Computer Science and Control Engineering,Chinese Academy of Sciences,Shenzhen,China,518055"],"affiliations":[{"raw_affiliation_string":"Shenzhen Institute of Advanced Technology,Faculty of Computer Science and Control Engineering,Chinese Academy of Sciences,Shenzhen,China,518055","institution_ids":["https://openalex.org/I4210145761","https://openalex.org/I19820366"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5102641220"],"corresponding_institution_ids":["https://openalex.org/I88830068"],"apc_list":null,"apc_paid":null,"fwci":2.5297,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.91446779,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"7","issue":"1","first_page":"142","last_page":"155"},"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9954000115394592,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.6809401512145996},{"id":"https://openalex.org/keywords/solubility","display_name":"Solubility","score":0.6015073657035828},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.5675190687179565},{"id":"https://openalex.org/keywords/encode","display_name":"ENCODE","score":0.5413560271263123},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.5288318991661072},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4641519784927368},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.39071330428123474},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2416868507862091},{"id":"https://openalex.org/keywords/voltage","display_name":"Voltage","score":0.11125335097312927},{"id":"https://openalex.org/keywords/organic-chemistry","display_name":"Organic chemistry","score":0.0884363055229187},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08599728345870972},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08445408940315247}],"concepts":[{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.6809401512145996},{"id":"https://openalex.org/C155574463","wikidata":"https://www.wikidata.org/wiki/Q170731","display_name":"Solubility","level":2,"score":0.6015073657035828},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.5675190687179565},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.5413560271263123},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.5288318991661072},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4641519784927368},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.39071330428123474},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2416868507862091},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.11125335097312927},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0884363055229187},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08599728345870972},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08445408940315247},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","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}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.26599/bdma.2023.9020009","is_oa":true,"landing_page_url":"https://doi.org/10.26599/bdma.2023.9020009","pdf_url":"https://ieeexplore.ieee.org/ielx7/8254253/10372994/10373001.pdf","source":{"id":"https://openalex.org/S4210209060","display_name":"Big Data Mining and Analytics","issn_l":"2096-0654","issn":["2096-0654"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311901","host_organization_name":"Tsinghua University Press","host_organization_lineage":["https://openalex.org/P4310311901"],"host_organization_lineage_names":["Tsinghua University Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Big Data Mining and Analytics","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:d8b0e9f8a84f4fd4aa2e1221577e300a","is_oa":true,"landing_page_url":"https://doaj.org/article/d8b0e9f8a84f4fd4aa2e1221577e300a","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":"Big Data Mining and Analytics, Vol 7, Iss 1, Pp 142-155 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.26599/bdma.2023.9020009","is_oa":true,"landing_page_url":"https://doi.org/10.26599/bdma.2023.9020009","pdf_url":"https://ieeexplore.ieee.org/ielx7/8254253/10372994/10373001.pdf","source":{"id":"https://openalex.org/S4210209060","display_name":"Big Data Mining and Analytics","issn_l":"2096-0654","issn":["2096-0654"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311901","host_organization_name":"Tsinghua University Press","host_organization_lineage":["https://openalex.org/P4310311901"],"host_organization_lineage_names":["Tsinghua University Press"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Big Data Mining and Analytics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G450443699","display_name":null,"funder_award_id":"61972451","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4785461891","display_name":null,"funder_award_id":"U22A2041","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6311684539","display_name":null,"funder_award_id":"202204","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6579278899","display_name":null,"funder_award_id":"62272288","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"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390205041.pdf","grobid_xml":"https://content.openalex.org/works/W4390205041.grobid-xml"},"referenced_works_count":53,"referenced_works":["https://openalex.org/W1583912456","https://openalex.org/W1975147762","https://openalex.org/W1997764055","https://openalex.org/W2020859943","https://openalex.org/W2023818227","https://openalex.org/W2034549041","https://openalex.org/W2087563523","https://openalex.org/W2096541451","https://openalex.org/W2529996553","https://openalex.org/W2578240541","https://openalex.org/W2618625858","https://openalex.org/W2765224015","https://openalex.org/W2768118983","https://openalex.org/W2793945656","https://openalex.org/W2803615944","https://openalex.org/W2805002767","https://openalex.org/W2887447356","https://openalex.org/W2900090807","https://openalex.org/W2900694120","https://openalex.org/W2963609389","https://openalex.org/W2964308564","https://openalex.org/W2966357564","https://openalex.org/W2997058986","https://openalex.org/W3009321976","https://openalex.org/W3045928028","https://openalex.org/W3087716567","https://openalex.org/W3100358278","https://openalex.org/W3112113844","https://openalex.org/W3116865743","https://openalex.org/W3209056694","https://openalex.org/W3209708391","https://openalex.org/W4212815277","https://openalex.org/W4220802400","https://openalex.org/W4221138292","https://openalex.org/W4225983336","https://openalex.org/W4229590462","https://openalex.org/W4236316962","https://openalex.org/W4284898351","https://openalex.org/W4289436753","https://openalex.org/W4289761690","https://openalex.org/W4297796727","https://openalex.org/W4297798428","https://openalex.org/W4385245566","https://openalex.org/W6635084905","https://openalex.org/W6679434410","https://openalex.org/W6714644935","https://openalex.org/W6733974131","https://openalex.org/W6737665993","https://openalex.org/W6738599175","https://openalex.org/W6747927160","https://openalex.org/W6752245542","https://openalex.org/W6752910514","https://openalex.org/W6804214328"],"related_works":["https://openalex.org/W2468279273","https://openalex.org/W2354198838","https://openalex.org/W1989130879","https://openalex.org/W2103419012","https://openalex.org/W1990608904","https://openalex.org/W1539400370","https://openalex.org/W2988126442","https://openalex.org/W1974414866","https://openalex.org/W2007219878","https://openalex.org/W1934224411"],"abstract_inverted_index":{"Generating":[0],"novel":[1],"molecules":[2,160,175],"to":[3,31,39,82,101,123,155,158,176],"satisfy":[4,40,177],"specific":[5,21,37,42,84,162,178],"properties":[6,34,43],"is":[7],"a":[8,20,36,83,90],"challenging":[9],"task":[10],"in":[11,78,126],"modern":[12],"drug":[13],"discovery,":[14],"which":[15,53],"requires":[16],"the":[17,33,41,45,55,70,79,87,110,114,118,127,138,150,167,173],"optimization":[18,71],"of":[19,35,44,89,120],"objective":[22],"based":[23,116],"on":[24,117],"satisfying":[25],"chemical":[26],"rules.":[27],"Herein,":[28],"we":[29,112],"aim":[30],"optimize":[32,172],"molecule":[38],"generated":[46],"molecule.":[47],"The":[48,73],"Matched":[49],"Molecular":[50],"Pairs":[51],"(MMPs),":[52],"contain":[54],"source":[56,174],"and":[57,63,65,95,104,129,134,141],"target":[58],"molecules,":[59],"are":[60,67,98,147],"used":[61,100],"herein,":[62],"logD":[64,103],"solubility":[66,105],"selected":[68],"as":[69,137],"properties.":[72,163,179],"main":[74],"innovative":[75],"work":[76],"lies":[77],"calculation":[80],"related":[81],"transformer":[85,168],"from":[86],"perspective":[88],"matrix":[91],"dimension.":[92],"Threshold":[93],"intervals":[94],"state":[96],"changes":[97],"then":[99],"encode":[102],"for":[106],"subsequent":[107],"tests.":[108],"During":[109],"experiments,":[111],"screen":[113],"data":[115],"proportion":[119],"heavy":[121],"atoms":[122,125],"all":[124],"groups":[128],"select":[130],"12":[131],"365,":[132],"1503,":[133],"1570":[135],"MMPs":[136],"training,":[139],"validation,":[140],"test":[142],"sets,":[143],"respectively.":[144],"Transformer":[145],"models":[146,152],"compared":[148],"with":[149,153,161],"baseline":[151],"respect":[154],"their":[156],"abilities":[157],"generate":[159],"Results":[164],"show":[165],"that":[166],"model":[169],"can":[170],"accurately":[171]},"counts_by_year":[{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":5}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
