{"id":"https://openalex.org/W4385784138","doi":"https://doi.org/10.1007/s10489-023-04915-8","title":"SELF-EdiT: Structure-constrained molecular optimisation using SELFIES editing transformer","display_name":"SELF-EdiT: Structure-constrained molecular optimisation using SELFIES editing transformer","publication_year":2023,"publication_date":"2023-08-12","ids":{"openalex":"https://openalex.org/W4385784138","doi":"https://doi.org/10.1007/s10489-023-04915-8"},"language":"en","primary_location":{"id":"doi:10.1007/s10489-023-04915-8","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10489-023-04915-8","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10489-023-04915-8.pdf","source":{"id":"https://openalex.org/S74726891","display_name":"Applied Intelligence","issn_l":"0924-669X","issn":["0924-669X","1573-7497"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Applied Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s10489-023-04915-8.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014258113","display_name":"Shengmin \u200dPiao","orcid":"https://orcid.org/0000-0003-2358-9797"},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Shengmin Piao","raw_affiliation_strings":["Department of Computer Science, Yonsei University, Yonsei-ro 50, Seoul, 03722, Republic of Korea"],"raw_orcid":"https://orcid.org/0000-0003-2358-9797","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Yonsei University, Yonsei-ro 50, Seoul, 03722, Republic of Korea","institution_ids":["https://openalex.org/I193775966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064308519","display_name":"Jonghwan Choi","orcid":"https://orcid.org/0000-0002-8429-4135"},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jonghwan Choi","raw_affiliation_strings":["Department of Computer Science, Yonsei University, Yonsei-ro 50, Seoul, 03722, Republic of Korea","UBLBio Corporation, Yeongtong-ro 237, Suwon, 16679, Gyeonggi-do, Republic of Korea"],"raw_orcid":"https://orcid.org/0000-0002-8429-4135","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Yonsei University, Yonsei-ro 50, Seoul, 03722, Republic of Korea","institution_ids":["https://openalex.org/I193775966"]},{"raw_affiliation_string":"UBLBio Corporation, Yeongtong-ro 237, Suwon, 16679, Gyeonggi-do, Republic of Korea","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102777941","display_name":"Sangmin Seo","orcid":"https://orcid.org/0000-0003-4883-3987"},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Sangmin Seo","raw_affiliation_strings":["Department of Computer Science, Yonsei University, Yonsei-ro 50, Seoul, 03722, Republic of Korea","UBLBio Corporation, Yeongtong-ro 237, Suwon, 16679, Gyeonggi-do, Republic of Korea"],"raw_orcid":"https://orcid.org/0000-0003-4883-3987","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Yonsei University, Yonsei-ro 50, Seoul, 03722, Republic of Korea","institution_ids":["https://openalex.org/I193775966"]},{"raw_affiliation_string":"UBLBio Corporation, Yeongtong-ro 237, Suwon, 16679, Gyeonggi-do, Republic of Korea","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100322270","display_name":"Sanghyun Park","orcid":"https://orcid.org/0000-0002-5196-6193"},"institutions":[{"id":"https://openalex.org/I193775966","display_name":"Yonsei University","ror":"https://ror.org/01wjejq96","country_code":"KR","type":"education","lineage":["https://openalex.org/I193775966"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Sanghyun Park","raw_affiliation_strings":["Department of Computer Science, Yonsei University, Yonsei-ro 50, Seoul, 03722, Republic of Korea"],"raw_orcid":"https://orcid.org/0000-0002-5196-6193","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Yonsei University, Yonsei-ro 50, Seoul, 03722, Republic of Korea","institution_ids":["https://openalex.org/I193775966"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100322270"],"corresponding_institution_ids":["https://openalex.org/I193775966"],"apc_list":{"value":2390,"currency":"EUR","value_usd":2990},"apc_paid":{"value":2390,"currency":"EUR","value_usd":2990},"fwci":1.3011,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.83306699,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"53","issue":"21","first_page":"25868","last_page":"25880"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9993000030517578,"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":0.9993000030517578,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9993000030517578,"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/T12534","display_name":"Protein Degradation and Inhibitors","score":0.9952999949455261,"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":0.8675099015235901},{"id":"https://openalex.org/keywords/levenshtein-distance","display_name":"Levenshtein distance","score":0.6049690246582031},{"id":"https://openalex.org/keywords/edit-distance","display_name":"Edit distance","score":0.5318624377250671},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.4172738194465637},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3729812502861023},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3600011169910431},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.32202044129371643}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8675099015235901},{"id":"https://openalex.org/C2777515626","wikidata":"https://www.wikidata.org/wiki/Q496939","display_name":"Levenshtein distance","level":2,"score":0.6049690246582031},{"id":"https://openalex.org/C44359876","wikidata":"https://www.wikidata.org/wiki/Q5338467","display_name":"Edit distance","level":2,"score":0.5318624377250671},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.4172738194465637},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3729812502861023},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3600011169910431},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32202044129371643},{"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/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/s10489-023-04915-8","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10489-023-04915-8","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10489-023-04915-8.pdf","source":{"id":"https://openalex.org/S74726891","display_name":"Applied Intelligence","issn_l":"0924-669X","issn":["0924-669X","1573-7497"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Applied Intelligence","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1007/s10489-023-04915-8","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10489-023-04915-8","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10489-023-04915-8.pdf","source":{"id":"https://openalex.org/S74726891","display_name":"Applied Intelligence","issn_l":"0924-669X","issn":["0924-669X","1573-7497"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","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":"Applied Intelligence","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6200000047683716,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G2519687455","display_name":null,"funder_award_id":"2019R1A2C3005212","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"},{"id":"https://openalex.org/G4634960091","display_name":null,"funder_award_id":"RS-2023-00229822","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4385784138.pdf"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1972091733","https://openalex.org/W1975147762","https://openalex.org/W1981276685","https://openalex.org/W2018668003","https://openalex.org/W2023818227","https://openalex.org/W2034549041","https://openalex.org/W2046813714","https://openalex.org/W2138621090","https://openalex.org/W2151697120","https://openalex.org/W2154777073","https://openalex.org/W2160592148","https://openalex.org/W2166550586","https://openalex.org/W2240536489","https://openalex.org/W2529996553","https://openalex.org/W2610148085","https://openalex.org/W2797867047","https://openalex.org/W2803615944","https://openalex.org/W2909240409","https://openalex.org/W2985931096","https://openalex.org/W3087999580","https://openalex.org/W3130822715","https://openalex.org/W3156636935","https://openalex.org/W3158331815","https://openalex.org/W3168385357","https://openalex.org/W3210813272","https://openalex.org/W4221110561","https://openalex.org/W4229372746","https://openalex.org/W4281743220","https://openalex.org/W4285179478","https://openalex.org/W4315473675"],"related_works":["https://openalex.org/W2461708070","https://openalex.org/W2003932770","https://openalex.org/W1531307672","https://openalex.org/W4362583275","https://openalex.org/W2575897682","https://openalex.org/W4321609555","https://openalex.org/W2844405045","https://openalex.org/W4285090010","https://openalex.org/W4280559639","https://openalex.org/W2788104449"],"abstract_inverted_index":{"Abstract":[0],"Structure-constrained":[1],"molecular":[2,19,34,63,126,160],"optimisation":[3,26,35,127],"aims":[4],"to":[5,28,95,110,176,186,190,193,207],"improve":[6,151],"the":[7,18,30,86,106,139,147,152,159,171,177,183,191,209],"target":[8],"pharmacological":[9,153],"properties":[10,154],"of":[11,17,32,58,133,158],"input":[12],"molecules":[13,83],"through":[14,162],"small":[15],"perturbations":[16,157],"structures.":[20],"Previous":[21],"studies":[22,39],"have":[23,40],"exploited":[24],"various":[25],"techniques":[27],"satisfy":[29],"requirements":[31],"structure-constrained":[33,125],"tasks.":[36],"However,":[37],"several":[38],"encountered":[41],"difficulties":[42],"in":[43],"producing":[44],"property-improved":[45],"and":[46,55,75,105,135],"synthetically":[47],"feasible":[48],"molecules.":[49],"To":[50],"achieve":[51],"both":[52],"property":[53],"improvement":[54],"synthetic":[56],"feasibility":[57],"molecules,":[59],"we":[60,144],"proposed":[61,148],"a":[62,100,130],"structure":[64],"editing":[65,116,188],"model":[66,109,149],"called":[67],"SELF-EdiT":[68,80,98,122,181],"that":[69,84,121,146],"uses":[70],"self-referencing":[71],"embedded":[72],"strings":[73],"(SELFIES)":[74],"Levenshtein":[76,107],"transformer":[77,108],"models.":[78],"The":[79,97],"generates":[81],"new":[82],"resemble":[85],"seed":[87],"molecule":[88],"by":[89,129],"iteratively":[90],"applying":[91],"fragment-based":[92,167],"deletion-and-insertion":[93,113],"operations":[94,114,189],"SELFIES.":[96,117,210],"exploits":[99],"grammar-based":[101],"SELFIES":[102,172,192],"tokenization":[103],"method":[104],"efficiently":[111],"learn":[112],"for":[115,203],"Our":[118],"results":[119],"demonstrated":[120],"outperformed":[123],"existing":[124,178],"models":[128],"considerable":[131],"margin":[132],"success":[134],"total":[136],"scores":[137],"on":[138],"two":[140],"benchmark":[141],"datasets.":[142],"Furthermore,":[143],"confirmed":[145],"could":[150],"without":[155],"large":[156],"structures":[161],"edit-path":[163],"analysis.":[164],"Moreover,":[165],"our":[166],"approach":[168],"significantly":[169],"relieved":[170],"collapse":[173],"problem":[174],"compared":[175],"SELFIES-based":[179],"model.":[180],"is":[182],"first":[184],"attempt":[185],"apply":[187],"design":[194],"an":[195],"effective":[196],"editing-based":[197],"optimisation,":[198],"which":[199],"can":[200],"be":[201],"helpful":[202],"fellow":[204],"researchers":[205],"planning":[206],"utilise":[208]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-13T06:13:01.061226","created_date":"2025-10-10T00:00:00"}
