{"id":"https://openalex.org/W4289936378","doi":"https://doi.org/10.1093/bioinformatics/btac545","title":"MICER: a pre-trained encoder\u2013decoder architecture for molecular image captioning","display_name":"MICER: a pre-trained encoder\u2013decoder architecture for molecular image captioning","publication_year":2022,"publication_date":"2022-08-05","ids":{"openalex":"https://openalex.org/W4289936378","doi":"https://doi.org/10.1093/bioinformatics/btac545","pmid":"https://pubmed.ncbi.nlm.nih.gov/35929794"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac545","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac545","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/A5066240587","display_name":"Jiacai Yi","orcid":"https://orcid.org/0000-0001-6823-1882"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiacai Yi","raw_affiliation_strings":["School of Computer Science, National University of Defense Technology , Changsha 410073, China"],"raw_orcid":"https://orcid.org/0000-0001-6823-1882","affiliations":[{"raw_affiliation_string":"School of Computer Science, National University of Defense Technology , Changsha 410073, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054335730","display_name":"Chengkun Wu","orcid":"https://orcid.org/0000-0002-9688-5311"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chengkun Wu","raw_affiliation_strings":["Institute for Quantum Information & State Key Laboratory of High-Performance Computing, College of Computer Science and Technology, National University of Defense Technology , Changsha 410073, China"],"raw_orcid":"https://orcid.org/0000-0002-9688-5311","affiliations":[{"raw_affiliation_string":"Institute for Quantum Information & State Key Laboratory of High-Performance Computing, College of Computer Science and Technology, National University of Defense Technology , Changsha 410073, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100458555","display_name":"Xiaochen Zhang","orcid":"https://orcid.org/0000-0002-7154-5337"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaochen Zhang","raw_affiliation_strings":["School of Computer Science, National University of Defense Technology , Changsha 410073, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, National University of Defense Technology , Changsha 410073, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073490951","display_name":"Xinyi Xiao","orcid":"https://orcid.org/0009-0009-2854-8477"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinyi Xiao","raw_affiliation_strings":["School of Computer Science, National University of Defense Technology , Changsha 410073, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, National University of Defense Technology , Changsha 410073, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019512392","display_name":"Yanlong Qiu","orcid":"https://orcid.org/0000-0003-4940-5546"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanlong Qiu","raw_affiliation_strings":["School of Computer Science, National University of Defense Technology , Changsha 410073, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, National University of Defense Technology , Changsha 410073, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103149594","display_name":"Wentao Zhao","orcid":"https://orcid.org/0000-0002-2906-3238"},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Wentao Zhao","raw_affiliation_strings":["School of Computer Science, National University of Defense Technology , Changsha 410073, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, National University of Defense Technology , Changsha 410073, China","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028525523","display_name":"Tingjun Hou","orcid":"https://orcid.org/0000-0001-7227-2580"},"institutions":[{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]},{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tingjun Hou","raw_affiliation_strings":["Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, China"],"raw_orcid":"https://orcid.org/0000-0001-7227-2580","affiliations":[{"raw_affiliation_string":"Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University , Hangzhou 310058, China","institution_ids":["https://openalex.org/I4210123185","https://openalex.org/I76130692"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083809384","display_name":"Dongsheng Cao","orcid":"https://orcid.org/0000-0003-3604-3785"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Dongsheng Cao","raw_affiliation_strings":["Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University , Changsha 410013, China","Xiangya School of Pharmaceutical Sciences, Central South University , Changsha 410003, China"],"raw_orcid":"https://orcid.org/0000-0003-3604-3785","affiliations":[{"raw_affiliation_string":"Hunan Key Laboratory of Diagnostic and Therapeutic Drug Research for Chronic Diseases, Central South University , Changsha 410013, China","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"Xiangya School of Pharmaceutical Sciences, Central South University , Changsha 410003, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5028525523","https://openalex.org/A5083809384","https://openalex.org/A5103149594"],"corresponding_institution_ids":["https://openalex.org/I139660479","https://openalex.org/I170215575","https://openalex.org/I4210123185","https://openalex.org/I76130692"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.5864,"has_fulltext":false,"cited_by_count":22,"citation_normalized_percentile":{"value":0.90894201,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"38","issue":"19","first_page":"4562","last_page":"4572"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.2401999980211258,"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":0.2401999980211258,"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":0.20909999310970306,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.11729999631643295,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/closed-captioning","display_name":"Closed captioning","score":0.9507806301116943},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.8347931504249573},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8145796060562134},{"id":"https://openalex.org/keywords/image","display_name":"Image (mathematics)","score":0.5717035531997681},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.5576448440551758},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45746782422065735},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.38595038652420044},{"id":"https://openalex.org/keywords/speech-recognition","display_name":"Speech recognition","score":0.37109166383743286},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.052104949951171875}],"concepts":[{"id":"https://openalex.org/C157657479","wikidata":"https://www.wikidata.org/wiki/Q2367247","display_name":"Closed captioning","level":3,"score":0.9507806301116943},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.8347931504249573},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8145796060562134},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.5717035531997681},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.5576448440551758},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45746782422065735},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.38595038652420044},{"id":"https://openalex.org/C28490314","wikidata":"https://www.wikidata.org/wiki/Q189436","display_name":"Speech recognition","level":1,"score":0.37109166383743286},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.052104949951171875},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac545","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac545","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35929794","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35929794","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.46000000834465027,"display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G4135978206","display_name":null,"funder_award_id":"U1811462","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7632230142","display_name":null,"funder_award_id":"22173118","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8590540938","display_name":null,"funder_award_id":"2021YFF1201400","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program 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/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W1686810756","https://openalex.org/W1966456689","https://openalex.org/W1988037271","https://openalex.org/W1989405983","https://openalex.org/W2001496424","https://openalex.org/W2027482274","https://openalex.org/W2064675550","https://openalex.org/W2076063813","https://openalex.org/W2077357770","https://openalex.org/W2112796928","https://openalex.org/W2132289924","https://openalex.org/W2166468803","https://openalex.org/W2170973067","https://openalex.org/W2752386593","https://openalex.org/W2896348597","https://openalex.org/W2963734039","https://openalex.org/W3006781240","https://openalex.org/W3007750971","https://openalex.org/W3009321976","https://openalex.org/W3037585619","https://openalex.org/W3041133507","https://openalex.org/W3045928028","https://openalex.org/W3092396754","https://openalex.org/W3094640617","https://openalex.org/W3097598035","https://openalex.org/W3103383152","https://openalex.org/W3107609030","https://openalex.org/W3210813272","https://openalex.org/W4206174637","https://openalex.org/W4244568576","https://openalex.org/W4288364646","https://openalex.org/W4394670654","https://openalex.org/W6637373629","https://openalex.org/W6642027612","https://openalex.org/W6743837088","https://openalex.org/W6762269264","https://openalex.org/W6779720960","https://openalex.org/W6796281881","https://openalex.org/W6826938794","https://openalex.org/W6864277861"],"related_works":["https://openalex.org/W4210416330","https://openalex.org/W3088136942","https://openalex.org/W3164229987","https://openalex.org/W3215212336","https://openalex.org/W4290852288","https://openalex.org/W3122720459","https://openalex.org/W4298897568","https://openalex.org/W3217388757","https://openalex.org/W1938708284","https://openalex.org/W4380190185"],"abstract_inverted_index":{"MOTIVATION:":[0],"Automatic":[1],"recognition":[2,41],"of":[3,16,34,102,124,139],"chemical":[4,207],"structures":[5],"from":[6,39],"molecular":[7,35,81,105,126,200],"images":[8,36,127],"provides":[9,190],"an":[10,76],"important":[11],"avenue":[12],"for":[13,80,154,194],"the":[14,31,121,125,129,137,148,152,155,160,165,170],"rediscovery":[15],"chemicals.":[17],"Traditional":[18],"rule-based":[19],"approaches":[20],"that":[21,50,120,164],"rely":[22],"on":[23,112,136,173],"expert":[24],"knowledge":[25],"and":[26,43,55,65,68,89,95,109,128,151,159,180,186,189,197],"fail":[27],"to":[28,92,146,183,204],"consider":[29],"all":[30],"stylistic":[32],"variations":[33],"usually":[37],"suffer":[38],"cumbersome":[40],"processes":[42],"low":[44],"generalization":[45],"ability.":[46],"Deep":[47],"learning-based":[48],"methods":[49,172],"integrate":[51],"different":[52,98],"image":[53,82],"styles":[54],"automatically":[56],"learn":[57],"valuable":[58],"features":[59,123],"are":[60,69,217],"flexible,":[61],"but":[62],"currently":[63],"under-researched":[64],"have":[66,132],"limitations,":[67],"therefore":[70],"not":[71],"fully":[72],"exploited.":[73],"RESULTS:":[74],"MICER,":[75],"encoder-decoder-based,":[77],"reconstructed":[78],"architecture":[79],"captioning,":[83],"combines":[84],"transfer":[85,187],"learning,":[86],"attention":[87],"mechanisms":[88],"several":[90],"strategies":[91],"strengthen":[93],"effectiveness":[94],"plasticity":[96],"in":[97],"datasets.":[99,175],"The":[100],"effects":[101],"stereochemical":[103],"information,":[104],"complexity,":[106],"data":[107,216],"volume":[108],"pre-trained":[110],"encoders":[111],"MICER":[113,166,176],"performance":[114,138],"were":[115],"evaluated.":[116],"Experimental":[117],"results":[118,162],"show":[119],"intrinsic":[122],"sub-model":[130],"match":[131],"a":[133,191],"significant":[134],"impact":[135],"this":[140],"task.":[141],"These":[142],"findings":[143],"inspire":[144],"us":[145],"design":[147],"training":[149],"dataset":[150],"encoder":[153],"final":[156],"validation":[157],"model,":[158],"experimental":[161],"suggest":[163],"model":[167],"consistently":[168],"outperforms":[169],"state-of-the-art":[171],"four":[174],"was":[177],"more":[178],"reliable":[179],"scalable":[181],"due":[182],"its":[184],"interpretability":[185],"capacity":[188],"practical":[192],"framework":[193],"developing":[195],"comprehensive":[196],"accurate":[198],"automated":[199],"structure":[201],"identification":[202],"tools":[203],"explore":[205],"unknown":[206],"space.":[208],"AVAILABILITY":[209],"AND":[210],"IMPLEMENTATION:":[211],"https://github.com/Jiacai-Yi/MICER.":[212],"SUPPLEMENTARY":[213],"INFORMATION:":[214],"Supplementary":[215],"available":[218],"at":[219],"Bioinformatics":[220],"online.":[221]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":7}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
