{"id":"https://openalex.org/W4390992168","doi":"https://doi.org/10.1109/bibm58861.2023.10385903","title":"De Novo Molecular Structure Generation from Mass Spectra","display_name":"De Novo Molecular Structure Generation from Mass Spectra","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390992168","doi":"https://doi.org/10.1109/bibm58861.2023.10385903"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10385903","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10385903","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5084905540","display_name":"Yanmin Liu","orcid":"https://orcid.org/0000-0002-1571-5370"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yanmin Liu","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China","School of Computer Science and Technology, Shandong University, Qingdao, China"],"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]},{"raw_affiliation_string":"School of Computer Science and Technology, Shandong University, Qingdao, China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100342872","display_name":"Xuan Zhang","orcid":"https://orcid.org/0000-0001-5329-7272"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuan Zhang","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China","School of Computer Science and Technology, Shandong University, Qingdao, China"],"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]},{"raw_affiliation_string":"School of Computer Science and Technology, Shandong University, Qingdao, China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100434561","display_name":"Wei Zhao","orcid":"https://orcid.org/0000-0003-0699-3501"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I4391767886","display_name":"State Key Laboratory of Microbial Technology","ror":"https://ror.org/03x08qn04","country_code":null,"type":"facility","lineage":["https://openalex.org/I154099455","https://openalex.org/I4391767886"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wei Zhao","raw_affiliation_strings":["Shandong University,State Key Laboratory of Microbial Technology,Qingdao,China","State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China"],"affiliations":[{"raw_affiliation_string":"Shandong University,State Key Laboratory of Microbial Technology,Qingdao,China","institution_ids":["https://openalex.org/I154099455","https://openalex.org/I4391767886"]},{"raw_affiliation_string":"State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China","institution_ids":["https://openalex.org/I154099455","https://openalex.org/I4391767886"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100548068","display_name":"Daming Zhu","orcid":null},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Daming Zhu","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China","School of Computer Science and Technology, Shandong University, Qingdao, China"],"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]},{"raw_affiliation_string":"School of Computer Science and Technology, Shandong University, Qingdao, China","institution_ids":["https://openalex.org/I80143920"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101906222","display_name":"Xuefeng Cui","orcid":"https://orcid.org/0000-0002-8816-3482"},"institutions":[{"id":"https://openalex.org/I80143920","display_name":"Shandong University of Science and Technology","ror":"https://ror.org/04gtjhw98","country_code":"CN","type":"education","lineage":["https://openalex.org/I80143920"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuefeng Cui","raw_affiliation_strings":["Shandong University,School of Computer Science and Technology,Qingdao,China","School of Computer Science and Technology, Shandong University, Qingdao, China"],"affiliations":[{"raw_affiliation_string":"Shandong University,School of Computer Science and Technology,Qingdao,China","institution_ids":["https://openalex.org/I80143920"]},{"raw_affiliation_string":"School of Computer Science and Technology, Shandong University, Qingdao, China","institution_ids":["https://openalex.org/I80143920"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5084905540"],"corresponding_institution_ids":["https://openalex.org/I80143920"],"apc_list":null,"apc_paid":null,"fwci":1.1139,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.78882919,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"373","last_page":"378"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9998999834060669,"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/T11667","display_name":"Advanced Chemical Sensor Technologies","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10908","display_name":"Analytical Chemistry and Chromatography","score":0.9919999837875366,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"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":0.6430329084396362},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5493375062942505},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.48374509811401367},{"id":"https://openalex.org/keywords/hydrogen","display_name":"Hydrogen","score":0.483467161655426},{"id":"https://openalex.org/keywords/mass-spectrum","display_name":"Mass spectrum","score":0.4762292504310608},{"id":"https://openalex.org/keywords/molecule","display_name":"Molecule","score":0.460737407207489},{"id":"https://openalex.org/keywords/spectral-line","display_name":"Spectral line","score":0.44657957553863525},{"id":"https://openalex.org/keywords/reliability","display_name":"Reliability (semiconductor)","score":0.41603535413742065},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.40426304936408997},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.35192421078681946},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33934128284454346},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2672607898712158},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.2010766863822937}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6430329084396362},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5493375062942505},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.48374509811401367},{"id":"https://openalex.org/C512968161","wikidata":"https://www.wikidata.org/wiki/Q556","display_name":"Hydrogen","level":2,"score":0.483467161655426},{"id":"https://openalex.org/C40325409","wikidata":"https://www.wikidata.org/wiki/Q2360668","display_name":"Mass spectrum","level":3,"score":0.4762292504310608},{"id":"https://openalex.org/C32909587","wikidata":"https://www.wikidata.org/wiki/Q11369","display_name":"Molecule","level":2,"score":0.460737407207489},{"id":"https://openalex.org/C4839761","wikidata":"https://www.wikidata.org/wiki/Q212111","display_name":"Spectral line","level":2,"score":0.44657957553863525},{"id":"https://openalex.org/C43214815","wikidata":"https://www.wikidata.org/wiki/Q7310987","display_name":"Reliability (semiconductor)","level":3,"score":0.41603535413742065},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.40426304936408997},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.35192421078681946},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33934128284454346},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2672607898712158},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.2010766863822937},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0},{"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/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm58861.2023.10385903","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10385903","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W2064675550","https://openalex.org/W2069936863","https://openalex.org/W2101394823","https://openalex.org/W2110485445","https://openalex.org/W2148797284","https://openalex.org/W2179948434","https://openalex.org/W2285468881","https://openalex.org/W2504691963","https://openalex.org/W2603853601","https://openalex.org/W2767683865","https://openalex.org/W2788277448","https://openalex.org/W2888792171","https://openalex.org/W2900694120","https://openalex.org/W2921388451","https://openalex.org/W2922522932","https://openalex.org/W2970413753","https://openalex.org/W3030363843","https://openalex.org/W3036061391","https://openalex.org/W3094361883","https://openalex.org/W3162917764","https://openalex.org/W3217248762","https://openalex.org/W4214893857","https://openalex.org/W4225160382","https://openalex.org/W4281688302","https://openalex.org/W4308449887","https://openalex.org/W4310295249","https://openalex.org/W4313525610","https://openalex.org/W4385245566","https://openalex.org/W6739901393","https://openalex.org/W6757251034"],"related_works":["https://openalex.org/W2029490476","https://openalex.org/W3186870842","https://openalex.org/W2557857968","https://openalex.org/W2004176732","https://openalex.org/W4387333010","https://openalex.org/W2019947875","https://openalex.org/W182336420","https://openalex.org/W1977853483","https://openalex.org/W2036032105","https://openalex.org/W2166757835"],"abstract_inverted_index":{"Mass":[0],"spectrometry":[1],"is":[2,66],"a":[3,54,67,92,173],"key":[4],"technology":[5],"for":[6,38,70],"the":[7,30,60,71,108,127,133,142,145,153,182],"identification":[8],"of":[9,41,63,73,120,144,165,176],"small":[10],"molecules.":[11],"However,":[12],"traditional":[13],"methods":[14],"that":[15,26,59,95],"rely":[16],"on":[17,123],"database":[18],"comparisons":[19],"have":[20,57],"difficulty":[21],"with":[22],"newly":[23],"discovered":[24],"molecules":[25],"are":[27,79],"not":[28,80],"in":[29,34,83],"database.":[31,55],"Recent":[32],"advances":[33],"deep":[35],"learning":[36],"allow":[37],"direct":[39],"analysis":[40],"mass":[42],"spectra,":[43],"which":[44],"makes":[45],"it":[46,160],"possible":[47],"to":[48,102,110,181],"predict":[49,111],"chemical":[50,74,139],"structures":[51],"without":[52],"using":[53,152],"We":[56,149],"found":[58],"accurate":[61],"prediction":[62,72,163],"hydrogen":[64,97,116],"atoms":[65,98,114,117],"major":[68],"challenge":[69],"structures,":[75,140],"especially":[76],"since":[77],"they":[78],"explicitly":[81],"represented":[82],"SMILES.":[84],"To":[85],"address":[86],"this":[87],"challenge,":[88],"we":[89],"introduce":[90],"MS2SMILES,":[91],"novel":[93],"approach":[94],"treats":[96],"as":[99],"implicitly":[100],"linked":[101],"heavy":[103,113,124],"atoms.":[104],"This":[105],"method":[106],"enables":[107],"model":[109],"both":[112],"and":[115,155,159,167,178],"accurately":[118],"(instead":[119],"just":[121],"focusing":[122],"atoms)":[125],"during":[126],"training":[128],"phase.":[129],"Additionally,":[130],"MS2SMILES":[131,151],"incorporates":[132],"SMILES":[134,147,162],"grammatical":[135],"rules":[136],"when":[137],"predicting":[138],"increasing":[141],"reliability":[143],"generated":[146],"representations.":[148],"tested":[150],"GNPS":[154],"CASMI":[156],"2016":[157],"datasets,":[158],"achieved":[161],"accuracies":[164],"53.6%":[166],"63.8%,":[168],"respectively.":[169],"These":[170],"results":[171],"demonstrate":[172],"significant":[174],"improvement":[175],"19.9%":[177],"10.9%":[179],"compared":[180],"current":[183],"leading":[184],"method.":[185]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4}],"updated_date":"2026-02-25T23:00:34.991745","created_date":"2025-10-10T00:00:00"}
