{"id":"https://openalex.org/W4390970098","doi":"https://doi.org/10.1109/bibm58861.2023.10385774","title":"Learned Fingerprint Embedding for Large-Scale Peptide Mass Spectra Retrieval","display_name":"Learned Fingerprint Embedding for Large-Scale Peptide Mass Spectra Retrieval","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390970098","doi":"https://doi.org/10.1109/bibm58861.2023.10385774"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10385774","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10385774","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/A5013431919","display_name":"Yongshuai Wang","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":true,"raw_author_name":"Yongshuai Wang","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/A5100733931","display_name":"Defeng Li","orcid":"https://orcid.org/0000-0002-9316-3313"},"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":"Defeng Li","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/A5101559654","display_name":"Cheng Chen","orcid":"https://orcid.org/0000-0001-9017-9195"},"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":"Cheng Chen","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/A5103199799","display_name":"Xiaojun Cai","orcid":"https://orcid.org/0000-0003-1586-375X"},"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":"Xiaojun Cai","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/A5108903761","display_name":"Shiwei Sun","orcid":"https://orcid.org/0000-0002-0351-3720"},"institutions":[{"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"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shiwei Sun","raw_affiliation_strings":["Chinese Academy of Sciences,Key Lab of Intelligent Information Processing, Institute of Computing Technology,Beijing,China","Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China"],"affiliations":[{"raw_affiliation_string":"Chinese Academy of Sciences,Key Lab of Intelligent Information Processing, Institute of Computing Technology,Beijing,China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]},{"raw_affiliation_string":"Key Lab of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]}]},{"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":6,"corresponding_author_ids":["https://openalex.org/A5013431919"],"corresponding_institution_ids":["https://openalex.org/I80143920"],"apc_list":null,"apc_paid":null,"fwci":0.7628,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.68293152,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"306","last_page":"311"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9998999834060669,"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"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9998000264167786,"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"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.998199999332428,"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/fingerprint","display_name":"Fingerprint (computing)","score":0.7787584066390991},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7315167784690857},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6205378174781799},{"id":"https://openalex.org/keywords/pooling","display_name":"Pooling","score":0.6071823835372925},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5264878273010254},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4928281605243683},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.47193261981010437},{"id":"https://openalex.org/keywords/fingerprint-recognition","display_name":"Fingerprint recognition","score":0.4625486731529236},{"id":"https://openalex.org/keywords/tandem-mass-spectrometry","display_name":"Tandem mass spectrometry","score":0.4474918842315674},{"id":"https://openalex.org/keywords/mass-spectrum","display_name":"Mass spectrum","score":0.43014946579933167},{"id":"https://openalex.org/keywords/mass-spectrometry","display_name":"Mass spectrometry","score":0.3767409026622772},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.27473771572113037},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.0949571430683136},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07733267545700073}],"concepts":[{"id":"https://openalex.org/C2777826928","wikidata":"https://www.wikidata.org/wiki/Q3745713","display_name":"Fingerprint (computing)","level":2,"score":0.7787584066390991},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7315167784690857},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6205378174781799},{"id":"https://openalex.org/C70437156","wikidata":"https://www.wikidata.org/wiki/Q7228652","display_name":"Pooling","level":2,"score":0.6071823835372925},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5264878273010254},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4928281605243683},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.47193261981010437},{"id":"https://openalex.org/C168406668","wikidata":"https://www.wikidata.org/wiki/Q178022","display_name":"Fingerprint recognition","level":3,"score":0.4625486731529236},{"id":"https://openalex.org/C31827203","wikidata":"https://www.wikidata.org/wiki/Q874296","display_name":"Tandem mass spectrometry","level":3,"score":0.4474918842315674},{"id":"https://openalex.org/C40325409","wikidata":"https://www.wikidata.org/wiki/Q2360668","display_name":"Mass spectrum","level":3,"score":0.43014946579933167},{"id":"https://openalex.org/C162356407","wikidata":"https://www.wikidata.org/wiki/Q180809","display_name":"Mass spectrometry","level":2,"score":0.3767409026622772},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.27473771572113037},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0949571430683136},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07733267545700073},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm58861.2023.10385774","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10385774","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":[{"display_name":"Clean water and sanitation","id":"https://metadata.un.org/sdg/6","score":0.8299999833106995}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1981593008","https://openalex.org/W2006015763","https://openalex.org/W2026465178","https://openalex.org/W2037837681","https://openalex.org/W2072099326","https://openalex.org/W2079056345","https://openalex.org/W2080258378","https://openalex.org/W2105889769","https://openalex.org/W2130706354","https://openalex.org/W2138621090","https://openalex.org/W2161574105","https://openalex.org/W2736859409","https://openalex.org/W2765736339","https://openalex.org/W2888985586","https://openalex.org/W2899760200","https://openalex.org/W2903819617","https://openalex.org/W2919115771","https://openalex.org/W2945525532","https://openalex.org/W2945901478","https://openalex.org/W2947763854","https://openalex.org/W2949278902","https://openalex.org/W2964308564","https://openalex.org/W2970104449","https://openalex.org/W2990072002","https://openalex.org/W3176766392","https://openalex.org/W4221112332","https://openalex.org/W4225763451","https://openalex.org/W4281911083","https://openalex.org/W4310295249","https://openalex.org/W4313525610","https://openalex.org/W4376270841","https://openalex.org/W4385245566","https://openalex.org/W6679434410"],"related_works":["https://openalex.org/W4389371618","https://openalex.org/W3014822659","https://openalex.org/W2117826006","https://openalex.org/W4362496757","https://openalex.org/W2566091814","https://openalex.org/W2114937328","https://openalex.org/W4312797710","https://openalex.org/W2148654711","https://openalex.org/W2608025327","https://openalex.org/W1621827506"],"abstract_inverted_index":{"Tandem":[0],"mass":[1,53],"spectrometry":[2],"(MS/MS)":[3],"is":[4,89,116],"a":[5,41,82,101],"widely":[6],"used":[7,76,90],"technique":[8],"for":[9,119],"protein":[10],"identification,":[11],"post-translational":[12],"modifications,":[13],"immunotherapy,":[14],"and":[15,62,81,143],"other":[16],"applications.":[17],"As":[18],"the":[19,57,113,120,124,133,136],"amount":[20],"of":[21,51,105],"MS/MS":[22],"spectra":[23,125],"data":[24],"increases,":[25],"new":[26],"computational":[27],"methods":[28,109],"are":[29,75,146],"needed":[30],"to":[31,47,77,91,130,149],"efficiently":[32],"search":[33],"through":[34],"these":[35],"databases.":[36],"This":[37],"study":[38],"introduces":[39],"MS2VEC,":[40],"novel":[42,83],"fingerprint":[43,65,93,150],"embedding":[44],"model":[45],"designed":[46],"facilitate":[48],"large-scale":[49],"retrieval":[50,103,121],"peptide":[52],"spectra.":[54],"MS2VEC":[55,99],"captures":[56],"relationships":[58],"between":[59],"distant":[60],"peaks":[61],"incorporates":[63],"position-aware":[64,84],"features":[66],"from":[67],"all":[68],"peaks.":[69],"To":[70],"do":[71],"this,":[72],"dilated":[73],"convolutions":[74],"capture":[78],"remote":[79],"relationships,":[80],"multi-head":[85],"attention":[86],"pooling":[87],"mechanism":[88],"abstract":[92],"features.":[94,151],"The":[95],"results":[96,137],"demonstrate":[97],"that":[98,139],"achieves":[100],"top-1":[102],"accuracy":[104],"0.810,":[106],"outperforming":[107],"existing":[108],"by":[110],"5.1%.":[111],"Interestingly,":[112],"precursor":[114],"charge":[115],"not":[117],"essential":[118],"task,":[122],"as":[123],"itself":[126],"contains":[127],"enough":[128],"information":[129],"accurately":[131],"predict":[132],"charge.":[134],"Additionally,":[135],"suggest":[138],"weight-balanced":[140],"fragment":[141],"ions":[142],"water":[144],"losses":[145],"important":[147],"contributors":[148]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
