{"id":"https://openalex.org/W7126026536","doi":"https://doi.org/10.1109/bibm66473.2025.11356833","title":"TheProtein: Evolutionarily Informed Graph-Surface Protein Representation","display_name":"TheProtein: Evolutionarily Informed Graph-Surface Protein Representation","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126026536","doi":"https://doi.org/10.1109/bibm66473.2025.11356833"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356833","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356833","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 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/A5124187154","display_name":"Seungyong Lee","orcid":null},"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":"Seungyong Lee","raw_affiliation_strings":["Yonsei University,Department of Computer Science,Seoul,Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Yonsei University,Department of Computer Science,Seoul,Republic of Korea","institution_ids":["https://openalex.org/I193775966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018589974","display_name":"Seungyeon Choi","orcid":null},"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":"Seungyeon Choi","raw_affiliation_strings":["Yonsei University,Department of Computer Science,Seoul,Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Yonsei University,Department of Computer Science,Seoul,Republic of Korea","institution_ids":["https://openalex.org/I193775966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087507166","display_name":"Hwanhee C. Kim","orcid":null},"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":"Hwanhee Kim","raw_affiliation_strings":["Yonsei University,Department of Computer Science,Seoul,Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Yonsei University,Department of Computer Science,Seoul,Republic of Korea","institution_ids":["https://openalex.org/I193775966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015082756","display_name":"Hyoung\u2010Joon Park","orcid":"https://orcid.org/0000-0003-2938-0740"},"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":"Hyoungjoon Park","raw_affiliation_strings":["Yonsei University,Department of Computer Science,Seoul,Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Yonsei University,Department of Computer Science,Seoul,Republic of Korea","institution_ids":["https://openalex.org/I193775966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055128033","display_name":"Youngchang Kim","orcid":"https://orcid.org/0000-0002-1610-4889"},"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":"Yoonju Kim","raw_affiliation_strings":["Yonsei University,Department of Computer Science,Seoul,Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Yonsei University,Department of Computer Science,Seoul,Republic of Korea","institution_ids":["https://openalex.org/I193775966"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124173311","display_name":"Hyunseo Yang","orcid":null},"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":"Hyunseo Yang","raw_affiliation_strings":["Yonsei University,Department of Computer Science,Seoul,Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Yonsei University,Department of Computer Science,Seoul,Republic of Korea","institution_ids":["https://openalex.org/I193775966"]}]},{"author_position":"last","author":{"id":null,"display_name":"Sanghyun Park","orcid":null},"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":"Sanghyun Park","raw_affiliation_strings":["Yonsei University,Department of Computer Science,Seoul,Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Yonsei University,Department of Computer Science,Seoul,Republic of Korea","institution_ids":["https://openalex.org/I193775966"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5124187154"],"corresponding_institution_ids":["https://openalex.org/I193775966"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.65138756,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"6929","last_page":"6935"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.46399998664855957,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.46399998664855957,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.11140000075101852,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.09929999709129333,"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/representation","display_name":"Representation (politics)","score":0.7107999920845032},{"id":"https://openalex.org/keywords/initialization","display_name":"Initialization","score":0.690500020980835},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6208999752998352},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5929999947547913},{"id":"https://openalex.org/keywords/surface","display_name":"Surface (topology)","score":0.4496999979019165},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.4002000093460083},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.3871999979019165}],"concepts":[{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.7107999920845032},{"id":"https://openalex.org/C114466953","wikidata":"https://www.wikidata.org/wiki/Q6034165","display_name":"Initialization","level":2,"score":0.690500020980835},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6474000215530396},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6208999752998352},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5929999947547913},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5128999948501587},{"id":"https://openalex.org/C2776799497","wikidata":"https://www.wikidata.org/wiki/Q484298","display_name":"Surface (topology)","level":2,"score":0.4496999979019165},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.4002000093460083},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.3871999979019165},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3865000009536743},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.3582000136375427},{"id":"https://openalex.org/C167528306","wikidata":"https://www.wikidata.org/wiki/Q5508776","display_name":"Function representation","level":3,"score":0.2870999872684479},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.2791000008583069},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.275299996137619},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.26759999990463257},{"id":"https://openalex.org/C61797465","wikidata":"https://www.wikidata.org/wiki/Q1188986","display_name":"Term (time)","level":2,"score":0.2630999982357025},{"id":"https://openalex.org/C159149176","wikidata":"https://www.wikidata.org/wiki/Q14489129","display_name":"Evolutionary algorithm","level":2,"score":0.2547000050544739},{"id":"https://openalex.org/C3019232848","wikidata":"https://www.wikidata.org/wiki/Q29548","display_name":"Surface protein","level":2,"score":0.2526000142097473}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356833","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356833","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"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":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W2008708467","https://openalex.org/W2992752586","https://openalex.org/W3159926201","https://openalex.org/W3177828909","https://openalex.org/W3185671814","https://openalex.org/W4213077304","https://openalex.org/W4282926916","https://openalex.org/W4293003482","https://openalex.org/W4311573042","https://openalex.org/W4327550249","https://openalex.org/W4385245566","https://openalex.org/W4399880448","https://openalex.org/W4400497719"],"related_works":[],"abstract_inverted_index":{"Protein":[0],"representation":[1,146],"learning":[2],"is":[3,94],"a":[4,19,62,78,97,149],"research":[5],"field":[6],"that":[7,13,68,82],"converts":[8],"proteins":[9],"into":[10],"numerical":[11],"representations":[12],"computational":[14],"models":[15,44],"can":[16],"process,":[17],"playing":[18],"crucial":[20],"role":[21],"in":[22,143],"areas":[23],"such":[24],"as":[25],"structure-based":[26],"drug":[27],"development":[28],"and":[29,48,76,90,106,122,147],"protein":[30,42,53,74,145],"function":[31],"prediction.":[32],"However,":[33],"existing":[34],"methods":[35],"struggle":[36],"to":[37,58],"integrate":[38],"global":[39,84,129],"information":[40,131],"from":[41],"language":[43],"with":[45,87,119,132],"local":[46,88,133],"structure":[47,89],"surface":[49,64,75,91,99],"data,":[50],"particularly":[51],"on":[52,115],"surfaces":[54],"which":[55],"are":[56],"key":[57],"interactions.":[59],"We":[60],"propose":[61],"novel":[63,79],"feature":[65,100],"initialization":[66,101],"method":[67,102],"maps":[69],"ESM":[70,104,130],"embeddings":[71,105],"onto":[72],"the":[73,116,138],"TheProtein,":[77],"multimodal":[80,144],"architecture":[81],"integrates":[83],"evolutionary":[85,141],"context":[86,142],"information.":[92],"This":[93],"achieved":[95,111],"through":[96],"new":[98,112],"using":[103],"dedicated":[107],"TheProtein":[108,110],"blocks.":[109],"state-of-the-art":[113],"performance":[114],"Atom3D":[117],"benchmark,":[118],"ablation":[120],"studies":[121],"visualizations":[123],"confirming":[124],"its":[125],"effective":[126],"integration":[127],"of":[128,140],"data.":[134],"Our":[135],"work":[136],"highlights":[137],"importance":[139],"offers":[148],"significant":[150],"methodological":[151],"advance.":[152]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2026-01-30T00:00:00"}
