{"id":"https://openalex.org/W4390971250","doi":"https://doi.org/10.1109/bibm58861.2023.10386059","title":"PESI: Paratope-Epitope Set Interaction for SARS-CoV-2 Neutralization Prediction","display_name":"PESI: Paratope-Epitope Set Interaction for SARS-CoV-2 Neutralization Prediction","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390971250","doi":"https://doi.org/10.1109/bibm58861.2023.10386059"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10386059","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10386059","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/A5034623010","display_name":"Zhang Wan","orcid":"https://orcid.org/0000-0003-2767-8949"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":true,"raw_author_name":"Zhang Wan","raw_affiliation_strings":["Nanyang Technological University,School of Computer Science and Engineering,Singapore","School of Computer Science and Engineering, Nanyang Technological University, Singapore"],"affiliations":[{"raw_affiliation_string":"Nanyang Technological University,School of Computer Science and Engineering,Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010951535","display_name":"Zhuoyi Lin","orcid":"https://orcid.org/0000-0003-4942-160X"},"institutions":[{"id":"https://openalex.org/I3005327000","display_name":"Institute for Infocomm Research","ror":"https://ror.org/053rfa017","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I3005327000","https://openalex.org/I91275662"]},{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Zhuoyi Lin","raw_affiliation_strings":["Technology and Research (A*STAR),Institute for Infocomm Research, Agency for Science,Singapore","Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR), Singapore"],"affiliations":[{"raw_affiliation_string":"Technology and Research (A*STAR),Institute for Infocomm Research, Agency for Science,Singapore","institution_ids":["https://openalex.org/I3005327000","https://openalex.org/I115228651"]},{"raw_affiliation_string":"Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR), Singapore","institution_ids":["https://openalex.org/I3005327000","https://openalex.org/I115228651"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037891222","display_name":"Shamima Rashid","orcid":"https://orcid.org/0000-0002-0157-6525"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Shamima Rashid","raw_affiliation_strings":["Nanyang Technological University,School of Computer Science and Engineering,Singapore","School of Computer Science and Engineering, Nanyang Technological University, Singapore"],"affiliations":[{"raw_affiliation_string":"Nanyang Technological University,School of Computer Science and Engineering,Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104230593","display_name":"Shaun Yue-Hao Ng","orcid":null},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Shaun Yue-Hao Ng","raw_affiliation_strings":["Nanyang Technological University,School of Chemical and Biomolecular Engineering,Singapore","School of Chemical and Biomolecular Engineering, Nanyang Technological University, Singapore"],"affiliations":[{"raw_affiliation_string":"Nanyang Technological University,School of Chemical and Biomolecular Engineering,Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Chemical and Biomolecular Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077105641","display_name":"Rui Yin","orcid":"https://orcid.org/0000-0002-1403-0396"},"institutions":[{"id":"https://openalex.org/I2800717037","display_name":"University of Florida Health","ror":"https://ror.org/04tk2gy88","country_code":"US","type":"education","lineage":["https://openalex.org/I2800717037"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rui Yin","raw_affiliation_strings":["University of Florida,Department of Health Outcome and Biomedical Informatics,Gainesville,FL,USA","Department of Health Outcome and Biomedical Informatics, University of Florida, Gainesville, FL, USA"],"affiliations":[{"raw_affiliation_string":"University of Florida,Department of Health Outcome and Biomedical Informatics,Gainesville,FL,USA","institution_ids":["https://openalex.org/I2800717037"]},{"raw_affiliation_string":"Department of Health Outcome and Biomedical Informatics, University of Florida, Gainesville, FL, USA","institution_ids":["https://openalex.org/I2800717037"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083824197","display_name":"J. Senthilnath","orcid":"https://orcid.org/0000-0002-1737-7985"},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I3005327000","display_name":"Institute for Infocomm Research","ror":"https://ror.org/053rfa017","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I3005327000","https://openalex.org/I91275662"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"J. Senthilnath","raw_affiliation_strings":["Technology and Research (A*STAR),Institute for Infocomm Research, Agency for Science,Singapore","Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR), Singapore"],"affiliations":[{"raw_affiliation_string":"Technology and Research (A*STAR),Institute for Infocomm Research, Agency for Science,Singapore","institution_ids":["https://openalex.org/I3005327000","https://openalex.org/I115228651"]},{"raw_affiliation_string":"Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR), Singapore","institution_ids":["https://openalex.org/I3005327000","https://openalex.org/I115228651"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027208445","display_name":"Chee Keong Kwoh","orcid":"https://orcid.org/0000-0002-8547-6387"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Chee-Keong Kwoh","raw_affiliation_strings":["Nanyang Technological University,School of Computer Science and Engineering,Singapore","School of Computer Science and Engineering, Nanyang Technological University, Singapore"],"affiliations":[{"raw_affiliation_string":"Nanyang Technological University,School of Computer Science and Engineering,Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5034623010"],"corresponding_institution_ids":["https://openalex.org/I172675005"],"apc_list":null,"apc_paid":null,"fwci":0.3181,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.65440966,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"49","last_page":"56"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9990000128746033,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9990000128746033,"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/T10167","display_name":"Influenza Virus Research Studies","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9966999888420105,"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/paratope","display_name":"Paratope","score":0.939399242401123},{"id":"https://openalex.org/keywords/neutralization","display_name":"Neutralization","score":0.8243486881256104},{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.661104142665863},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5161986947059631},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.48620694875717163},{"id":"https://openalex.org/keywords/severe-acute-respiratory-syndrome-coronavirus-2","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","score":0.47340187430381775},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.4251770079135895},{"id":"https://openalex.org/keywords/coronavirus-disease-2019","display_name":"Coronavirus disease 2019 (COVID-19)","score":0.39816075563430786},{"id":"https://openalex.org/keywords/antibody","display_name":"Antibody","score":0.18821755051612854},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14148840308189392},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.09324488043785095},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.08950638771057129},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.07528743147850037}],"concepts":[{"id":"https://openalex.org/C9086966","wikidata":"https://www.wikidata.org/wiki/Q489135","display_name":"Paratope","level":4,"score":0.939399242401123},{"id":"https://openalex.org/C14086860","wikidata":"https://www.wikidata.org/wiki/Q337120","display_name":"Neutralization","level":3,"score":0.8243486881256104},{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.661104142665863},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5161986947059631},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.48620694875717163},{"id":"https://openalex.org/C3007834351","wikidata":"https://www.wikidata.org/wiki/Q82069695","display_name":"Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)","level":5,"score":0.47340187430381775},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.4251770079135895},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.39816075563430786},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.18821755051612854},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14148840308189392},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.09324488043785095},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.08950638771057129},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.07528743147850037},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C524204448","wikidata":"https://www.wikidata.org/wiki/Q788926","display_name":"Infectious disease (medical specialty)","level":3,"score":0.0},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibm58861.2023.10386059","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10386059","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"},{"id":"pmh:oai:dr.ntu.edu.sg:10356/178506","is_oa":false,"landing_page_url":"https://doi.org/10.1109/BIBM58861.2023.10386059","pdf_url":null,"source":{"id":"https://openalex.org/S4306402609","display_name":"DR-NTU (Nanyang Technological University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I172675005","host_organization_name":"Nanyang Technological University","host_organization_lineage":["https://openalex.org/I172675005"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"Conference Paper"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.4099999964237213,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":53,"referenced_works":["https://openalex.org/W1832693441","https://openalex.org/W1856085589","https://openalex.org/W2003652884","https://openalex.org/W2017956110","https://openalex.org/W2045080704","https://openalex.org/W2064675550","https://openalex.org/W2101234009","https://openalex.org/W2110036226","https://openalex.org/W2131774270","https://openalex.org/W2131859684","https://openalex.org/W2152565070","https://openalex.org/W2194775991","https://openalex.org/W2400041270","https://openalex.org/W2620760558","https://openalex.org/W2808159893","https://openalex.org/W2808491442","https://openalex.org/W2896457183","https://openalex.org/W2957436444","https://openalex.org/W2999309192","https://openalex.org/W2999958881","https://openalex.org/W3022788428","https://openalex.org/W3039131048","https://openalex.org/W3049166744","https://openalex.org/W3122210777","https://openalex.org/W3124415907","https://openalex.org/W3138783506","https://openalex.org/W3146944767","https://openalex.org/W3150505176","https://openalex.org/W3156522942","https://openalex.org/W3166142427","https://openalex.org/W3187580872","https://openalex.org/W3202850396","https://openalex.org/W3206187363","https://openalex.org/W3209435597","https://openalex.org/W4200104219","https://openalex.org/W4221141645","https://openalex.org/W4225285785","https://openalex.org/W4225321559","https://openalex.org/W4280625391","https://openalex.org/W4283068487","https://openalex.org/W4285030803","https://openalex.org/W4300861364","https://openalex.org/W4307814667","https://openalex.org/W4318679072","https://openalex.org/W4385245566","https://openalex.org/W6651075283","https://openalex.org/W6675354045","https://openalex.org/W6739901393","https://openalex.org/W6752249467","https://openalex.org/W6755207826","https://openalex.org/W6755477022","https://openalex.org/W6780226713","https://openalex.org/W6846613353"],"related_works":["https://openalex.org/W2972990938","https://openalex.org/W2100617793","https://openalex.org/W1977627421","https://openalex.org/W4206669628","https://openalex.org/W4224279380","https://openalex.org/W4205317059","https://openalex.org/W3176864053","https://openalex.org/W4206651655","https://openalex.org/W4206548596","https://openalex.org/W2037745559"],"abstract_inverted_index":{"Prediction":[0],"of":[1,9,41,71,102,147,167,186,192],"neutralization":[2,67,131],"antibodies":[3,181],"is":[4,200],"important":[5],"for":[6,129,182],"the":[7,26,125,141,190],"development":[8],"effective":[10],"vaccines":[11],"and":[12,52,73,99,127,143,255],"antibody-based":[13],"therapeutics.":[14],"Traditional":[15],"methods":[16],"rely":[17],"on":[18,21,170,241,259],"features":[19],"based":[20,64],"first":[22,221],"principles":[23,222],"derived":[24],"from":[25,37],"binding":[27],"interface.":[28],"However,":[29],"they":[30],"are":[31,160],"burdened":[32],"by":[33,203,220],"arduous":[34],"data":[35],"preprocessing":[36],"a":[38,107,119,135,152,172,215,229,238,250,256],"limited":[39],"quantity":[40],"protein":[42],"structures.":[43],"In":[44,58,114],"comparison,":[45],"deep":[46,175],"learning":[47,176],"allows":[48],"automatic":[49],"substructure":[50],"characterization":[51],"representation":[53],"without":[54],"hand-crafted":[55,151],"feature":[56],"engineering.":[57],"particular,":[59],"large":[60],"language":[61],"models":[62,177],"(LLMs)":[63],"method":[65],"predicts":[66],"using":[68],"Fv":[69,80],"sequences":[70,81],"antibody":[72],"antigen.":[74],"Despite":[75],"LLM\u2019s":[76],"success,":[77],"incorporating":[78],"full-length":[79],"suffers":[82],"from:":[83],"1)":[84],"inaccurate":[85,193],"sequence-level":[86,194],"labels":[87],"in":[88,110],"existing":[89,264],"datasets,":[90],"2)":[91],"inefficient":[92],"modeling":[93,138,198,217],"due":[94],"to":[95,163,178,263],"noisy":[96],"non-contributing":[97,205],"motifs,":[98],"3)":[100],"ignorance":[101],"non-bonded":[103],"interactions":[104,227],"that":[105,122,139,223,247],"play":[106],"key":[108],"role":[109],"facilitating":[111],"epitope-paratope":[112],"pairing.":[113],"this":[115],"paper,":[116],"we":[117,150,208,236],"propose":[118,210],"novel":[120,136],"approach":[121],"incorporates":[123],"only":[124],"paratope":[126,142],"epitope":[128,144],"antibody-antigen":[130],"prediction":[132],"while":[133],"adopting":[134],"set":[137,212,216],"regards":[140],"as":[145,261],"bags":[146],"residues.":[148],"Specifically,":[149],"dataset":[153,173],"containing":[154],"neutralizing":[155,180],"paratope-epitope":[156,211],"pairs":[157],"where":[158],"epitopes":[159],"potentially":[161],"generalizable":[162],"future":[164],"unseen":[165],"variants":[166,185],"SARS-CoV-2.":[168],"Training":[169],"such":[171],"enables":[174],"predict":[179],"prospective":[183],"mutated":[184],"SARS-CoV-2,":[187],"meanwhile":[188],"addressing":[189],"problem":[191],"labels.":[195],"A":[196],"higher":[197],"efficiency":[199],"also":[201,209],"achieved":[202],"disregarding":[204],"motifs.":[206],"Furthermore,":[207],"interaction":[213],"(PESI),":[214],"model":[218],"inspired":[219],"learns":[224],"intra-inter":[225],"non-covalent":[226],"through":[228],"global":[230],"attention":[231],"mechanism.":[232],"To":[233],"validate":[234],"PESI,":[235],"perform":[237],"10-fold":[239],"cross-validation":[240],"our":[242],"dataset.":[243],"Experimental":[244],"results":[245],"show":[246],"PESI":[248],"achieves":[249],"more":[251],"balanced":[252],"overall":[253],"performance":[254],"significant":[257],"improvement":[258],"MCC":[260],"compared":[262],"architectures.":[265]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
