{"id":"https://openalex.org/W3197505096","doi":"https://doi.org/10.1109/tcbb.2021.3108971","title":"IAV-CNN: A 2D Convolutional Neural Network Model to Predict Antigenic Variants of Influenza A Virus","display_name":"IAV-CNN: A 2D Convolutional Neural Network Model to Predict Antigenic Variants of Influenza A Virus","publication_year":2021,"publication_date":"2021-09-01","ids":{"openalex":"https://openalex.org/W3197505096","doi":"https://doi.org/10.1109/tcbb.2021.3108971","mag":"3197505096","pmid":"https://pubmed.ncbi.nlm.nih.gov/34469306"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2021.3108971","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3108971","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5077105641","display_name":"Rui Yin","orcid":"https://orcid.org/0000-0002-1403-0396"},"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":"Rui Yin","raw_affiliation_strings":["School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore"],"raw_orcid":"https://orcid.org/0000-0002-1403-0396","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042055696","display_name":"Nyi Nyi Thwin","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":"Nyi Nyi Thwin","raw_affiliation_strings":["School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084325598","display_name":"Pei Zhuang","orcid":"https://orcid.org/0000-0003-2370-8813"},"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":"Pei Zhuang","raw_affiliation_strings":["School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, Singapore"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mechanical and Aerospace Engineering, Nanyang Technological University, Singapore, 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/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":"Zhuoyi Lin","raw_affiliation_strings":["School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore"],"raw_orcid":"https://orcid.org/0000-0003-4942-160X","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"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":["School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore"],"raw_orcid":"https://orcid.org/0000-0002-8547-6387","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I172675005"],"apc_list":null,"apc_paid":null,"fwci":2.5697,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.90503878,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"19","issue":"6","first_page":"3497","last_page":"3506"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10167","display_name":"Influenza Virus Research Studies","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T10167","display_name":"Influenza Virus Research Studies","score":0.9998000264167786,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9994000196456909,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.9991999864578247,"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/computer-science","display_name":"Computer science","score":0.7171770930290222},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6690787672996521},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5482221245765686},{"id":"https://openalex.org/keywords/influenza-a-virus","display_name":"Influenza A virus","score":0.5338426828384399},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5184842944145203},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.4811505079269409},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4328344166278839},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.37525808811187744},{"id":"https://openalex.org/keywords/virus","display_name":"Virus","score":0.23023861646652222},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1603373885154724},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.12006443738937378}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7171770930290222},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6690787672996521},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5482221245765686},{"id":"https://openalex.org/C2777546802","wikidata":"https://www.wikidata.org/wiki/Q834390","display_name":"Influenza A virus","level":3,"score":0.5338426828384399},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5184842944145203},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.4811505079269409},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4328344166278839},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.37525808811187744},{"id":"https://openalex.org/C2522874641","wikidata":"https://www.wikidata.org/wiki/Q808","display_name":"Virus","level":2,"score":0.23023861646652222},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1603373885154724},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.12006443738937378},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000956","descriptor_name":"Antigens, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000956","descriptor_name":"Antigens, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000956","descriptor_name":"Antigens, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007251","descriptor_name":"Influenza, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009980","descriptor_name":"Influenza A virus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009980","descriptor_name":"Influenza A virus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009980","descriptor_name":"Influenza A virus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019267","descriptor_name":"Hemagglutinin Glycoproteins, Influenza Virus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019267","descriptor_name":"Hemagglutinin Glycoproteins, Influenza Virus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019267","descriptor_name":"Hemagglutinin Glycoproteins, Influenza Virus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2021.3108971","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2021.3108971","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34469306","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34469306","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":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320751","display_name":"Ministry of Education - Singapore","ror":"https://ror.org/01kcva023"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":71,"referenced_works":["https://openalex.org/W6908809","https://openalex.org/W114517082","https://openalex.org/W121013250","https://openalex.org/W1501531009","https://openalex.org/W1522301498","https://openalex.org/W1546047689","https://openalex.org/W1584308190","https://openalex.org/W1598661758","https://openalex.org/W1665214252","https://openalex.org/W1686810756","https://openalex.org/W1979158913","https://openalex.org/W2009914637","https://openalex.org/W2031908280","https://openalex.org/W2041646166","https://openalex.org/W2067284235","https://openalex.org/W2071644795","https://openalex.org/W2076048958","https://openalex.org/W2077845498","https://openalex.org/W2101234009","https://openalex.org/W2121731372","https://openalex.org/W2123156966","https://openalex.org/W2131744502","https://openalex.org/W2148853951","https://openalex.org/W2160378127","https://openalex.org/W2163605009","https://openalex.org/W2171288396","https://openalex.org/W2264077953","https://openalex.org/W2270365003","https://openalex.org/W2313411748","https://openalex.org/W2327300044","https://openalex.org/W2345051977","https://openalex.org/W2415353984","https://openalex.org/W2509094238","https://openalex.org/W2523246573","https://openalex.org/W2583907533","https://openalex.org/W2587183882","https://openalex.org/W2605343262","https://openalex.org/W2610635081","https://openalex.org/W2752782242","https://openalex.org/W2757165800","https://openalex.org/W2795792036","https://openalex.org/W2797060233","https://openalex.org/W2896988999","https://openalex.org/W2899771611","https://openalex.org/W2906578344","https://openalex.org/W2906904975","https://openalex.org/W2909727437","https://openalex.org/W2917557027","https://openalex.org/W2951793362","https://openalex.org/W2963347351","https://openalex.org/W2963745697","https://openalex.org/W3003415212","https://openalex.org/W3003920946","https://openalex.org/W3013637395","https://openalex.org/W3094518056","https://openalex.org/W4231170962","https://openalex.org/W4294170691","https://openalex.org/W6600284362","https://openalex.org/W6631190155","https://openalex.org/W6632634077","https://openalex.org/W6637242042","https://openalex.org/W6637373629","https://openalex.org/W6675354045","https://openalex.org/W6679775712","https://openalex.org/W6682691769","https://openalex.org/W6684191040","https://openalex.org/W6704695948","https://openalex.org/W6727249380","https://openalex.org/W6750454948","https://openalex.org/W6756040250","https://openalex.org/W6758485811"],"related_works":["https://openalex.org/W4293226380","https://openalex.org/W4313906399","https://openalex.org/W4321487865","https://openalex.org/W2811106690","https://openalex.org/W4239306820","https://openalex.org/W2947043951","https://openalex.org/W2318112981","https://openalex.org/W4312417841","https://openalex.org/W2062195135","https://openalex.org/W4225147082"],"abstract_inverted_index":{"The":[0,23],"rapid":[1],"evolution":[2],"of":[3,11,18,26,63,71,79,82,88,106,115,141,153,163,230,256],"influenza":[4,13,76,116,130,164,200],"viruses":[5],"constantly":[6],"leads":[7],"to":[8,31,56,102,128,150,176],"the":[9,58,66,69,75,93,104,112,208,223,228,234,254],"emergence":[10],"novel":[12],"strains":[14],"that":[15,146,173,241],"are":[16,42],"capable":[17],"escaping":[19],"from":[20],"population":[21],"immunity.":[22],"timely":[24],"determination":[25],"antigenic":[27,59,131,257],"variants":[28,60,132],"is":[29,98,171],"critical":[30],"vaccine":[32],"design.":[33],"Empirical":[34],"experimental":[35],"methods":[36],"like":[37],"hemagglutination":[38],"inhibition":[39],"(HI)":[40],"assays":[41],"time-consuming":[43],"and":[44,90,110,161,186,227,250],"labor-intensive,":[45],"requiring":[46],"live":[47],"viruses.":[48],"Recently,":[49],"many":[50],"computational":[51],"models":[52,232],"have":[53,85,119],"been":[54],"developed":[55],"predict":[57],"without":[61],"considerations":[62],"explicitly":[64],"modeling":[65],"interdependencies":[67],"between":[68],"channels":[70],"feature":[72,225],"maps.":[73],"Moreover,":[74],"sequences":[77],"consisting":[78],"similar":[80],"distribution":[81],"residues":[83],"will":[84,91],"high":[86],"degrees":[87],"similarity":[89],"affect":[92],"prediction":[94,255],"outcome.":[95],"Consequently,":[96],"it":[97],"challenging":[99],"but":[100],"vital":[101],"determine":[103],"importance":[105],"different":[107],"residue":[108,180],"sites":[109],"enhance":[111],"predictive":[113],"performance":[114,206],"antigenicity.":[117],"We":[118],"proposed":[120,214],"a":[121,137,151,166,248],"2D":[122,167],"convolutional":[123],"neural":[124],"network":[125],"(CNN)":[126],"model":[127,243],"infer":[129],"(IAV-CNN).":[133],"Specifically,":[134],"we":[135,239],"apply":[136],"new":[138,209],"distributed":[139,210],"representation":[140,211],"amino":[142],"acids,":[143],"named":[144],"ProtVec":[145],"can":[147,244],"be":[148,245],"applied":[149],"variety":[152],"downstream":[154],"proteomic":[155],"machine":[156,220],"learning":[157],"tasks.":[158],"After":[159],"splittings":[160],"embeddings":[162],"strains,":[165],"squeeze-and-excitation":[168],"CNN":[169],"architecture":[170],"constructed":[172],"enables":[174],"networks":[175],"focus":[177],"on":[178,198],"informative":[179],"features":[181],"by":[182],"fusing":[183],"both":[184,218],"spatial":[185],"channel-wise":[187],"information":[188],"with":[189,212,222],"local":[190],"receptive":[191],"fields":[192],"at":[193],"each":[194],"layer.":[195],"Experimental":[196],"results":[197],"three":[199],"datasets":[201],"show":[202],"IAV-CNN":[203],"achieves":[204],"state-of-the-art":[205],"combining":[207],"our":[213,242],"architecture.":[215],"It":[216],"outperforms":[217],"traditional":[219],"algorithms":[221],"same":[224],"representations":[226],"majority":[229],"existing":[231],"in":[233],"independent":[235],"test":[236],"data.":[237],"Therefore":[238],"believe":[240],"served":[246],"as":[247],"reliable":[249],"robust":[251],"tool":[252],"for":[253],"variants.":[258]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":5}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
