{"id":"https://openalex.org/W4377297592","doi":"https://doi.org/10.48550/arxiv.2305.11194","title":"Vaxformer: Antigenicity-controlled Transformer for Vaccine Design Against SARS-CoV-2","display_name":"Vaxformer: Antigenicity-controlled Transformer for Vaccine Design Against SARS-CoV-2","publication_year":2023,"publication_date":"2023-05-18","ids":{"openalex":"https://openalex.org/W4377297592","doi":"https://doi.org/10.48550/arxiv.2305.11194"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2305.11194","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2305.11194","pdf_url":"https://arxiv.org/pdf/2305.11194","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2305.11194","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080213009","display_name":"Aryo Pradipta Gema","orcid":"https://orcid.org/0009-0007-1163-3531"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Gema, Aryo Pradipta","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091998597","display_name":"Micha\u0142 Kobiela","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kobiela, Micha\u0142","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112920694","display_name":"Achille Fraisse","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fraisse, Achille","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079075574","display_name":"Ajitha Rajan","orcid":"https://orcid.org/0000-0003-3765-3075"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rajan, Ajitha","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016017194","display_name":"Diego A. Oyarz\u00fan","orcid":"https://orcid.org/0000-0002-0381-5278"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Oyarz\u00fan, Diego A.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5012272783","display_name":"Javier A. Alfaro","orcid":"https://orcid.org/0000-0002-5553-6991"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Alfaro, Javier Antonio","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5080213009"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12576","display_name":"vaccines and immunoinformatics approaches","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/T12576","display_name":"vaccines and immunoinformatics approaches","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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9983000159263611,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9980999827384949,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/antigenicity","display_name":"Antigenicity","score":0.9278500080108643},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5031861662864685},{"id":"https://openalex.org/keywords/virology","display_name":"Virology","score":0.44075533747673035},{"id":"https://openalex.org/keywords/spike","display_name":"Spike (software development)","score":0.42838752269744873},{"id":"https://openalex.org/keywords/pandemic","display_name":"Pandemic","score":0.4171094298362732},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40436112880706787},{"id":"https://openalex.org/keywords/coronavirus-disease-2019","display_name":"Coronavirus disease 2019 (COVID-19)","score":0.3242976665496826},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3220334053039551},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.2830556631088257},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.24411866068840027},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.1677381694316864},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.12863147258758545}],"concepts":[{"id":"https://openalex.org/C2779026604","wikidata":"https://www.wikidata.org/wiki/Q4774742","display_name":"Antigenicity","level":3,"score":0.9278500080108643},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5031861662864685},{"id":"https://openalex.org/C159047783","wikidata":"https://www.wikidata.org/wiki/Q7215","display_name":"Virology","level":1,"score":0.44075533747673035},{"id":"https://openalex.org/C2781390188","wikidata":"https://www.wikidata.org/wiki/Q25203449","display_name":"Spike (software development)","level":2,"score":0.42838752269744873},{"id":"https://openalex.org/C89623803","wikidata":"https://www.wikidata.org/wiki/Q12184","display_name":"Pandemic","level":5,"score":0.4171094298362732},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40436112880706787},{"id":"https://openalex.org/C3008058167","wikidata":"https://www.wikidata.org/wiki/Q84263196","display_name":"Coronavirus disease 2019 (COVID-19)","level":4,"score":0.3242976665496826},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3220334053039551},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2830556631088257},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.24411866068840027},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.1677381694316864},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.12863147258758545},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"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/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:arXiv.org:2305.11194","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2305.11194","pdf_url":"https://arxiv.org/pdf/2305.11194","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"pmh:oai:pure.ed.ac.uk:publications/8b56671b-9c26-4f23-b26b-12914bb7be3f","is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/en/publications/8b56671b-9c26-4f23-b26b-12914bb7be3f","pdf_url":null,"source":{"id":"https://openalex.org/S4406922455","display_name":"Edinburgh Research Explorer","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Gema, A P, Kobiela, M, Fraisse, A, Rajan, A, Oyarz\u00fan, D A & Alfaro, J A 2023 'Vaxformer : Antigenicity-controlled transformer for vaccine design against SARS-CoV-2'. https://doi.org/10.48550/arXiv.2305.11194","raw_type":"workingPaper"},{"id":"doi:10.48550/arxiv.2305.11194","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2305.11194","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2305.11194","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2305.11194","pdf_url":"https://arxiv.org/pdf/2305.11194","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.7900000214576721,"display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G3186036607","display_name":null,"funder_award_id":"EP/S02431X/1","funder_id":"https://openalex.org/F4320314731","funder_display_name":"UK Research and Innovation"},{"id":"https://openalex.org/G581313191","display_name":null,"funder_award_id":"EP/T022159/","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G7002347110","display_name":"Cambridge Service for Data Driven Discovery (CSD3) - A National Data Intensive Science Cloud for Converged Simulation, AI &amp; Analytics","funder_award_id":"EP/T022159/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G7603489359","display_name":"UKRI Centre for Doctoral Training in Biomedical Artificial Intelligence","funder_award_id":"EP/S02431X/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320312927","display_name":"Dell EMC","ror":"https://ror.org/05rejmm18"},{"id":"https://openalex.org/F4320314731","display_name":"UK Research and Innovation","ror":"https://ror.org/001aqnf71"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320334632","display_name":"Science and Technology Facilities Council","ror":"https://ror.org/057g20z61"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4377297592.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W786416207","https://openalex.org/W2367852944","https://openalex.org/W2115812853","https://openalex.org/W2004255297","https://openalex.org/W2078727461","https://openalex.org/W2008472229","https://openalex.org/W2435839362","https://openalex.org/W2396550544","https://openalex.org/W4380730574","https://openalex.org/W294199537"],"abstract_inverted_index":{"The":[0,23,121],"SARS-CoV-2":[1,43,94],"pandemic":[2],"has":[3],"emphasised":[4],"the":[5,21,48,53,84],"importance":[6],"of":[7,20,52,110],"developing":[8],"a":[9,27,65],"universal":[10],"vaccine":[11,76,111],"that":[12,81],"can":[13],"protect":[14],"against":[15],"current":[16],"and":[17,64,113],"future":[18],"variants":[19],"virus.":[22],"present":[24],"study":[25,126],"proposes":[26],"novel":[28],"conditional":[29,103],"protein":[30,50,58],"Language":[31],"Model":[32],"architecture,":[33],"called":[34],"Vaxformer,":[35],"which":[36],"is":[37,127],"designed":[38],"to":[39,71,91,106],"produce":[40],"natural-looking":[41],"antigenicity-controlled":[42,93],"spike":[44,95],"proteins.":[45,96],"We":[46],"evaluate":[47],"generated":[49],"sequences":[51],"Vaxformer":[54,82],"model":[55,90],"using":[56],"DDGun":[57],"stability":[59],"measure,":[60],"netMHCpan":[61],"antigenicity":[62],"score,":[63],"structure":[66],"fidelity":[67],"score":[68],"with":[69],"AlphaFold":[70],"gauge":[72],"its":[73],"viability":[74],"for":[75,102],"development.":[77],"Our":[78],"results":[79],"show":[80],"outperforms":[83],"existing":[85],"state-of-the-art":[86],"Conditional":[87],"Variational":[88],"Autoencoder":[89],"generate":[92],"These":[97],"findings":[98],"suggest":[99],"promising":[100],"opportunities":[101],"Transformer":[104],"models":[105],"expand":[107],"our":[108],"understanding":[109],"design":[112],"their":[114],"role":[115],"in":[116,124],"mitigating":[117],"global":[118],"health":[119],"challenges.":[120],"code":[122],"used":[123],"this":[125],"available":[128],"at":[129],"https://github.com/aryopg/vaxformer":[130],".":[131]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-16T08:24:45.110214","created_date":"2023-05-23T00:00:00"}
