{"id":"https://openalex.org/W7138002032","doi":"https://doi.org/10.1109/tcbbio.2026.3674782","title":"A Contrastive Learning Framework for Efficient Viral Escape Prediction","display_name":"A Contrastive Learning Framework for Efficient Viral Escape Prediction","publication_year":2026,"publication_date":"2026-03-17","ids":{"openalex":"https://openalex.org/W7138002032","doi":"https://doi.org/10.1109/tcbbio.2026.3674782","pmid":"https://pubmed.ncbi.nlm.nih.gov/41843532"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2026.3674782","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2026.3674782","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE 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/A5066344615","display_name":"Samet Tenekeci","orcid":"https://orcid.org/0000-0001-8875-4111"},"institutions":[{"id":"https://openalex.org/I120217413","display_name":"Izmir Institute of Technology","ror":"https://ror.org/03stptj97","country_code":"TR","type":"education","lineage":["https://openalex.org/I120217413"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Samet Tenekeci","raw_affiliation_strings":["Department of Computer Engineering, &#x0130;zmir Institute of Technology, &#x0130;zmir, T&#x00FC;rkiye"],"raw_orcid":"https://orcid.org/0000-0001-8875-4111","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, &#x0130;zmir Institute of Technology, &#x0130;zmir, T&#x00FC;rkiye","institution_ids":["https://openalex.org/I120217413"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119322752","display_name":"Efe Sezgin","orcid":null},"institutions":[{"id":"https://openalex.org/I120217413","display_name":"Izmir Institute of Technology","ror":"https://ror.org/03stptj97","country_code":"TR","type":"education","lineage":["https://openalex.org/I120217413"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Efe Sezgin","raw_affiliation_strings":["Department of Food Engineering, &#x0130;zmir Institute of Technology, &#x0130;zmir, T&#x00FC;rkiye"],"raw_orcid":"https://orcid.org/0000-0002-8000-7485","affiliations":[{"raw_affiliation_string":"Department of Food Engineering, &#x0130;zmir Institute of Technology, &#x0130;zmir, T&#x00FC;rkiye","institution_ids":["https://openalex.org/I120217413"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030858892","display_name":"SELMA TEK\u0130R","orcid":null},"institutions":[{"id":"https://openalex.org/I120217413","display_name":"Izmir Institute of Technology","ror":"https://ror.org/03stptj97","country_code":"TR","type":"education","lineage":["https://openalex.org/I120217413"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Selma Tekir","raw_affiliation_strings":["Department of Computer Engineering, &#x0130;zmir Institute of Technology, &#x0130;zmir, T&#x00FC;rkiye"],"raw_orcid":"https://orcid.org/0000-0002-0488-9682","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, &#x0130;zmir Institute of Technology, &#x0130;zmir, T&#x00FC;rkiye","institution_ids":["https://openalex.org/I120217413"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I120217413"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.30436317,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"23","issue":"3","first_page":"1277","last_page":"1289"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11241","display_name":"Advanced Malware Detection Techniques","score":0.07119999825954437,"subfield":{"id":"https://openalex.org/subfields/1711","display_name":"Signal Processing"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11241","display_name":"Advanced Malware Detection Techniques","score":0.07119999825954437,"subfield":{"id":"https://openalex.org/subfields/1711","display_name":"Signal Processing"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11448","display_name":"Face recognition and analysis","score":0.0681999996304512,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10400","display_name":"Network Security and Intrusion Detection","score":0.059300001710653305,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/statistical-learning","display_name":"Statistical learning","score":0.27799999713897705},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.27160000801086426},{"id":"https://openalex.org/keywords/sequence-learning","display_name":"Sequence learning","score":0.25060001015663147},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.24169999361038208},{"id":"https://openalex.org/keywords/immune-escape","display_name":"Immune escape","score":0.23929999768733978}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5788000226020813},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5595999956130981},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.31130000948905945},{"id":"https://openalex.org/C2982736386","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Statistical learning","level":2,"score":0.27799999713897705},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.27160000801086426},{"id":"https://openalex.org/C40506919","wikidata":"https://www.wikidata.org/wiki/Q7452469","display_name":"Sequence learning","level":2,"score":0.25060001015663147},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.24639999866485596},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.24169999361038208},{"id":"https://openalex.org/C3018558359","wikidata":"https://www.wikidata.org/wiki/Q1660157","display_name":"Immune escape","level":3,"score":0.23929999768733978},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.23770000040531158}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":true},{"descriptor_ui":"D000098437","descriptor_name":"Prediction Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098437","descriptor_name":"Prediction Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000940","descriptor_name":"Antigenic Variation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000940","descriptor_name":"Antigenic Variation","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":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057131","descriptor_name":"Immune Evasion","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D057131","descriptor_name":"Immune Evasion","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000276","qualifier_name":"immunology","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D064370","descriptor_name":"Spike Glycoprotein, Coronavirus","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1109/tcbbio.2026.3674782","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2026.3674782","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41843532","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41843532","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 transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:gcris.iyte.edu.tr:11147/19080","is_oa":false,"landing_page_url":"https://hdl.handle.net/11147/19080","pdf_url":null,"source":{"id":"https://openalex.org/S4306400894","display_name":"\u0130YTE (\u0130ZM\u0130R Y\u00dcKSEK TEKNOLOJ\u0130 ENST\u0130T\u00dcS\u00dc)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I120217413","host_organization_name":"Izmir Institute of Technology","host_organization_lineage":["https://openalex.org/I120217413"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Understanding":[0],"the":[1],"complex":[2],"rules":[3],"and":[4,46,71,108,123,144,170],"mechanisms":[5],"behind":[6],"viral":[7,38,109],"evolution":[8],"is":[9],"crucial":[10],"for":[11,33],"developing":[12],"better":[13],"preventive":[14],"treatments,":[15],"yet":[16],"predicting":[17],"immune-evading":[18],"mutations":[19],"remains":[20],"challenging.":[21],"Recent":[22],"advances":[23],"in":[24,34,132,140,167],"protein":[25,79],"language":[26,80],"models":[27],"have":[28],"led":[29],"to":[30,105,111,153],"novel":[31,118],"approaches":[32],"silico":[35,168],"analysis":[36],"of":[37,138,172],"escape.":[39],"We":[40,114],"introduce":[41],"CoV-SNN,":[42,55],"unifying":[43],"variant":[44,134,142],"classification":[45],"escape":[47,90,126,146],"prediction":[48],"within":[49],"an":[50,93,136],"efficient":[51],"contrastive":[52,162],"learning":[53,163],"framework.":[54],"built":[56],"on":[57,83,117],"a":[58,77,154],"Siamese":[59],"neural":[60],"network":[61],"architecture,":[62],"classifies":[63],"previously":[64],"unseen":[65],"variants":[66],"by":[67],"modeling":[68],"sequence-level":[69],"similarities":[70],"differences":[72],"through":[73],"embeddings":[74],"from":[75],"CoV-RoBERTa,":[76],"lightweight":[78],"model":[81],"trained":[82],"high-quality":[84],"SARS-CoV-2":[85],"Spike":[86],"sequences.":[87],"It":[88],"prioritizes":[89],"sequences":[91,119],"using":[92],"enhanced":[94],"Constrained":[95],"Semantic":[96],"Change":[97],"Search":[98],"(CSCS)":[99],"function":[100],"that":[101,161],"maps":[102],"antigenic":[103],"variation":[104],"semantic":[106],"change":[107],"fitness":[110],"sequence":[112],"probability.":[113],"evaluate":[115],"CoV-SNN":[116,128],"containing":[120],"both":[121],"wet-lab-verified":[122],"computationally":[124],"generated":[125],"mutations.":[127,174],"achieves":[129],"98.8%":[130],"accuracy":[131],"multi-class":[133],"classification,":[135,143],"AUC":[137],"0.909":[139],"zero-shot":[141],"97.7%":[145],"precision":[147],"at":[148],"Top-10%,":[149],"while":[150],"providing":[151],"up":[152],"125-fold":[155],"inference":[156],"speedup.":[157],"These":[158],"results":[159],"suggest":[160],"can":[164],"support":[165],"scalable":[166],"surveillance":[169],"prioritization":[171],"immune-evasive":[173]},"counts_by_year":[],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2026-03-18T00:00:00"}
