{"id":"https://openalex.org/W4417466324","doi":"https://doi.org/10.48550/arxiv.2512.14011","title":"Accelerating MHC-II Epitope Discovery via Multi-Scale Prediction in Antigen Presentation","display_name":"Accelerating MHC-II Epitope Discovery via Multi-Scale Prediction in Antigen Presentation","publication_year":2025,"publication_date":"2025-12-16","ids":{"openalex":"https://openalex.org/W4417466324","doi":"https://doi.org/10.48550/arxiv.2512.14011"},"language":null,"primary_location":{"id":"pmh:oai:arXiv.org:2512.14011","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2512.14011","pdf_url":"https://arxiv.org/pdf/2512.14011","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":null,"raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2512.14011","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Wan, Yue","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wan, Yue","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067607368","display_name":"Jiayi Yuan","orcid":"https://orcid.org/0009-0007-0121-4990"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yuan, Jiayi","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076924374","display_name":"Zhiwei Feng","orcid":"https://orcid.org/0000-0001-6533-8932"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Feng, Zhiwei","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5001445783","display_name":"Xiaowei Jia","orcid":"https://orcid.org/0000-0001-8544-5233"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jia, Xiaowei","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"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":0.9979000091552734,"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":0.9979000091552734,"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/T10580","display_name":"Immunotherapy and Immune Responses","score":0.0010000000474974513,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10031","display_name":"T-cell and B-cell Immunology","score":0.00039999998989515007,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/epitope","display_name":"Epitope","score":0.8571000099182129},{"id":"https://openalex.org/keywords/major-histocompatibility-complex","display_name":"Major histocompatibility complex","score":0.5428000092506409},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.4733999967575073},{"id":"https://openalex.org/keywords/antigen","display_name":"Antigen","score":0.4713999927043915},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4505999982357025},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.3621000051498413},{"id":"https://openalex.org/keywords/immune-recognition","display_name":"Immune recognition","score":0.3555000126361847}],"concepts":[{"id":"https://openalex.org/C195616568","wikidata":"https://www.wikidata.org/wiki/Q128711","display_name":"Epitope","level":3,"score":0.8571000099182129},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6873999834060669},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6478999853134155},{"id":"https://openalex.org/C207936829","wikidata":"https://www.wikidata.org/wiki/Q423163","display_name":"Major histocompatibility complex","level":3,"score":0.5428000092506409},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.4733999967575073},{"id":"https://openalex.org/C147483822","wikidata":"https://www.wikidata.org/wiki/Q103537","display_name":"Antigen","level":2,"score":0.4713999927043915},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4505999982357025},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.38589999079704285},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3621000051498413},{"id":"https://openalex.org/C3018252375","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune recognition","level":3,"score":0.3555000126361847},{"id":"https://openalex.org/C188280979","wikidata":"https://www.wikidata.org/wiki/Q911125","display_name":"Human leukocyte antigen","level":3,"score":0.35530000925064087},{"id":"https://openalex.org/C83464605","wikidata":"https://www.wikidata.org/wiki/Q575296","display_name":"Antigen presentation","level":4,"score":0.3513000011444092},{"id":"https://openalex.org/C108249834","wikidata":"https://www.wikidata.org/wiki/Q3922363","display_name":"Antigen processing","level":5,"score":0.3458000123500824},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.3456000089645386},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34220001101493835},{"id":"https://openalex.org/C2781241564","wikidata":"https://www.wikidata.org/wiki/Q1347450","display_name":"Epitope mapping","level":4,"score":0.3393000066280365},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3206000030040741},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.30230000615119934},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.3009999990463257},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.30059999227523804},{"id":"https://openalex.org/C2777601897","wikidata":"https://www.wikidata.org/wiki/Q3409113","display_name":"Presentation (obstetrics)","level":2,"score":0.27300000190734863}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2512.14011","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2512.14011","pdf_url":"https://arxiv.org/pdf/2512.14011","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2512.14011","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2512.14011","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2512.14011","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2512.14011","pdf_url":"https://arxiv.org/pdf/2512.14011","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"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":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4417466324.pdf"},"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Antigenic":[0],"epitope":[1,32,183],"presented":[2],"by":[3],"major":[4,109],"histocompatibility":[5],"complex":[6,40],"II":[7],"(MHC-II)":[8],"proteins":[9],"plays":[10],"an":[11],"essential":[12],"role":[13],"in":[14,24,180],"immunotherapy.":[15],"However,":[16],"compared":[17],"to":[18,38,142,155],"the":[19,27,74,125,130],"more":[20,35],"widely":[21],"studied":[22],"MHC-I":[23],"computational":[25,172],"immunotherapy,":[26,173],"study":[28],"of":[29,114,188],"MHC-II":[30,51,131],"antigenic":[31],"poses":[33],"significantly":[34],"challenges":[36],"due":[37],"its":[39],"binding":[41],"specificity":[42],"and":[43,55,79,87,119,185],"ambiguous":[44],"motif":[45],"patterns.":[46],"Consequently,":[47],"existing":[48,89,144],"datasets":[49],"for":[50,61,170,177],"interactions":[52],"are":[53],"smaller":[54],"less":[56],"standardized":[57],"than":[58],"those":[59],"available":[60],"MHC-I.":[62],"To":[63],"address":[64],"these":[65],"challenges,":[66],"we":[67,106],"present":[68],"a":[69,95,138,148,159,167,175],"well-curated":[70],"dataset":[71,98],"derived":[72],"from":[73],"Immune":[75],"Epitope":[76],"Database":[77],"(IEDB)":[78],"other":[80],"public":[81],"sources.":[82],"It":[83],"not":[84],"only":[85],"extends":[86],"standardizes":[88],"peptide-MHC-II":[90],"datasets,":[91],"but":[92],"also":[93],"introduces":[94],"novel":[96],"antigen-MHC-II":[97],"with":[99,147,158],"richer":[100],"biological":[101,127],"context.":[102],"Leveraging":[103],"this":[104,156,163],"dataset,":[105],"formulate":[107],"three":[108],"machine":[110],"learning":[111],"(ML)":[112],"tasks":[113],"peptide":[115,117],"binding,":[116],"presentation,":[118,121],"antigen":[120,132],"which":[122],"progressively":[123],"capture":[124],"broader":[126],"processes":[128],"within":[129],"presentation":[133],"pathway.":[134],"We":[135],"further":[136],"employ":[137],"multi-scale":[139],"evaluation":[140],"framework":[141],"benchmark":[143],"models,":[145],"along":[146],"comprehensive":[149],"analysis":[150],"over":[151],"various":[152],"modeling":[153,187],"designs":[154],"problem":[157],"modular":[160],"framework.":[161],"Overall,":[162],"work":[164],"serves":[165],"as":[166],"valuable":[168],"resource":[169],"advancing":[171],"providing":[174],"foundation":[176],"future":[178],"research":[179],"ML":[181],"guided":[182],"discovery":[184],"predictive":[186],"immune":[189],"responses.":[190]},"counts_by_year":[],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-12-18T00:00:00"}
