{"id":"https://openalex.org/W4406261478","doi":"https://doi.org/10.1109/bibm62325.2024.10822216","title":"Interpretable deep learning quantifies the impact of genomic variations on CD8+ T cell infiltration","display_name":"Interpretable deep learning quantifies the impact of genomic variations on CD8+ T cell infiltration","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406261478","doi":"https://doi.org/10.1109/bibm62325.2024.10822216"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822216","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822216","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","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/A5101912769","display_name":"Yi He","orcid":"https://orcid.org/0009-0004-5363-1102"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi He","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Changsha,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Changsha,China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019478505","display_name":"Li\u2010Wen Xu","orcid":"https://orcid.org/0000-0001-5705-0015"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liwen Xu","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Changsha,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Changsha,China","institution_ids":["https://openalex.org/I16609230"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065663582","display_name":"Xiang Wang","orcid":"https://orcid.org/0000-0001-5900-8486"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]},{"id":"https://openalex.org/I4210159865","display_name":"Xiangya Hospital Central South University","ror":"https://ror.org/05c1yfj14","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159865"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiang Wang","raw_affiliation_strings":["Central South University,2nd Xiangya Hospital,Department of Thoracic Surgery,Changsha,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Central South University,2nd Xiangya Hospital,Department of Thoracic Surgery,Changsha,China","institution_ids":["https://openalex.org/I4210159865","https://openalex.org/I139660479"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108008219","display_name":"Shaoliang Peng","orcid":"https://orcid.org/0000-0002-4647-2615"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shaoliang Peng","raw_affiliation_strings":["Hunan University,College of Computer Science and Electronic Engineering,Changsha,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hunan University,College of Computer Science and Electronic Engineering,Changsha,China","institution_ids":["https://openalex.org/I16609230"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"932","last_page":"937"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.935699999332428,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.935699999332428,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9139000177383423,"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/infiltration","display_name":"Infiltration (HVAC)","score":0.6902732849121094},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4978194236755371},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.482045978307724},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.1440710723400116},{"id":"https://openalex.org/keywords/meteorology","display_name":"Meteorology","score":0.06239989399909973}],"concepts":[{"id":"https://openalex.org/C153400128","wikidata":"https://www.wikidata.org/wiki/Q3150731","display_name":"Infiltration (HVAC)","level":2,"score":0.6902732849121094},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4978194236755371},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.482045978307724},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.1440710723400116},{"id":"https://openalex.org/C153294291","wikidata":"https://www.wikidata.org/wiki/Q25261","display_name":"Meteorology","level":1,"score":0.06239989399909973}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822216","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822216","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1994993231","https://openalex.org/W2003730490","https://openalex.org/W2039123767","https://openalex.org/W2123879591","https://openalex.org/W2340636398","https://openalex.org/W2465860350","https://openalex.org/W2779503684","https://openalex.org/W2790362775","https://openalex.org/W2796408191","https://openalex.org/W2884910323","https://openalex.org/W2894573839","https://openalex.org/W2898682581","https://openalex.org/W2906255446","https://openalex.org/W2923548794","https://openalex.org/W2938818098","https://openalex.org/W2981114563","https://openalex.org/W3003320500","https://openalex.org/W3028523516","https://openalex.org/W3029490475","https://openalex.org/W3035912217","https://openalex.org/W3045946240","https://openalex.org/W3201390648","https://openalex.org/W3203575974","https://openalex.org/W3211011084","https://openalex.org/W4206693666","https://openalex.org/W4220661685","https://openalex.org/W4292511002","https://openalex.org/W4381046896"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2355608013"],"abstract_inverted_index":{"Immune":[0],"checkpoint":[1],"inhibitors":[2],"(ICIs)":[3],"have":[4],"revolutionized":[5],"cancer":[6],"treatment,":[7],"but":[8],"challenges":[9],"remain":[10],"in":[11,47,108,135],"identifying":[12],"molecular":[13],"determinants":[14],"of":[15,71,125,132],"clinical":[16,146],"response.":[17],"To":[18],"address":[19],"this,":[20],"we":[21],"developed":[22],"a":[23],"Transformer-based":[24],"model,":[25],"ImmRegVar,":[26],"to":[27],"predict":[28],"CD8+":[29,88],"T":[30,89],"cell":[31,90],"infiltration":[32],"using":[33],"somatic":[34],"genomic":[35],"variations":[36],"from":[37],"7972":[38],"solid":[39],"tumor":[40],"samples.":[41],"ImmRegVar":[42,148],"outperforms":[43],"traditional":[44],"regression":[45],"methods":[46],"predictive":[48],"accuracy":[49],"and":[50,106,137,145,149],"model":[51],"performance.":[52],"We":[53],"introduce":[54],"an":[55,79],"innovative":[56],"explanatory":[57,151],"factor":[58,77,152],"that":[59],"combines":[60],"Transformer":[61],"attention":[62],"weights":[63],"with":[64,116],"feature":[65],"ablation":[66],"techniques,":[67],"allowing":[68],"precise":[69],"quantification":[70],"each":[72],"gene":[73],"mutation\u2019s":[74],"contribution.":[75],"This":[76,127],"offers":[78],"interpretable":[80],"metric":[81],"for":[82,141],"understanding":[83,131],"how":[84],"specific":[85],"mutations":[86],"affect":[87],"infiltration,":[91],"shedding":[92],"light":[93],"on":[94],"immune":[95,118,143],"regulatory":[96,119],"mechanisms.":[97],"Validation":[98],"through":[99],"random":[100],"permutation":[101],"tests":[102],"confirms":[103],"its":[104],"robustness":[105],"stability":[107],"high-dimensional":[109],"sparse":[110],"data.":[111],"Our":[112],"analysis":[113],"also":[114],"aligns":[115],"known":[117],"genes,":[120],"supporting":[121],"the":[122,130,150],"biological":[123],"credibility":[124],"ImmRegVar.":[126],"research":[128],"advances":[129],"key":[133],"factors":[134],"immunotherapy":[136],"opens":[138],"new":[139],"pathways":[140],"exploring":[142],"regulation":[144],"applications.":[147],"are":[153],"available":[154],"at":[155],"//github.com/Liwen-Liberty/ImmRegVar.":[156]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
