{"id":"https://openalex.org/W4405442410","doi":"https://doi.org/10.1145/3698587.3701379","title":"MVFormer: Predicting the pathogenicity of missense variants using gated transformers","display_name":"MVFormer: Predicting the pathogenicity of missense variants using gated transformers","publication_year":2024,"publication_date":"2024-11-22","ids":{"openalex":"https://openalex.org/W4405442410","doi":"https://doi.org/10.1145/3698587.3701379"},"language":"en","primary_location":{"id":"doi:10.1145/3698587.3701379","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3698587.3701379","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"article","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/A5113309704","display_name":"Z. J. Li","orcid":"https://orcid.org/0009-0008-6099-9895"},"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"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zong-Xuan Li","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, Hunan, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, Hunan, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110609940","display_name":"Wenkui Huang","orcid":null},"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"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wen-Kui Huang","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, Hunan, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, Hunan, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101819060","display_name":"Hong\u2010Dong Li","orcid":null},"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"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hong-Dong Li","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, Hunan, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, Hunan, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5113309704"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":null,"apc_paid":null,"fwci":0.5506,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.76416938,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9994999766349792,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9962999820709229,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9955000281333923,"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/missense-mutation","display_name":"Missense mutation","score":0.8410003781318665},{"id":"https://openalex.org/keywords/pathogenicity","display_name":"Pathogenicity","score":0.7118352651596069},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.4416252672672272},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3950692415237427},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3771725296974182},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3407548666000366},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3100956678390503},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.19498711824417114},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.13359323143959045},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1199176013469696},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.08760344982147217},{"id":"https://openalex.org/keywords/voltage","display_name":"Voltage","score":0.0770498514175415},{"id":"https://openalex.org/keywords/microbiology","display_name":"Microbiology","score":0.05778723955154419}],"concepts":[{"id":"https://openalex.org/C75563809","wikidata":"https://www.wikidata.org/wiki/Q2656896","display_name":"Missense mutation","level":4,"score":0.8410003781318665},{"id":"https://openalex.org/C64502627","wikidata":"https://www.wikidata.org/wiki/Q170065","display_name":"Pathogenicity","level":2,"score":0.7118352651596069},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.4416252672672272},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3950692415237427},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3771725296974182},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3407548666000366},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3100956678390503},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.19498711824417114},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.13359323143959045},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1199176013469696},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.08760344982147217},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0770498514175415},{"id":"https://openalex.org/C89423630","wikidata":"https://www.wikidata.org/wiki/Q7193","display_name":"Microbiology","level":1,"score":0.05778723955154419}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3698587.3701379","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3698587.3701379","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 15th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1563940013","https://openalex.org/W1970413157","https://openalex.org/W2051391520","https://openalex.org/W2051978340","https://openalex.org/W2059145105","https://openalex.org/W2063714349","https://openalex.org/W2069197202","https://openalex.org/W2072931688","https://openalex.org/W2089335658","https://openalex.org/W2100867326","https://openalex.org/W2115787060","https://openalex.org/W2161978970","https://openalex.org/W2167852161","https://openalex.org/W2171777347","https://openalex.org/W2225726427","https://openalex.org/W2256016639","https://openalex.org/W2342878844","https://openalex.org/W2417483443","https://openalex.org/W2521967673","https://openalex.org/W2535426958","https://openalex.org/W2562408240","https://openalex.org/W2773354488","https://openalex.org/W2883972171","https://openalex.org/W2891643925","https://openalex.org/W2949886398","https://openalex.org/W3029661147","https://openalex.org/W3107322429","https://openalex.org/W3123287010","https://openalex.org/W4200580850","https://openalex.org/W4281260498","https://openalex.org/W4309563206","https://openalex.org/W4400064739","https://openalex.org/W6959643953"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W3004443428","https://openalex.org/W4361004911","https://openalex.org/W1971719088","https://openalex.org/W2625862723","https://openalex.org/W2612068534","https://openalex.org/W4289526060","https://openalex.org/W2594013754","https://openalex.org/W2388990391","https://openalex.org/W2032061938"],"abstract_inverted_index":{"Accurately":[0],"predicting":[1],"the":[2,21,37,40,58,97,147,155,163,186],"pathogenicity":[3,22,89,136,187],"of":[4,24,42,66,91,107,165,180,189],"missense":[5,25,92,108,190],"variants":[6,26,109],"is":[7,33,75],"a":[8,82,125,131],"challenge":[9],"in":[10,100],"clinical":[11],"diagnosis":[12],"and":[13,73,110,129,146,194],"genomics":[14],"studies.":[15],"Although":[16],"previous":[17,43],"methods":[18,44],"have":[19,52],"facilitated":[20],"prediction":[23,90,188],"using":[27,85],"machine":[28],"learning":[29],"algorithms,":[30],"their":[31,61],"performance":[32],"still":[34,76],"limited.":[35],"On":[36,57],"one":[38],"hand,":[39,60],"features":[41,51,65,106,112,166,179],"are":[45,196],"mostly":[46],"protein-level":[47],"or":[48],"genome-level.":[49],"Transcriptlevel":[50],"not":[53],"received":[54],"enough":[55],"attention.":[56],"other":[59,148,156],"ability":[62],"to":[63,104,113,121,133,167,184],"exploit":[64,178],"diverse":[67,181],"data":[68,145,182,193],"types":[69,183],"(e.g.":[70],"textual/categorical,":[71],"numerical,":[72],"binary)":[74],"lacking.":[77],"Here,":[78],"we":[79,95,117,161,174],"propose":[80],"MVFormer,":[81],"novel":[83],"method":[84],"gated":[86,126],"transformers":[87],"for":[88],"variants.":[93,191],"Firstly,":[94],"use":[96,130],"tokenization-embedding":[98],"paradigm":[99],"natural":[101],"language":[102],"processing":[103],"encode":[105],"convert":[111,118],"token-level":[114,119],"embeddings.":[115],"Then,":[116],"embeddings":[120,123],"sample-level":[122],"by":[124,140,170],"transformer":[127],"model":[128],"classifier":[132],"generate":[134],"final":[135],"scores.":[137],"Secondly,":[138],"evaluated":[139],"cancer":[141],"somatic":[142],"variant":[143],"hotspot":[144],"6":[149],"independent":[150],"test":[151],"sets,":[152],"MVFormer":[153,168,176],"outperforms":[154],"8":[157],"state-of-the-art":[158],"methods.":[159],"Thirdly,":[160],"investigate":[162],"contribution":[164],"predictions":[169],"cross-one-group-out":[171],"experiments.":[172],"Overall,":[173],"demonstrate":[175],"can":[177],"improve":[185],"The":[192],"codes":[195],"available":[197],"at":[198],"https://github.com/genemine/MVFormer.git.":[199]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
