{"id":"https://openalex.org/W4412475032","doi":"https://doi.org/10.1007/s10489-025-06607-x","title":"TransSSVs: a Transformer-based deep learning model for accurate detection of somatic small variants in paired tumor and normal sequencing data","display_name":"TransSSVs: a Transformer-based deep learning model for accurate detection of somatic small variants in paired tumor and normal sequencing data","publication_year":2025,"publication_date":"2025-07-16","ids":{"openalex":"https://openalex.org/W4412475032","doi":"https://doi.org/10.1007/s10489-025-06607-x"},"language":"en","primary_location":{"id":"doi:10.1007/s10489-025-06607-x","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10489-025-06607-x","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10489-025-06607-x.pdf","source":{"id":"https://openalex.org/S74726891","display_name":"Applied Intelligence","issn_l":"0924-669X","issn":["0924-669X","1573-7497"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Applied Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://link.springer.com/content/pdf/10.1007/s10489-025-06607-x.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101824404","display_name":"Jing Meng","orcid":"https://orcid.org/0000-0002-9485-5645"},"institutions":[{"id":"https://openalex.org/I4387155285","display_name":"Suqian University","ror":"https://ror.org/00f93gn72","country_code":null,"type":"education","lineage":["https://openalex.org/I4387155285"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Meng","raw_affiliation_strings":["School of Information Engineering, Suqian University, Suqian, 223800, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Suqian University, Suqian, 223800, China","institution_ids":["https://openalex.org/I4387155285"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030269757","display_name":"Jiangyuan Wang","orcid":"https://orcid.org/0000-0001-9810-0912"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jiangyuan Wang","raw_affiliation_strings":["Guangzhou National Laboratory, Guangzhou, 510005, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Guangzhou National Laboratory, Guangzhou, 510005, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108777850","display_name":"Jingze Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I200296433","display_name":"Chinese Academy of Medical Sciences & Peking Union Medical College","ror":"https://ror.org/02drdmm93","country_code":"CN","type":"education","lineage":["https://openalex.org/I200296433"]},{"id":"https://openalex.org/I4210122727","display_name":"Suzhou Institute of Systems Medicine","ror":"https://ror.org/02szepc22","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210122727","https://openalex.org/I4210141683"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jingze Liu","raw_affiliation_strings":["State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, Jiangsu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, Jiangsu, China","institution_ids":["https://openalex.org/I200296433","https://openalex.org/I4210122727"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114056696","display_name":"Wenkai Song","orcid":null},"institutions":[{"id":"https://openalex.org/I24185976","display_name":"Sichuan University","ror":"https://ror.org/011ashp19","country_code":"CN","type":"education","lineage":["https://openalex.org/I24185976"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenkai Song","raw_affiliation_strings":["College of Computer Science, Sichuan University, Chengdu, 610065, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Computer Science, Sichuan University, Chengdu, 610065, China","institution_ids":["https://openalex.org/I24185976"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100351382","display_name":"Ming Li","orcid":"https://orcid.org/0000-0002-1218-2804"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Ming Li","raw_affiliation_strings":["Zhejiang Institute of Optoelectronics, Jinhua, 321004, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Zhejiang Institute of Optoelectronics, Jinhua, 321004, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047692460","display_name":"Aiping Wu","orcid":"https://orcid.org/0000-0002-5869-651X"},"institutions":[{"id":"https://openalex.org/I200296433","display_name":"Chinese Academy of Medical Sciences & Peking Union Medical College","ror":"https://ror.org/02drdmm93","country_code":"CN","type":"education","lineage":["https://openalex.org/I200296433"]},{"id":"https://openalex.org/I4210122727","display_name":"Suzhou Institute of Systems Medicine","ror":"https://ror.org/02szepc22","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210122727","https://openalex.org/I4210141683"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Aiping Wu","raw_affiliation_strings":["State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, Jiangsu, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, Jiangsu, China","institution_ids":["https://openalex.org/I200296433","https://openalex.org/I4210122727"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062116814","display_name":"Taijiao Jiang","orcid":"https://orcid.org/0000-0002-6280-6347"},"institutions":[{"id":"https://openalex.org/I200296433","display_name":"Chinese Academy of Medical Sciences & Peking Union Medical College","ror":"https://ror.org/02drdmm93","country_code":"CN","type":"education","lineage":["https://openalex.org/I200296433"]},{"id":"https://openalex.org/I4210098361","display_name":"First Affiliated Hospital of Guangzhou Medical University","ror":"https://ror.org/00z0j0d77","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210098361"]},{"id":"https://openalex.org/I4210122727","display_name":"Suzhou Institute of Systems Medicine","ror":"https://ror.org/02szepc22","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210122727","https://openalex.org/I4210141683"]},{"id":"https://openalex.org/I92039509","display_name":"Guangzhou Medical University","ror":"https://ror.org/00zat6v61","country_code":"CN","type":"education","lineage":["https://openalex.org/I92039509"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Taijiao Jiang","raw_affiliation_strings":["Guangzhou National Laboratory, Guangzhou, 510005, China","State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, Jiangsu, China","State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, China"],"raw_orcid":"https://orcid.org/0000-0002-6280-6347","affiliations":[{"raw_affiliation_string":"Guangzhou National Laboratory, Guangzhou, 510005, China","institution_ids":[]},{"raw_affiliation_string":"State Key Laboratory of Common Mechanism Research for Major Diseases, Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical College, Suzhou, 215123, Jiangsu, China","institution_ids":["https://openalex.org/I200296433","https://openalex.org/I4210122727"]},{"raw_affiliation_string":"State Key Laboratory of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, 510120, China","institution_ids":["https://openalex.org/I4210098361","https://openalex.org/I92039509"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5047692460","https://openalex.org/A5062116814"],"corresponding_institution_ids":["https://openalex.org/I200296433","https://openalex.org/I4210098361","https://openalex.org/I4210122727","https://openalex.org/I92039509"],"apc_list":{"value":2390,"currency":"EUR","value_usd":2990},"apc_paid":{"value":2390,"currency":"EUR","value_usd":2990},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.2091002,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"55","issue":"12","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9998000264167786,"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":0.9998000264167786,"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/T12422","display_name":"Radiomics and Machine Learning in Medical Imaging","score":0.9926999807357788,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11369","display_name":"Genetic factors in colorectal cancer","score":0.9837999939918518,"subfield":{"id":"https://openalex.org/subfields/2734","display_name":"Pathology and Forensic Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8294275403022766},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.6745615005493164},{"id":"https://openalex.org/keywords/somatic-cell","display_name":"Somatic cell","score":0.6355781555175781},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4801746904850006},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3589637875556946},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14602482318878174},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12115460634231567},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09571006894111633},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.08601224422454834}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8294275403022766},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.6745615005493164},{"id":"https://openalex.org/C134305767","wikidata":"https://www.wikidata.org/wiki/Q725508","display_name":"Somatic cell","level":3,"score":0.6355781555175781},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4801746904850006},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3589637875556946},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14602482318878174},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12115460634231567},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09571006894111633},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.08601224422454834},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/s10489-025-06607-x","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10489-025-06607-x","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10489-025-06607-x.pdf","source":{"id":"https://openalex.org/S74726891","display_name":"Applied Intelligence","issn_l":"0924-669X","issn":["0924-669X","1573-7497"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Applied Intelligence","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1007/s10489-025-06607-x","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s10489-025-06607-x","pdf_url":"https://link.springer.com/content/pdf/10.1007/s10489-025-06607-x.pdf","source":{"id":"https://openalex.org/S74726891","display_name":"Applied Intelligence","issn_l":"0924-669X","issn":["0924-669X","1573-7497"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Applied Intelligence","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6665687486","display_name":null,"funder_award_id":"32070678","funder_id":"https://openalex.org/F4320315254","funder_display_name":"Innovative Research Group Project of the National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320315254","display_name":"Innovative Research Group Project of the National Natural Science Foundation of China","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412475032.pdf","grobid_xml":"https://content.openalex.org/works/W4412475032.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W1959574505","https://openalex.org/W1972701998","https://openalex.org/W1985384725","https://openalex.org/W1989840284","https://openalex.org/W2023560061","https://openalex.org/W2034937344","https://openalex.org/W2076063813","https://openalex.org/W2104750097","https://openalex.org/W2112005039","https://openalex.org/W2112794562","https://openalex.org/W2119180969","https://openalex.org/W2138601221","https://openalex.org/W2147733682","https://openalex.org/W2155943701","https://openalex.org/W2163922914","https://openalex.org/W2192272998","https://openalex.org/W2338589459","https://openalex.org/W2765534399","https://openalex.org/W2794000666","https://openalex.org/W2887469830","https://openalex.org/W2919115771","https://openalex.org/W2952570350","https://openalex.org/W2963351448","https://openalex.org/W3099717514","https://openalex.org/W3147574308","https://openalex.org/W3163306278","https://openalex.org/W3203588026","https://openalex.org/W4220655797","https://openalex.org/W4220657176","https://openalex.org/W4286586290","https://openalex.org/W4315641887","https://openalex.org/W4316096017","https://openalex.org/W4365513261","https://openalex.org/W4385737488","https://openalex.org/W4386832358","https://openalex.org/W4391758720","https://openalex.org/W4401455022","https://openalex.org/W4404688382"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"Accurate":[0],"identification":[1],"of":[2,31,46,72,100,113,134,169,176],"somatic":[3,16,40,48,65,78,94,118,177,189],"small":[4,95],"variants":[5],"in":[6,12,27,138],"tumors":[7],"plays":[8],"a":[9,39,64,110,116],"crucial":[10],"role":[11],"cancer":[13],"diagnosis.":[14],"Various":[15],"mutation":[17],"callers":[18],"have":[19],"been":[20],"developed;":[21],"however,":[22],"existing":[23],"methods":[24,158],"face":[25],"limitations":[26],"modeling":[28],"mapping":[29,132],"information":[30],"flanking":[32,73,122,170],"genomic":[33,74,123,136,171],"sites":[34,36,75,124,137,172,178,190],"(genomic":[35],"adjacent":[37],"to":[38,54,89,142,173],"site)":[41],"that":[42,149],"influence":[43],"the":[44,47,59,70,77,84,104,126,139,167,174],"state":[45],"site.":[49,79],"Additionally,":[50],"they":[51],"are":[52,179,191],"unable":[53],"analyze":[55],"inter-site":[56],"interactions":[57,114],"within":[58,125],"context":[60,127,140],"sequence":[61,141],"centered":[62],"around":[63],"site":[66,119],"or":[67],"appropriately":[68],"weigh":[69],"effects":[71],"on":[76,103,159],"To":[80],"address":[81],"these":[82],"limitations,":[83],"Transformer":[85],"model":[86],"is":[87],"utilized":[88],"develop":[90],"TransSSVs":[91,101,129,150],"for":[92,185],"detecting":[93],"variants.":[96],"The":[97],"core":[98],"functionality":[99],"relies":[102],"multi-head":[105],"attention":[106,182],"mechanism,":[107],"which":[108],"generates":[109],"reliable":[111],"representation":[112],"between":[115],"candidate":[117],"and":[120,162,181,187],"its":[121],"sequence.":[128],"effectively":[130],"extract":[131],"features":[133],"various":[135],"enhance":[143],"prediction":[144],"accuracy.":[145],"Benchmarking":[146],"experiments":[147],"demonstrate":[148],"exhibit":[151],"robust":[152],"performance":[153],"when":[154],"compared":[155],"with":[156],"state-of-the-art":[157],"well-characterized":[160],"real":[161],"simulated":[163],"tumor":[164],"datasets.":[165],"Furthermore,":[166],"contributions":[168],"detection":[175],"assessed,":[180],"weight":[183],"patterns":[184],"positive":[186],"negative":[188],"analyzed.":[192]},"counts_by_year":[],"updated_date":"2026-06-13T06:13:01.061226","created_date":"2025-10-10T00:00:00"}