{"id":"https://openalex.org/W4405427266","doi":"https://doi.org/10.1145/3698587.3701335","title":"Spatiotemporal attention boosts calling of complicated variations from long reads' alignment data","display_name":"Spatiotemporal attention boosts calling of complicated variations from long reads' alignment data","publication_year":2024,"publication_date":"2024-11-22","ids":{"openalex":"https://openalex.org/W4405427266","doi":"https://doi.org/10.1145/3698587.3701335"},"language":"en","primary_location":{"id":"doi:10.1145/3698587.3701335","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3698587.3701335","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"gold","oa_url":"https://doi.org/10.1145/3698587.3701335","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101787464","display_name":"Ying Shi","orcid":"https://orcid.org/0000-0003-1443-1912"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]},{"id":"https://openalex.org/I181877577","display_name":"Shanxi University","ror":"https://ror.org/03y3e3s17","country_code":"CN","type":"education","lineage":["https://openalex.org/I181877577"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ying Shi","raw_affiliation_strings":["School of Computer and Information Technology, Shanxi University Taiyuan, Shanxi, China, Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"School of Computer and Information Technology, Shanxi University Taiyuan, Shanxi, China, Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I180726961","https://openalex.org/I181877577"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Shifu Luo","orcid":"https://orcid.org/0000-0001-9735-4670"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]},{"id":"https://openalex.org/I204512498","display_name":"University of Macau","ror":"https://ror.org/01r4q9n85","country_code":"MO","type":"education","lineage":["https://openalex.org/I204512498"]}],"countries":["CN","MO"],"is_corresponding":false,"raw_author_name":"Shifu Luo","raw_affiliation_strings":["Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, Guangdong, China, Health Sciences, University of Macau, Taipa, Macau SAR, China"],"affiliations":[{"raw_affiliation_string":"Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, Guangdong, China, Health Sciences, University of Macau, Taipa, Macau SAR, China","institution_ids":["https://openalex.org/I180726961","https://openalex.org/I204512498"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101465265","display_name":"Yi Pan","orcid":"https://orcid.org/0000-0002-2766-3096"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi Pan","raw_affiliation_strings":["Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, Guangdong, China, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, Guangdong, China, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I4210145761","https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083170497","display_name":"Hao Wu","orcid":"https://orcid.org/0000-0003-1269-7354"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Wu","raw_affiliation_strings":["Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, Guangdong, China Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"Computer Science and Control Engineering, Shenzhen University of Advanced Technology, Shenzhen, Guangdong, China Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I4210145761","https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100773704","display_name":"Wenjian Wang","orcid":"https://orcid.org/0000-0002-8276-3639"},"institutions":[{"id":"https://openalex.org/I181877577","display_name":"Shanxi University","ror":"https://ror.org/03y3e3s17","country_code":"CN","type":"education","lineage":["https://openalex.org/I181877577"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenjian Wang","raw_affiliation_strings":["School of Computer and Information Technology, Shanxi University, Taiyuan, Shanxi, China"],"affiliations":[{"raw_affiliation_string":"School of Computer and Information Technology, Shanxi University, Taiyuan, Shanxi, China","institution_ids":["https://openalex.org/I181877577"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017861049","display_name":"Jinyan Li","orcid":"https://orcid.org/0000-0003-1833-7413"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]},{"id":"https://openalex.org/I4210145761","display_name":"Shenzhen Institutes of Advanced Technology","ror":"https://ror.org/04gh4er46","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210145761"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinyan Li","raw_affiliation_strings":["Computer Science and Control Engineering, Shenzhen University of Advanced Technology Shenzhen, Guangdong, China Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China"],"affiliations":[{"raw_affiliation_string":"Computer Science and Control Engineering, Shenzhen University of Advanced Technology Shenzhen, Guangdong, China Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I4210145761","https://openalex.org/I180726961"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5101787464"],"corresponding_institution_ids":["https://openalex.org/I180726961","https://openalex.org/I181877577"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.20829354,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"10"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11307","display_name":"Domain Adaptation and Few-Shot Learning","score":0.989300012588501,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T11307","display_name":"Domain Adaptation and Few-Shot Learning","score":0.989300012588501,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9876000285148621,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9843000173568726,"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/computer-science","display_name":"Computer science","score":0.6856471300125122},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.40324991941452026}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6856471300125122},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.40324991941452026}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3698587.3701335","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3698587.3701335","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":{"id":"doi:10.1145/3698587.3701335","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3698587.3701335","pdf_url":null,"source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4118435245","display_name":null,"funder_award_id":"No.U21A20513, No.62476157, No.62076154","funder_id":"https://openalex.org/F4320323817","funder_display_name":"Universitas Brawijaya"}],"funders":[{"id":"https://openalex.org/F4320323817","display_name":"Universitas Brawijaya","ror":"https://ror.org/01wk3d929"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W2109255472","https://openalex.org/W2233072870","https://openalex.org/W2297084330","https://openalex.org/W2607669908","https://openalex.org/W2762638728","https://openalex.org/W2889664156","https://openalex.org/W2916803445","https://openalex.org/W2919717584","https://openalex.org/W2950993016","https://openalex.org/W2951331911","https://openalex.org/W2979942779","https://openalex.org/W3014232442","https://openalex.org/W3033870872","https://openalex.org/W3196566472","https://openalex.org/W3208186059","https://openalex.org/W4236965008","https://openalex.org/W4313430580","https://openalex.org/W4315707395","https://openalex.org/W6696884364","https://openalex.org/W6743731764","https://openalex.org/W6753412334","https://openalex.org/W6754484989","https://openalex.org/W6768952390"],"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/W4396696052"],"abstract_inverted_index":{"With":[0],"the":[1,5,32,48,79,97,102,119,138,145,150,155,158,168,172,195,211,217,224,230,236,256,262,272,291,300,304,306,311,315,318],"latest":[2],"Q20":[3,85,177],"technology,":[4],"base":[6,34,307],"error":[7,35,308],"rate":[8,36,309],"in":[9,37,42,47,149,171],"ONT":[10,80],"long-read":[11],"sequencing":[12,22,142,312],"has":[13],"been":[14],"down":[15],"to":[16,62,75,117,136],"1%.":[17],"However,":[18],"such":[19],"rates":[20],"of":[21,52,121,132,180,245,251,267,302,310],"errors":[23,143],"(base":[24],"insertions,":[25],"deletions":[26],"or":[27,90],"substitutions)":[28],"still":[29,283],"lag":[30],"behind":[31],"0.1%":[33],"NGS":[38],"short":[39],"reads,":[40],"resulting":[41],"many":[43],"complicated":[44,98,126,169,237,297,317],"variation":[45,99,122,127,238],"regions":[46,100,170],"full":[49],"alignment":[50,151,173,220,293,319],"data":[51,152,174,294,320],"deeply":[53],"sequenced":[54],"long":[55,81],"reads":[56,82,103,292],"and":[57,144,204,229,270,285,314],"posing":[58],"a":[59,87,110,265],"big":[60],"challenge":[61],"germline":[63,147],"variant":[64],"calling.":[65],"For":[66],"example,":[67],"current":[68,191,212],"deep":[69,113],"learning":[70,114],"methods":[71,247],"could":[72,91],"misidentify":[73,92],"20,000":[74],"30,000":[76,95],"variants":[77],"from":[78,190],"basecalled":[83,104,175],"by":[84,105,157,176,188,200,205,226,232,264,274],"on":[86,124,167,178,202,207,216,235,248,255],"single":[88],"chromosome,":[89],"more":[93,296,316],"than":[94],"at":[96,162],"when":[101,290],"Guppy":[106,218,257],"v5.0.14.":[107],"We":[108,240],"proposed":[109],"spatiotemporal":[111,133],"attention":[112,134],"method":[115],"(Attdeepcaller)":[116],"boost":[118],"performance":[120],"calling":[123],"these":[125,246],"regions.":[128,239],"The":[129],"novel":[130],"use":[131],"is":[135,198],"modulate":[137],"confusion":[139],"between":[140],"genuine":[141],"true":[146],"variations":[148],"so":[153],"that":[154,280],"identification":[156],"algorithms":[159],"becomes":[160,295],"clear":[161],"most":[163],"cases.":[164],"As":[165],"tested":[166,215],"chr1":[179],"HG002,":[181],"Attdeepcaller":[182,222,260,281],"made":[183],"only":[184],"22,739":[185],"misidentifications,":[186],"reduced":[187,199],"12.69%":[189],"26,043":[192],"misidentifications.":[193],"Similarly,":[194],"misidentification":[196],"number":[197],"16.49%":[201],"HG003":[203],"23.58%":[206],"HG004":[208],"compared":[209],"with":[210],"best.":[213],"When":[214],"5":[219],"data,":[221,313],"improved":[223,271],"precision":[225,263],"3":[227],"percent":[228,234,269],"recall":[231,273],"1":[233],"also":[241],"conducted":[242],"comparative":[243],"analysis":[244],"old":[249],"versions":[250],"guppy":[252],"data.":[253],"Specifically":[254],"v3.4.5":[258],"datasets,":[259],"boosted":[261],"jump":[266],"16":[268],"10":[275],"percent.":[276],"This":[277],"result":[278],"suggests":[279],"can":[282,286],"work":[284,287],"substantially":[288],"better":[289],"(the":[298],"older":[299],"version":[301],"basecalling,":[303],"higher":[305],"is).":[321]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
