{"id":"https://openalex.org/W3107396733","doi":"https://doi.org/10.1145/3400286.3418243","title":"Accelerating Variant Calling with Parallelized DeepVariant","display_name":"Accelerating Variant Calling with Parallelized DeepVariant","publication_year":2020,"publication_date":"2020-10-13","ids":{"openalex":"https://openalex.org/W3107396733","doi":"https://doi.org/10.1145/3400286.3418243","mag":"3107396733"},"language":"en","primary_location":{"id":"doi:10.1145/3400286.3418243","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3400286.3418243","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Research in Adaptive and Convergent Systems","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/A5076832732","display_name":"Chih-Han Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Chih-Han Yang","raw_affiliation_strings":["National Taiwan University"],"affiliations":[{"raw_affiliation_string":"National Taiwan University","institution_ids":["https://openalex.org/I16733864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074230745","display_name":"Jhih-Wun Zeng","orcid":null},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Jhih-Wun Zeng","raw_affiliation_strings":["National Taiwan University"],"affiliations":[{"raw_affiliation_string":"National Taiwan University","institution_ids":["https://openalex.org/I16733864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047375832","display_name":"Cheng-Yueh Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Cheng-Yueh Liu","raw_affiliation_strings":["National Taiwan University"],"affiliations":[{"raw_affiliation_string":"National Taiwan University","institution_ids":["https://openalex.org/I16733864"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020028710","display_name":"Shih\u2010Hao Hung","orcid":"https://orcid.org/0000-0003-2043-2663"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Shih-Hao Hung","raw_affiliation_strings":["National Taiwan University"],"affiliations":[{"raw_affiliation_string":"National Taiwan University","institution_ids":["https://openalex.org/I16733864"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5076832732"],"corresponding_institution_ids":["https://openalex.org/I16733864"],"apc_list":null,"apc_paid":null,"fwci":0.2486,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.54552024,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"13","last_page":"18"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994999766349792,"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":0.9904999732971191,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9868999719619751,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8102847337722778},{"id":"https://openalex.org/keywords/workstation","display_name":"Workstation","score":0.7771008610725403},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6864035129547119},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5767908692359924},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5463725328445435},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5157651901245117},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.48477524518966675},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4603763222694397},{"id":"https://openalex.org/keywords/program-optimization","display_name":"Program optimization","score":0.441805899143219},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2667275667190552},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.205440491437912},{"id":"https://openalex.org/keywords/compiler","display_name":"Compiler","score":0.141454815864563},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13753053545951843}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8102847337722778},{"id":"https://openalex.org/C67953723","wikidata":"https://www.wikidata.org/wiki/Q192525","display_name":"Workstation","level":2,"score":0.7771008610725403},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6864035129547119},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5767908692359924},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5463725328445435},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5157651901245117},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.48477524518966675},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4603763222694397},{"id":"https://openalex.org/C139571649","wikidata":"https://www.wikidata.org/wiki/Q1156793","display_name":"Program optimization","level":3,"score":0.441805899143219},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2667275667190552},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.205440491437912},{"id":"https://openalex.org/C169590947","wikidata":"https://www.wikidata.org/wiki/Q47506","display_name":"Compiler","level":2,"score":0.141454815864563},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13753053545951843},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3400286.3418243","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3400286.3418243","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the International Conference on Research in Adaptive and Convergent Systems","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":10,"referenced_works":["https://openalex.org/W2091546524","https://openalex.org/W2104846587","https://openalex.org/W2108234281","https://openalex.org/W2119180969","https://openalex.org/W2396849069","https://openalex.org/W2513408092","https://openalex.org/W2590415818","https://openalex.org/W2596992411","https://openalex.org/W2763759902","https://openalex.org/W2889664156"],"related_works":["https://openalex.org/W2045348955","https://openalex.org/W2352028719","https://openalex.org/W2584886384","https://openalex.org/W2378667902","https://openalex.org/W2791088446","https://openalex.org/W2052769075","https://openalex.org/W4206808270","https://openalex.org/W1999130367","https://openalex.org/W2134078163","https://openalex.org/W3081644756"],"abstract_inverted_index":{"Due":[0],"to":[1,43,70,91,99,111,126],"the":[2,6,11,32,41,72,76,101,113,118,124,128,133,153,171],"rapid":[3],"evolution":[4],"of":[5,13,22,34,49,78,120,132,139,149],"next-generation":[7],"sequencing":[8],"(NGS)":[9],"technology,":[10],"sequence":[12],"an":[14,80],"individual's":[15],"genome":[16,50],"can":[17,151],"be":[18],"determined":[19],"from":[20],"billions":[21],"short":[23],"reads":[24],"at":[25],"a":[26,86,104,107,137,144],"decreasing":[27],"cost,":[28],"which":[29,84,166],"has":[30],"advanced":[31],"fields":[33],"medical":[35],"research":[36],"and":[37,67,122,130,163],"precision":[38],"medicine":[39],"with":[40,106,136],"ability":[42],"correlate":[44],"mutations":[45],"between":[46],"genomes.":[47],"Analysis":[48],"sequences,":[51],"especially":[52],"variant":[53],"calling,":[54],"is":[55],"exceedingly":[56],"computationally":[57],"intensive,":[58],"as":[59],"it":[60,95],"demands":[61],"large":[62],"storage":[63],"capacity,":[64],"computing":[65],"power,":[66],"high-speed":[68],"network":[69,89],"reduce":[71,127],"processing":[73],"time.":[74],"In":[75],"case":[77],"DeepVariant,":[79],"open-source":[81],"software":[82],"package":[83],"employs":[85],"deep":[87],"neural":[88],"(DNN)":[90],"calls":[92],"genetic":[93],"variants,":[94],"took":[96],"four":[97],"hours":[98],"complete":[100],"analysis":[102],"on":[103,159],"workstation":[105],"high-performance":[108],"GPU":[109],"device":[110],"accelerate":[112],"DNN.":[114],"Therefore,":[115],"we":[116],"profiled":[117],"performance":[119],"DeepVariant":[121,150],"refactored":[123],"code":[125,140],"time":[129],"cost":[131],"NGS":[134],"pipeline":[135],"series":[138],"optimization":[141],"works.":[142],"As":[143],"result,":[145],"our":[146],"distributed":[147],"version":[148],"finish":[152],"same":[154],"job":[155],"within":[156],"8":[157,160,164],"minutes":[158],"dual-CPU":[161],"nodes":[162],"GPUs,":[165],"outperforms":[167],"commercial":[168],"versions":[169],"in":[170],"market.":[172]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
