{"id":"https://openalex.org/W4288421329","doi":"https://doi.org/10.1145/3535508.3545551","title":"DeepViFi","display_name":"DeepViFi","publication_year":2022,"publication_date":"2022-07-28","ids":{"openalex":"https://openalex.org/W4288421329","doi":"https://doi.org/10.1145/3535508.3545551"},"language":"en","primary_location":{"id":"doi:10.1145/3535508.3545551","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3535508.3545551","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3535508.3545551","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 13th 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://dl.acm.org/doi/pdf/10.1145/3535508.3545551","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069555967","display_name":"Utkrisht Rajkumar","orcid":"https://orcid.org/0000-0002-2825-6310"},"institutions":[{"id":"https://openalex.org/I2800935791","display_name":"UC San Diego Health System","ror":"https://ror.org/01kbfgm16","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800935791"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Utkrisht Rajkumar","raw_affiliation_strings":["UC San Diego"],"affiliations":[{"raw_affiliation_string":"UC San Diego","institution_ids":["https://openalex.org/I2800935791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038620773","display_name":"Sara Javadzadeh","orcid":"https://orcid.org/0000-0001-8240-2860"},"institutions":[{"id":"https://openalex.org/I2800935791","display_name":"UC San Diego Health System","ror":"https://ror.org/01kbfgm16","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800935791"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sara Javadzadeh","raw_affiliation_strings":["UC San Diego"],"affiliations":[{"raw_affiliation_string":"UC San Diego","institution_ids":["https://openalex.org/I2800935791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007356332","display_name":"Mihir Bafna","orcid":"https://orcid.org/0000-0001-8182-5888"},"institutions":[{"id":"https://openalex.org/I130701444","display_name":"Georgia Institute of Technology","ror":"https://ror.org/01zkghx44","country_code":"US","type":"education","lineage":["https://openalex.org/I130701444"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mihir Bafna","raw_affiliation_strings":["Georgia Institute of Technology"],"affiliations":[{"raw_affiliation_string":"Georgia Institute of Technology","institution_ids":["https://openalex.org/I130701444"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100943740","display_name":"Dongxia Wu","orcid":"https://orcid.org/0009-0005-5059-2395"},"institutions":[{"id":"https://openalex.org/I2800935791","display_name":"UC San Diego Health System","ror":"https://ror.org/01kbfgm16","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800935791"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dongxia Wu","raw_affiliation_strings":["UC San Diego"],"affiliations":[{"raw_affiliation_string":"UC San Diego","institution_ids":["https://openalex.org/I2800935791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057778679","display_name":"Rose Yu","orcid":"https://orcid.org/0000-0002-8491-7937"},"institutions":[{"id":"https://openalex.org/I2800935791","display_name":"UC San Diego Health System","ror":"https://ror.org/01kbfgm16","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800935791"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rose Yu","raw_affiliation_strings":["UC San Diego"],"affiliations":[{"raw_affiliation_string":"UC San Diego","institution_ids":["https://openalex.org/I2800935791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039500313","display_name":"Jingbo Shang","orcid":"https://orcid.org/0000-0002-7249-4404"},"institutions":[{"id":"https://openalex.org/I2800935791","display_name":"UC San Diego Health System","ror":"https://ror.org/01kbfgm16","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800935791"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jingbo Shang","raw_affiliation_strings":["UC San Diego"],"affiliations":[{"raw_affiliation_string":"UC San Diego","institution_ids":["https://openalex.org/I2800935791"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028801735","display_name":"Vineet Bafna","orcid":"https://orcid.org/0000-0002-5810-6241"},"institutions":[{"id":"https://openalex.org/I2800935791","display_name":"UC San Diego Health System","ror":"https://ror.org/01kbfgm16","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2800935791"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vineet Bafna","raw_affiliation_strings":["UC San Diego"],"affiliations":[{"raw_affiliation_string":"UC San Diego","institution_ids":["https://openalex.org/I2800935791"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5069555967"],"corresponding_institution_ids":["https://openalex.org/I2800935791"],"apc_list":null,"apc_paid":null,"fwci":1.1721,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.78121939,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9919999837875366,"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/T11135","display_name":"Virology and Viral Diseases","score":0.9671000242233276,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"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":0.684131920337677},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6278293132781982},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.5471699237823486},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.49900221824645996},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4895413815975189},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4892001152038574},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.46851038932800293},{"id":"https://openalex.org/keywords/supervised-learning","display_name":"Supervised learning","score":0.4490070939064026},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4465152323246002},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.43974146246910095},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.419726699590683},{"id":"https://openalex.org/keywords/sensitivity","display_name":"Sensitivity (control systems)","score":0.41812649369239807},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3645331859588623},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.17523160576820374},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16538158059120178},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11682894825935364},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09011286497116089},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.07991474866867065}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.684131920337677},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6278293132781982},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.5471699237823486},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.49900221824645996},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4895413815975189},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4892001152038574},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.46851038932800293},{"id":"https://openalex.org/C136389625","wikidata":"https://www.wikidata.org/wiki/Q334384","display_name":"Supervised learning","level":3,"score":0.4490070939064026},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4465152323246002},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.43974146246910095},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.419726699590683},{"id":"https://openalex.org/C21200559","wikidata":"https://www.wikidata.org/wiki/Q7451068","display_name":"Sensitivity (control systems)","level":2,"score":0.41812649369239807},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3645331859588623},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.17523160576820374},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16538158059120178},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11682894825935364},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09011286497116089},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.07991474866867065},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C24326235","wikidata":"https://www.wikidata.org/wiki/Q126095","display_name":"Electronic engineering","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3535508.3545551","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3535508.3545551","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3535508.3545551","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 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.1145/3535508.3545551","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3535508.3545551","pdf_url":"https://dl.acm.org/doi/pdf/10.1145/3535508.3545551","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 13th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4288421329.pdf","grobid_xml":"https://content.openalex.org/works/W4288421329.grobid-xml"},"referenced_works_count":19,"referenced_works":["https://openalex.org/W1588320408","https://openalex.org/W1901129140","https://openalex.org/W2035322315","https://openalex.org/W2092987969","https://openalex.org/W2103441770","https://openalex.org/W2122855404","https://openalex.org/W2143680521","https://openalex.org/W2599642236","https://openalex.org/W2740018417","https://openalex.org/W2789624890","https://openalex.org/W2789682519","https://openalex.org/W2973098646","https://openalex.org/W2981137688","https://openalex.org/W3003110834","https://openalex.org/W3087291937","https://openalex.org/W3109425975","https://openalex.org/W3112321766","https://openalex.org/W3177828909","https://openalex.org/W3201424287"],"related_works":["https://openalex.org/W4380075502","https://openalex.org/W4223943233","https://openalex.org/W4312200629","https://openalex.org/W4360585206","https://openalex.org/W4364306694","https://openalex.org/W4380086463","https://openalex.org/W4225161397","https://openalex.org/W4220686584","https://openalex.org/W4246751904","https://openalex.org/W3192794374"],"abstract_inverted_index":{"We":[0,13,86],"consider":[1],"the":[2,15,43],"problem":[3,16],"of":[4,125],"identifying":[5,65],"viral":[6,40,44,67,94,126],"reads":[7,21,41,95],"in":[8,38,83,96,138],"human":[9],"host":[10],"genome":[11,99],"data.":[12,101],"pose":[14],"as":[17,20,28],"open-set":[18,84,139],"classification":[19],"can":[22,72],"originate":[23],"from":[24],"unknown":[25],"sources":[26],"such":[27],"bacterial":[29],"and":[30,59,131,133],"fungal":[31],"genomes.":[32],"Sequence-matching":[33],"methods":[34,71],"have":[35,52,80],"low":[36],"sensitivity":[37,54,82],"recognizing":[39],"when":[42],"family":[45],"is":[46],"highly":[47],"diverged.":[48],"Hidden":[49],"Markov":[50],"models":[51],"higher":[53],"but":[55,79],"require":[56],"domain-specific":[57,77,129],"training":[58],"are":[60],"difficult":[61],"to":[62,92,110,122],"repurpose":[63],"for":[64,112],"different":[66],"families.":[68],"Supervised":[69],"learning":[70,115],"be":[73],"trained":[74],"with":[75],"little":[76],"knowledge":[78],"reduced":[81],"scenarios.":[85],"present":[87],"DeepViFi,":[88],"a":[89,119],"transformer-based":[90],"pipeline,":[91],"detect":[93],"short-read":[97],"whole":[98],"sequence":[100],"At":[102],"90%":[103,107],"precision,":[104],"DeepViFi":[105,117],"achieves":[106],"recall":[108],"compared":[109],"15%":[111],"other":[113],"deep":[114],"methods.":[116],"provides":[118],"semi-supervised":[120],"framework":[121],"learn":[123],"representations":[124],"families":[127],"without":[128],"knowledge,":[130],"rapidly":[132],"accurately":[134],"identify":[135],"target":[136],"sequences":[137],"settings.":[140]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2022-07-29T00:00:00"}
