{"id":"https://openalex.org/W4408971081","doi":"https://doi.org/10.1109/tcbbio.2025.3555268","title":"NegSPQ: Similar Patient Query Based on Negative Representation of Genomic Data","display_name":"NegSPQ: Similar Patient Query Based on Negative Representation of Genomic Data","publication_year":2025,"publication_date":"2025-03-29","ids":{"openalex":"https://openalex.org/W4408971081","doi":"https://doi.org/10.1109/tcbbio.2025.3555268","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811371"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3555268","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3555268","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5101936847","display_name":"Dongdong Zhao","orcid":"https://orcid.org/0000-0002-4697-6901"},"institutions":[{"id":"https://openalex.org/I196699116","display_name":"Wuhan University of Technology","ror":"https://ror.org/03fe7t173","country_code":"CN","type":"education","lineage":["https://openalex.org/I196699116"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Dongdong Zhao","raw_affiliation_strings":["Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, Wuhan, China","Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, China"],"affiliations":[{"raw_affiliation_string":"Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, Wuhan, China","institution_ids":["https://openalex.org/I196699116"]},{"raw_affiliation_string":"Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, China","institution_ids":["https://openalex.org/I196699116"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109373598","display_name":"Qiuxiang Xu","orcid":"https://orcid.org/0009-0002-4233-5442"},"institutions":[{"id":"https://openalex.org/I196699116","display_name":"Wuhan University of Technology","ror":"https://ror.org/03fe7t173","country_code":"CN","type":"education","lineage":["https://openalex.org/I196699116"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiben Xu","raw_affiliation_strings":["Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, Wuhan, China","Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, China"],"affiliations":[{"raw_affiliation_string":"Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, Wuhan, China","institution_ids":["https://openalex.org/I196699116"]},{"raw_affiliation_string":"Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, China","institution_ids":["https://openalex.org/I196699116"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100373589","display_name":"Fan Li","orcid":"https://orcid.org/0000-0002-9338-3295"},"institutions":[{"id":"https://openalex.org/I196699116","display_name":"Wuhan University of Technology","ror":"https://ror.org/03fe7t173","country_code":"CN","type":"education","lineage":["https://openalex.org/I196699116"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fan Li","raw_affiliation_strings":["Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, Wuhan, China","Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, China"],"affiliations":[{"raw_affiliation_string":"Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, Wuhan, China","institution_ids":["https://openalex.org/I196699116"]},{"raw_affiliation_string":"Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, China","institution_ids":["https://openalex.org/I196699116"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002279622","display_name":"Yiheng Mao","orcid":"https://orcid.org/0000-0001-8314-7929"},"institutions":[{"id":"https://openalex.org/I196699116","display_name":"Wuhan University of Technology","ror":"https://ror.org/03fe7t173","country_code":"CN","type":"education","lineage":["https://openalex.org/I196699116"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yiheng Mao","raw_affiliation_strings":["Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, Wuhan, China","Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, China"],"affiliations":[{"raw_affiliation_string":"Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, Wuhan, China","institution_ids":["https://openalex.org/I196699116"]},{"raw_affiliation_string":"Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, China","institution_ids":["https://openalex.org/I196699116"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016677170","display_name":"Jianwen Xiang","orcid":"https://orcid.org/0000-0001-8440-4181"},"institutions":[{"id":"https://openalex.org/I196699116","display_name":"Wuhan University of Technology","ror":"https://ror.org/03fe7t173","country_code":"CN","type":"education","lineage":["https://openalex.org/I196699116"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianwen Xiang","raw_affiliation_strings":["Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, Wuhan, China","Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, China"],"affiliations":[{"raw_affiliation_string":"Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, Wuhan, China","institution_ids":["https://openalex.org/I196699116"]},{"raw_affiliation_string":"Hubei Key Laboratory of Transportation Internet of Things, School of Computer Science and Artificial Intelligence and Chongqing Research Institute, Wuhan University of Technology, China","institution_ids":["https://openalex.org/I196699116"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100641742","display_name":"Huanhuan Li","orcid":"https://orcid.org/0000-0003-0298-6435"},"institutions":[{"id":"https://openalex.org/I3124059619","display_name":"China University of Geosciences","ror":"https://ror.org/04gcegc37","country_code":"CN","type":"education","lineage":["https://openalex.org/I3124059619"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huanhuan Li","raw_affiliation_strings":["School of Computer Science, School of Mechanical Engineering and Electronic Information, China University of Geosciences, Wuhan, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, School of Mechanical Engineering and Electronic Information, China University of Geosciences, Wuhan, China","institution_ids":["https://openalex.org/I3124059619"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5101936847"],"corresponding_institution_ids":["https://openalex.org/I196699116"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.0661858,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"3","first_page":"1248","last_page":"1262"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.8939999938011169,"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/T10885","display_name":"Gene expression and cancer classification","score":0.8939999938011169,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.8228999972343445,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.781499981880188,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.5851342678070068},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.569279134273529},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5498341917991638},{"id":"https://openalex.org/keywords/query-optimization","display_name":"Query optimization","score":0.509512722492218},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3231462240219116},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17955458164215088},{"id":"https://openalex.org/keywords/political-science","display_name":"Political science","score":0.07885733246803284}],"concepts":[{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.5851342678070068},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.569279134273529},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5498341917991638},{"id":"https://openalex.org/C157692150","wikidata":"https://www.wikidata.org/wiki/Q2919848","display_name":"Query optimization","level":2,"score":0.509512722492218},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3231462240219116},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17955458164215088},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.07885733246803284},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3555268","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3555268","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811371","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811371","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4373705170","display_name":null,"funder_award_id":"2022YFC3321102","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G5659948335","display_name":null,"funder_award_id":"CSTC2021JCYJ-MSXMX0002","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5796742757","display_name":null,"funder_award_id":"2022YFB3104001","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7005849280","display_name":null,"funder_award_id":"61806151","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W334899620","https://openalex.org/W1970026646","https://openalex.org/W1987878615","https://openalex.org/W2017127020","https://openalex.org/W2024981950","https://openalex.org/W2028201288","https://openalex.org/W2043481183","https://openalex.org/W2065597619","https://openalex.org/W2074654811","https://openalex.org/W2087135382","https://openalex.org/W2091580995","https://openalex.org/W2125123691","https://openalex.org/W2131300413","https://openalex.org/W2136068515","https://openalex.org/W2142785340","https://openalex.org/W2166971704","https://openalex.org/W2222068751","https://openalex.org/W2343921789","https://openalex.org/W2604552141","https://openalex.org/W2737931494","https://openalex.org/W2767257195","https://openalex.org/W2803328845","https://openalex.org/W2806715823","https://openalex.org/W2895776019","https://openalex.org/W2900798344","https://openalex.org/W2901699113","https://openalex.org/W2913467662","https://openalex.org/W2986484195","https://openalex.org/W3008463130","https://openalex.org/W3030396178","https://openalex.org/W3038072559","https://openalex.org/W3082009980","https://openalex.org/W3138612854","https://openalex.org/W3162120725","https://openalex.org/W3175553310","https://openalex.org/W3211546111","https://openalex.org/W4210463533","https://openalex.org/W4213131502","https://openalex.org/W4240018112","https://openalex.org/W4312537905","https://openalex.org/W4387262027","https://openalex.org/W4387490186","https://openalex.org/W4387717560","https://openalex.org/W4400116172","https://openalex.org/W4401580217","https://openalex.org/W6636915900","https://openalex.org/W6787462171"],"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":[1,75,126,140,144,156,176,186,191,196,233,244,249,259],"development":[2],"of":[3,32,48,78,99,108,148,150,198,228,268],"genome":[4,213],"sequencing":[5],"technology,":[6],"genomic":[7,20,33,36,62,119,152,236],"data":[8,37,63],"have":[9],"been":[10],"widely":[11,112],"collected":[12],"and":[13,22,43,80,89,116,161,180,190,207,218,241,246,270,281],"used":[14,183,226],"in":[15,114,266],"real-world":[16],"scenarios,":[17],"such":[18],"as":[19],"medicine":[21],"similar":[23],"patient":[24],"query":[25,205,282],"(SPQ)":[26],"cases,":[27],"based":[28,91],"on":[29,92],"similarity":[30,109,252],"comparisons":[31],"sequences.":[34],"However,":[35],"are":[38,165,182],"unique":[39],"for":[40,131,251],"every":[41],"person":[42],"contain":[44],"a":[45,66,93],"large":[46],"amount":[47],"sensitive":[49],"information":[50,100],"involving":[51],"personal":[52],"privacy.":[53],"Therefore,":[54],"determining":[55],"how":[56],"to":[57,154,184,202,231],"protect":[58],"privacy":[59,76,132],"while":[60],"utilizing":[61],"has":[64],"become":[65],"key":[67],"issue.":[68],"In":[69],"this":[70],"paper,":[71],"we":[72,81],"mainly":[73],"investigate":[74],"protection":[77],"SPQs,":[79],"propose":[82],"five":[83,106],"algorithms":[84,104,261,292],"(NDB-ED,":[85],"NDB-Band,":[86],"NDB-Block,":[87],"NDB-SIS":[88,240],"NDB-SDS)":[90],"promising":[94,264],"technique":[95],"called":[96],"negative":[97,122],"representation":[98],"(NRI).":[101],"The":[102,254],"proposed":[103,260],"use":[105],"kinds":[107],"comparison":[110],"approaches":[111],"applied":[113],"SPQs":[115],"convert":[117],"all":[118],"sequences":[120,153],"into":[121],"databases":[123],"(NDBs,":[124],"among":[125],"most":[127],"important":[128],"NRI":[129],"forms)":[130],"protection.":[133],"When":[134],"performing":[135],"an":[136],"SPQ,":[137],"NDB-ED":[138],"approximates":[139],"edit":[141,159,163,169,188,193,229],"distance":[142,160,164,170,189,194,230],"between":[143,195,235,248],"sketches":[145,197],"(the":[146],"statistics":[147],"NDBs)":[149],"two":[151,166],"evaluate":[155,232],"dissimilarity.":[157],"Banded":[158],"block-wise":[162,192],"effective":[167],"approximate":[168],"algorithms,":[171],"which":[172],"can":[173,223,262],"greatly":[174],"reduce":[175,208],"time":[177,283],"complexity.":[178],"NDB-Band":[179],"NDB-Block":[181],"estimate":[185,243],"banded":[187],"NDB":[199],"pairs,":[200],"respectively,":[201],"further":[203],"improve":[204],"efficiency":[206,271],"communication":[209],"overhead.":[210],"Besides,":[211],"private":[212],"set":[214,219],"intersection":[215],"size":[216,221],"(SIS)":[217],"difference":[220],"(SDS)":[222],"also":[224],"be":[225],"instead":[227],"dissimilarity":[234],"pairs":[237],"during":[238,293],"SPQs.":[239],"NDB-SDS":[242],"SIS":[245],"SDS":[247],"sketches,":[250],"comparison.":[253],"experimental":[255],"results":[256,265],"demonstrate":[257],"that":[258],"achieve":[263],"terms":[267],"accuracy":[269,276],"(Our":[272],"best":[273],"algorithm":[274],"improves":[275],"by":[277],"at":[278,285],"least":[279,286],"10%":[280],"is":[284],"700":[287],"times":[288],"faster":[289],"than":[290],"existing":[291],"SPQs).":[294]},"counts_by_year":[],"updated_date":"2025-12-28T23:10:05.387466","created_date":"2025-10-10T00:00:00"}
