{"id":"https://openalex.org/W3065829709","doi":"https://doi.org/10.1109/tcbb.2020.3017547","title":"CIPHER-SC: Disease-Gene Association Inference Using Graph Convolution on a Context-Aware Network With Single-Cell Data","display_name":"CIPHER-SC: Disease-Gene Association Inference Using Graph Convolution on a Context-Aware Network With Single-Cell Data","publication_year":2020,"publication_date":"2020-08-18","ids":{"openalex":"https://openalex.org/W3065829709","doi":"https://doi.org/10.1109/tcbb.2020.3017547","mag":"3065829709","pmid":"https://pubmed.ncbi.nlm.nih.gov/32809944"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2020.3017547","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.3017547","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM 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":null,"display_name":"Yiding Zhang","orcid":"https://orcid.org/0000-0001-9833-1729"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yiding Zhang","raw_affiliation_strings":["Department of Automation, MOE Key Laboratory of Bioinformatics, TCM-X Centre, Bioinformatics Division, BNRIST, Tsinghua University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0001-9833-1729","affiliations":[{"raw_affiliation_string":"Department of Automation, MOE Key Laboratory of Bioinformatics, TCM-X Centre, Bioinformatics Division, BNRIST, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077321785","display_name":"Lyujie Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lyujie Chen","raw_affiliation_strings":["Department of Computer Science and Technology, State Key Laboratory of Intelligent Technology and Systems, BNRIST, Tsinghua University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0002-5629-4517","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, State Key Laboratory of Intelligent Technology and Systems, BNRIST, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076576399","display_name":"Shao Li","orcid":"https://orcid.org/0000-0002-8709-9167"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shao Li","raw_affiliation_strings":["Department of Automation, MOE Key Laboratory of Bioinformatics, TCM-X Centre, Bioinformatics Division, BNRIST, Tsinghua University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0002-8709-9167","affiliations":[{"raw_affiliation_string":"Department of Automation, MOE Key Laboratory of Bioinformatics, TCM-X Centre, Bioinformatics Division, BNRIST, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I99065089"],"apc_list":null,"apc_paid":null,"fwci":0.895,"has_fulltext":false,"cited_by_count":30,"citation_normalized_percentile":{"value":0.72687464,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"19","issue":"2","first_page":"819","last_page":"829"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998000264167786,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9998000264167786,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9991000294685364,"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":0.7188405990600586},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.652420699596405},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.48780038952827454},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4571736454963684},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.45550039410591125},{"id":"https://openalex.org/keywords/cipher","display_name":"Cipher","score":0.4500551223754883},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.43212682008743286},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3799053430557251},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.36544299125671387},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3649081587791443},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.30729204416275024},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.2994554042816162},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19084331393241882},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13453787565231323},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.09144997596740723},{"id":"https://openalex.org/keywords/encryption","display_name":"Encryption","score":0.09076002240180969}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7188405990600586},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.652420699596405},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.48780038952827454},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4571736454963684},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45550039410591125},{"id":"https://openalex.org/C2780221543","wikidata":"https://www.wikidata.org/wiki/Q4681865","display_name":"Cipher","level":3,"score":0.4500551223754883},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.43212682008743286},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3799053430557251},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36544299125671387},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3649081587791443},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.30729204416275024},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.2994554042816162},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19084331393241882},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13453787565231323},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09144997596740723},{"id":"https://openalex.org/C148730421","wikidata":"https://www.wikidata.org/wiki/Q141090","display_name":"Encryption","level":2,"score":0.09076002240180969},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2020.3017547","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2020.3017547","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32809944","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32809944","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/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3408507975","display_name":null,"funder_award_id":"6201101081","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4675402369","display_name":null,"funder_award_id":"BNR2019TD01020","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4797519339","display_name":null,"funder_award_id":"81225025","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6429079033","display_name":"\u57fa\u4e8e\u751f\u7269\u7f51\u7edc\u7684\u75c5\u8bc1\u7ed3\u5408\u7814\u7a76\u65b9\u6cd5","funder_award_id":"81630103","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8199488517","display_name":null,"funder_award_id":"BNR2019RC01012","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8918435475","display_name":null,"funder_award_id":"TFIDT2018001","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":61,"referenced_works":["https://openalex.org/W90362830","https://openalex.org/W1533230146","https://openalex.org/W1856818388","https://openalex.org/W1955052620","https://openalex.org/W1981409633","https://openalex.org/W2057035541","https://openalex.org/W2074110893","https://openalex.org/W2097498614","https://openalex.org/W2100582962","https://openalex.org/W2102839669","https://openalex.org/W2103017472","https://openalex.org/W2109555487","https://openalex.org/W2119412782","https://openalex.org/W2119418518","https://openalex.org/W2120921989","https://openalex.org/W2126249571","https://openalex.org/W2136078375","https://openalex.org/W2136410628","https://openalex.org/W2145805672","https://openalex.org/W2154654747","https://openalex.org/W2194775991","https://openalex.org/W2274610632","https://openalex.org/W2313125707","https://openalex.org/W2409852956","https://openalex.org/W2512000099","https://openalex.org/W2523369352","https://openalex.org/W2551194178","https://openalex.org/W2570972025","https://openalex.org/W2577490495","https://openalex.org/W2600453489","https://openalex.org/W2614253029","https://openalex.org/W2624021832","https://openalex.org/W2624831627","https://openalex.org/W2767734009","https://openalex.org/W2791033272","https://openalex.org/W2794480084","https://openalex.org/W2799259690","https://openalex.org/W2890210261","https://openalex.org/W2897502144","https://openalex.org/W2899728356","https://openalex.org/W2907492528","https://openalex.org/W2916458303","https://openalex.org/W2918710707","https://openalex.org/W2919115771","https://openalex.org/W2944311410","https://openalex.org/W2944872709","https://openalex.org/W2949177718","https://openalex.org/W2949243209","https://openalex.org/W2950595506","https://openalex.org/W2950777612","https://openalex.org/W2951531839","https://openalex.org/W2962756421","https://openalex.org/W2963231572","https://openalex.org/W2972577058","https://openalex.org/W3008835119","https://openalex.org/W6603694148","https://openalex.org/W6631964550","https://openalex.org/W6632766574","https://openalex.org/W6720006811","https://openalex.org/W6726873649","https://openalex.org/W6748856961"],"related_works":["https://openalex.org/W2055243143","https://openalex.org/W4321636575","https://openalex.org/W2357796999","https://openalex.org/W2045526782","https://openalex.org/W2560421304","https://openalex.org/W2950199998","https://openalex.org/W2951387065","https://openalex.org/W2134575910","https://openalex.org/W4385727351","https://openalex.org/W4306798985"],"abstract_inverted_index":{"Inference":[0],"of":[1,8,42,122,164,186],"disease-gene":[2],"associations":[3],"helps":[4],"unravel":[5],"the":[6,13,36,53,119,131,154,169,184],"pathogenesis":[7],"diseases":[9],"and":[10,40,77,149,172],"contributes":[11],"to":[12,23,63,82,97,129,135,158,188],"treatment.":[14],"Although":[15],"many":[16],"machine":[17],"learning-based":[18],"methods":[19,55],"have":[20],"been":[21],"developed":[22],"predict":[24,130,136],"causative":[25],"genes,":[26],"accurate":[27],"association":[28],"inference":[29],"remains":[30],"challenging.":[31],"One":[32],"major":[33],"reason":[34],"is":[35,195],"inaccurate":[37],"feature":[38],"selection":[39],"accumulation":[41],"error":[43],"brought":[44],"by":[45],"commonly":[46],"used":[47],"multi-stage":[48],"training":[49],"architecture.":[50,103],"In":[51],"addition,":[52],"existing":[54],"do":[56],"not":[57],"incorporate":[58],"cell-type-specific":[59,179],"information,":[60],"thus":[61],"fail":[62],"study":[64,142],"gene":[65],"functions":[66],"at":[67,197],"a":[68,79,91,99],"higher":[69],"resolution.":[70],"Therefore,":[71],"we":[72,89],"introduce":[73],"single-cell":[74,165],"transcriptome":[75],"data":[76,86,151,166],"construct":[78],"context-aware":[80],"network":[81],"unbiasedly":[83],"integrate":[84],"all":[85],"sources.":[87],"Then":[88],"develop":[90],"graph":[92],"convolution-based":[93],"approach":[94,105],"named":[95],"CIPHER-SC":[96,187],"realize":[98],"complete":[100,146],"end-to-end":[101,147],"learning":[102],"Our":[104,193],"outperforms":[106],"four":[107],"state-of-the-art":[108],"approaches":[109],"in":[110,160],"five-fold":[111],"cross-validations":[112],"on":[113],"three":[114],"distinct":[115],"test":[116],"sets":[117],"with":[118,137],"best":[120],"AUC":[121],"0.9501,":[123],"demonstrating":[124],"its":[125],"stable":[126],"ability":[127,185],"either":[128],"novel":[132],"genes":[133],"or":[134],"genetic":[138],"basis.":[139],"The":[140,162],"ablation":[141],"shows":[143],"that":[144],"our":[145,174],"design":[148],"unbiased":[150],"integration":[152],"boost":[153],"performance":[155],"from":[156],"0.8727":[157],"0.9443":[159],"AUC.":[161],"addition":[163],"further":[167],"improves":[168],"prediction":[170],"accuracy":[171],"makes":[173],"results":[175,182],"be":[176],"enriched":[177],"for":[178],"genes.":[180,192],"These":[181],"confirm":[183],"discover":[189],"reliable":[190],"disease":[191],"implementation":[194],"available":[196],"http://github.com/YidingZhang117/CIPHER-SC.":[198]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":12},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
