{"id":"https://openalex.org/W4380303551","doi":"https://doi.org/10.1109/jbhi.2023.3284794","title":"Graph Neural Networks With Multiple Prior Knowledge for Multi-Omics Data Analysis","display_name":"Graph Neural Networks With Multiple Prior Knowledge for Multi-Omics Data Analysis","publication_year":2023,"publication_date":"2023-06-12","ids":{"openalex":"https://openalex.org/W4380303551","doi":"https://doi.org/10.1109/jbhi.2023.3284794","pmid":"https://pubmed.ncbi.nlm.nih.gov/37307177"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2023.3284794","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2023.3284794","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"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 Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://dr.ntu.edu.sg/bitstream/10356/171101/2/Graph%20Neural%20Networks%20with%20Multiple%20PriorKnowledge%20for%20Multi-Omics%20Data%20Analysis.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042079993","display_name":"Shunxin Xiao","orcid":"https://orcid.org/0000-0003-1187-8719"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]},{"id":"https://openalex.org/I80947539","display_name":"Fuzhou University","ror":"https://ror.org/011xvna82","country_code":"CN","type":"education","lineage":["https://openalex.org/I80947539"]}],"countries":["CN","SG"],"is_corresponding":false,"raw_author_name":"Shunxin Xiao","raw_affiliation_strings":["School of Computer Science and Engineering, Nanyang Technological University, Singapore","College of Computer and Data Science, Fuzhou University, Fuzhou, China"],"raw_orcid":"https://orcid.org/0000-0003-1187-8719","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]},{"raw_affiliation_string":"College of Computer and Data Science, Fuzhou University, Fuzhou, China","institution_ids":["https://openalex.org/I80947539"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036978677","display_name":"Huibin Lin","orcid":"https://orcid.org/0000-0002-7774-7722"},"institutions":[{"id":"https://openalex.org/I80947539","display_name":"Fuzhou University","ror":"https://ror.org/011xvna82","country_code":"CN","type":"education","lineage":["https://openalex.org/I80947539"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huibin Lin","raw_affiliation_strings":["College of Computer and Data Science, Fuzhou University, Fuzhou, China"],"raw_orcid":"https://orcid.org/0000-0002-7774-7722","affiliations":[{"raw_affiliation_string":"College of Computer and Data Science, Fuzhou University, Fuzhou, China","institution_ids":["https://openalex.org/I80947539"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004246659","display_name":"Conghao Wang","orcid":"https://orcid.org/0000-0002-6102-6576"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Conghao Wang","raw_affiliation_strings":["School of Computer Science and Engineering, Nanyang Technological University, Singapore"],"raw_orcid":"https://orcid.org/0000-0002-6102-6576","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100604225","display_name":"Shiping Wang","orcid":"https://orcid.org/0000-0001-5195-9682"},"institutions":[{"id":"https://openalex.org/I80947539","display_name":"Fuzhou University","ror":"https://ror.org/011xvna82","country_code":"CN","type":"education","lineage":["https://openalex.org/I80947539"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shiping Wang","raw_affiliation_strings":["College of Computer and Data Science, Fuzhou University, Fuzhou, China"],"raw_orcid":"https://orcid.org/0000-0001-5195-9682","affiliations":[{"raw_affiliation_string":"College of Computer and Data Science, Fuzhou University, Fuzhou, China","institution_ids":["https://openalex.org/I80947539"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026076885","display_name":"Jagath C. Rajapakse","orcid":"https://orcid.org/0000-0001-7944-1658"},"institutions":[{"id":"https://openalex.org/I172675005","display_name":"Nanyang Technological University","ror":"https://ror.org/02e7b5302","country_code":"SG","type":"education","lineage":["https://openalex.org/I172675005"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Jagath C. Rajapakse","raw_affiliation_strings":["School of Computer Science and Engineering, Nanyang Technological University, Singapore"],"raw_orcid":"https://orcid.org/0000-0001-7944-1658","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanyang Technological University, Singapore","institution_ids":["https://openalex.org/I172675005"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":5.1008,"has_fulltext":true,"cited_by_count":55,"citation_normalized_percentile":{"value":0.96825935,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"27","issue":"9","first_page":"4591","last_page":"4600"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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":0.9994000196456909,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9811999797821045,"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":0.7195183634757996},{"id":"https://openalex.org/keywords/omics","display_name":"Omics","score":0.6693405508995056},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5548111200332642},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5435521602630615},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5111268162727356},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4603554606437683},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3932774066925049},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2420189082622528},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.1602286994457245},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09937548637390137}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7195183634757996},{"id":"https://openalex.org/C157585117","wikidata":"https://www.wikidata.org/wiki/Q158666","display_name":"Omics","level":2,"score":0.6693405508995056},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5548111200332642},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5435521602630615},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5111268162727356},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4603554606437683},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3932774066925049},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2420189082622528},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.1602286994457245},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09937548637390137},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001709","descriptor_name":"Biotechnology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001709","descriptor_name":"Biotechnology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001709","descriptor_name":"Biotechnology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1109/jbhi.2023.3284794","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2023.3284794","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"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 Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:37307177","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37307177","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 journal of biomedical and health informatics","raw_type":null},{"id":"pmh:oai:dr.ntu.edu.sg:10356/171101","is_oa":true,"landing_page_url":"https://hdl.handle.net/10356/171101","pdf_url":"https://dr.ntu.edu.sg/bitstream/10356/171101/2/Graph%20Neural%20Networks%20with%20Multiple%20PriorKnowledge%20for%20Multi-Omics%20Data%20Analysis.pdf","source":{"id":"https://openalex.org/S4306402609","display_name":"DR-NTU (Nanyang Technological University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I172675005","host_organization_name":"Nanyang Technological University","host_organization_lineage":["https://openalex.org/I172675005"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"}],"best_oa_location":{"id":"pmh:oai:dr.ntu.edu.sg:10356/171101","is_oa":true,"landing_page_url":"https://hdl.handle.net/10356/171101","pdf_url":"https://dr.ntu.edu.sg/bitstream/10356/171101/2/Graph%20Neural%20Networks%20with%20Multiple%20PriorKnowledge%20for%20Multi-Omics%20Data%20Analysis.pdf","source":{"id":"https://openalex.org/S4306402609","display_name":"DR-NTU (Nanyang Technological University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I172675005","host_organization_name":"Nanyang Technological University","host_organization_lineage":["https://openalex.org/I172675005"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G203653162","display_name":null,"funder_award_id":"U21A20472 and 62276065","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G225997096","display_name":null,"funder_award_id":"202106650030","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"},{"id":"https://openalex.org/G2979006455","display_name":null,"funder_award_id":"62276065","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3794798619","display_name":null,"funder_award_id":"U21A20472","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8672504904","display_name":null,"funder_award_id":"2021YFB3600503","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/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4380303551.pdf","grobid_xml":"https://content.openalex.org/works/W4380303551.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1565746575","https://openalex.org/W2057559260","https://openalex.org/W2611138580","https://openalex.org/W2767593474","https://openalex.org/W2788281782","https://openalex.org/W2790295707","https://openalex.org/W2900569176","https://openalex.org/W2951209146","https://openalex.org/W2955502047","https://openalex.org/W2964015378","https://openalex.org/W2966234499","https://openalex.org/W2998662521","https://openalex.org/W3014654829","https://openalex.org/W3028304854","https://openalex.org/W3047056765","https://openalex.org/W3093053585","https://openalex.org/W3116278528","https://openalex.org/W3130891725","https://openalex.org/W3170986249","https://openalex.org/W3176966473","https://openalex.org/W3190730109","https://openalex.org/W3191368886","https://openalex.org/W3191867763","https://openalex.org/W3192157621","https://openalex.org/W3192677404","https://openalex.org/W4206781047","https://openalex.org/W4280605145","https://openalex.org/W4280617006","https://openalex.org/W4285723986","https://openalex.org/W4287812705","https://openalex.org/W6726873649","https://openalex.org/W6776700526"],"related_works":["https://openalex.org/W177137871","https://openalex.org/W4292302930","https://openalex.org/W4386960635","https://openalex.org/W2594649246","https://openalex.org/W2924366642","https://openalex.org/W3184567430","https://openalex.org/W4286491824","https://openalex.org/W2955498781","https://openalex.org/W4399390205","https://openalex.org/W4390585130"],"abstract_inverted_index":{"With":[0],"the":[1,92,99,112,135,175,178,184],"development":[2],"of":[3,8,94,177],"biotechnology,":[4],"a":[5,76,119,130,142,146,151,159],"large":[6],"amount":[7],"multi-omics":[9,46,77,108,156,169,180,204],"data":[10,78,109],"have":[11,51,60],"been":[12,35,61],"collected":[13],"for":[14,166],"precision":[15],"medicine.":[16],"There":[17],"exists":[18],"multiple":[19,67,83,104],"graph-based":[20],"prior":[21,84,105,127,138],"biological":[22],"knowledge":[23,65,85],"about":[24],"omics":[25],"data,":[26],"such":[27],"as":[28],"gene-gene":[29],"interaction":[30],"networks.":[31],"Recently,":[32],"there":[33],"has":[34],"an":[36],"increasing":[37],"interest":[38],"in":[39],"introducing":[40],"graph":[41,87],"neural":[42,88],"networks":[43,139],"(GNNs)":[44],"into":[45,86,107],"learning.":[47],"However,":[48],"existing":[49],"methods":[50,202],"not":[52],"fully":[53],"exploited":[54],"these":[55],"graphical":[56],"priors":[57],"since":[58],"none":[59],"able":[62],"to":[63,102,123,133,149,162],"integrate":[64],"from":[66,126,154],"sources":[68],"simultaneously.":[69],"To":[70,91],"solve":[71],"this":[72,97],"problem,":[73],"we":[74,173],"propose":[75],"analysis":[79,170],"framework":[80],"by":[81,140],"incorporating":[82],"network":[89],"(MPK-GNN).":[90],"best":[93],"our":[95],"knowledge,":[96],"is":[98],"first":[100],"attempt":[101],"introduce":[103],"graphs":[106],"analysis.":[110],"Specifically,":[111],"proposed":[113,179],"method":[114],"contains":[115],"four":[116],"parts:":[117],"(1)":[118],"feature-level":[120],"learning":[121,181,201],"module":[122,132,148,161],"aggregate":[124],"information":[125],"graphs;":[128],"(2)":[129],"projection":[131],"maximize":[134],"agreement":[136],"among":[137],"optimizing":[141],"contrastive":[143],"loss;":[144],"(3)":[145],"sample-level":[147],"learn":[150],"global":[152],"representation":[153],"input":[155],"features;":[157],"(4)":[158],"task-specific":[160],"flexibly":[163],"extend":[164],"MPK-GNN":[165,194],"various":[167],"downstream":[168],"tasks.":[171],"Finally,":[172],"verify":[174],"effectiveness":[176],"algorithm":[182],"on":[183],"cancer":[185],"molecular":[186],"subtype":[187],"classification":[188],"task.":[189],"Experimental":[190],"results":[191],"show":[192],"that":[193],"outperforms":[195],"other":[196],"state-of-the-art":[197],"algorithms,":[198],"including":[199],"multi-view":[200],"and":[203],"integrative":[205],"approaches.":[206]},"counts_by_year":[{"year":2026,"cited_by_count":14},{"year":2025,"cited_by_count":29},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":4}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
