{"id":"https://openalex.org/W4389577034","doi":"https://doi.org/10.1109/embc40787.2023.10340045","title":"Utilizing Graph Neural Networks for Breast Cancer Prognosis Prediction with High-dimensional Genomic Data","display_name":"Utilizing Graph Neural Networks for Breast Cancer Prognosis Prediction with High-dimensional Genomic Data","publication_year":2023,"publication_date":"2023-07-24","ids":{"openalex":"https://openalex.org/W4389577034","doi":"https://doi.org/10.1109/embc40787.2023.10340045","pmid":"https://pubmed.ncbi.nlm.nih.gov/38083007"},"language":"en","primary_location":{"id":"doi:10.1109/embc40787.2023.10340045","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/embc40787.2023.10340045","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 45th Annual International Conference of the IEEE Engineering in Medicine &amp; Biology Society (EMBC)","raw_type":"proceedings-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/A5072185245","display_name":"Tzu-Chen Huang","orcid":"https://orcid.org/0000-0002-8738-7695"},"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":"Tzu-Chen Huang","raw_affiliation_strings":["National Taiwan University (NTU),Graduate Institute of Communication Engineering,Taipei,Taiwan,10617"],"affiliations":[{"raw_affiliation_string":"National Taiwan University (NTU),Graduate Institute of Communication Engineering,Taipei,Taiwan,10617","institution_ids":["https://openalex.org/I16733864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026870554","display_name":"Te-Cheng Hsu","orcid":"https://orcid.org/0000-0003-2686-925X"},"institutions":[{"id":"https://openalex.org/I25846049","display_name":"National Tsing Hua University","ror":"https://ror.org/00zdnkx70","country_code":"TW","type":"education","lineage":["https://openalex.org/I25846049"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Te-Cheng Hsu","raw_affiliation_strings":["National Tsing-Hua University,Institute of Communications Engineering,Hsinchu,Taiwan,30013"],"affiliations":[{"raw_affiliation_string":"National Tsing-Hua University,Institute of Communications Engineering,Hsinchu,Taiwan,30013","institution_ids":["https://openalex.org/I25846049"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025960594","display_name":"Yi\u2010Hsien Hsieh","orcid":"https://orcid.org/0000-0003-4942-1888"},"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":"Yi-Hsien Hsieh","raw_affiliation_strings":["National Taiwan University (NTU),Graduate Institute of Communication Engineering,Taipei,Taiwan,10617"],"affiliations":[{"raw_affiliation_string":"National Taiwan University (NTU),Graduate Institute of Communication Engineering,Taipei,Taiwan,10617","institution_ids":["https://openalex.org/I16733864"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015929431","display_name":"Che-Lin","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"]},{"id":"https://openalex.org/I99613584","display_name":"National Taipei University","ror":"https://ror.org/03e29r284","country_code":"TW","type":"education","lineage":["https://openalex.org/I99613584"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Che-Lin","raw_affiliation_strings":["National Taiwan University (NTU),Graduate Institute of Communication Engineering,Taipei,Taiwan,10617","Department of Electrical Engineering, NTU, Taipei, Taiwan","Master's Program in Smart Medicine and Health Informatics, NTU, Taipei, Taiwan","Center for Computational and Systems Biology, NTU, Taipei, Taiwan"],"affiliations":[{"raw_affiliation_string":"National Taiwan University (NTU),Graduate Institute of Communication Engineering,Taipei,Taiwan,10617","institution_ids":["https://openalex.org/I16733864"]},{"raw_affiliation_string":"Department of Electrical Engineering, NTU, Taipei, Taiwan","institution_ids":["https://openalex.org/I99613584"]},{"raw_affiliation_string":"Master's Program in Smart Medicine and Health Informatics, NTU, Taipei, Taiwan","institution_ids":[]},{"raw_affiliation_string":"Center for Computational and Systems Biology, NTU, Taipei, Taiwan","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5072185245"],"corresponding_institution_ids":["https://openalex.org/I16733864"],"apc_list":null,"apc_paid":null,"fwci":0.3503,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.67355456,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"45","issue":null,"first_page":"1","last_page":"4"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.9993000030517578,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9990000128746033,"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":0.9940999746322632,"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/breast-cancer","display_name":"Breast cancer","score":0.6085229516029358},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.59635990858078},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5261273384094238},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.42779284715652466},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.35876214504241943},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.3508176803588867},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3452119827270508},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.20234879851341248},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18768414855003357},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.1865195333957672},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.14678481221199036}],"concepts":[{"id":"https://openalex.org/C530470458","wikidata":"https://www.wikidata.org/wiki/Q128581","display_name":"Breast cancer","level":3,"score":0.6085229516029358},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.59635990858078},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5261273384094238},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.42779284715652466},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.35876214504241943},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.3508176803588867},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3452119827270508},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.20234879851341248},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18768414855003357},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.1865195333957672},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.14678481221199036}],"mesh":[{"descriptor_ui":"D001007","descriptor_name":"Anxiety","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001007","descriptor_name":"Anxiety","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001007","descriptor_name":"Anxiety","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001007","descriptor_name":"Anxiety","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001007","descriptor_name":"Anxiety","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001940","descriptor_name":"Breast","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001940","descriptor_name":"Breast","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001940","descriptor_name":"Breast","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001940","descriptor_name":"Breast","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001940","descriptor_name":"Breast","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"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":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/embc40787.2023.10340045","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1109/embc40787.2023.10340045","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 45th Annual International Conference of the IEEE Engineering in Medicine &amp; Biology Society (EMBC)","raw_type":"proceedings-article"},{"id":"pmid:38083007","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38083007","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":"Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.8299999833106995}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322034","display_name":"Ministry of Health and Welfare","ror":"https://ror.org/00vxgjw72"},{"id":"https://openalex.org/F4320331164","display_name":"National Science and Technology Council","ror":"https://ror.org/00wnb9798"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1976526581","https://openalex.org/W2025183726","https://openalex.org/W2096283457","https://openalex.org/W2111547563","https://openalex.org/W2154039449","https://openalex.org/W2165698076","https://openalex.org/W2465015709","https://openalex.org/W2593104572","https://openalex.org/W2738632062","https://openalex.org/W2911964244","https://openalex.org/W2919115771","https://openalex.org/W2949098928","https://openalex.org/W2954996726","https://openalex.org/W2963351448","https://openalex.org/W2964015378","https://openalex.org/W2981126172","https://openalex.org/W3107527779","https://openalex.org/W3128646645","https://openalex.org/W4297733535","https://openalex.org/W4317989757","https://openalex.org/W4385245566","https://openalex.org/W6719270105","https://openalex.org/W6726873649","https://openalex.org/W6739901393","https://openalex.org/W6745537798","https://openalex.org/W6763479770"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2375584271","https://openalex.org/W1997105855","https://openalex.org/W4301030387","https://openalex.org/W2414286769","https://openalex.org/W2013223288","https://openalex.org/W2186113122","https://openalex.org/W1523310174","https://openalex.org/W3015743358","https://openalex.org/W2037827305"],"abstract_inverted_index":{"An":[0],"accurate":[1],"prediction":[2],"of":[3,19,109],"breast":[4,65],"cancer":[5,66],"is":[6,29],"essential":[7],"to":[8,15,32,54,64,92],"help":[9,108],"physicians":[10],"make":[11],"appropriate":[12],"treatment":[13],"recommendations":[14],"reduce":[16],"the":[17,69,95,100,107,111,114,122,125],"chance":[18],"excessive":[20],"treatment,":[21],"avoiding":[22],"unnecessary":[23],"anxiety":[24],"for":[25,51],"patients.":[26],"Cancer":[27],"prognosis":[28,67],"highly":[30],"related":[31,63],"patients'":[33],"genomic":[34,150],"features,":[35],"which":[36],"are":[37,60],"high-dimensional":[38,145],"in":[39,121],"nature.":[40],"In":[41],"this":[42],"study,":[43],"we":[44,77],"utilize":[45],"a":[46,79,85],"systems":[47],"biology":[48],"feature":[49],"selector":[50],"dimension":[52],"reduction":[53],"select":[55],"20":[56],"prognostic":[57],"biomarkers":[58],"that":[59,137],"considered":[61],"closely":[62],"from":[68,99],"high":[70],"dimensional":[71],"RNA":[72],"Sequencing":[73],"(RNA-Seq)":[74],"data.":[75,151],"Furthermore,":[76],"establish":[78],"graph":[80],"neural":[81],"network":[82,104],"(GNN)":[83],"and":[84,146],"multi-layer":[86],"perception":[87],"(MLP)":[88],"graph-level":[89],"readout":[90],"method":[91],"better":[93],"extract":[94,144],"underlying":[96],"gene":[97,102],"interactions":[98,148],"corresponding":[101],"interaction":[103],"(GIN).":[105],"With":[106],"GINs,":[110],"model":[112],"performs":[113],"best":[115],"among":[116],"all":[117],"baseline":[118],"models,":[119],"especially":[120],"area":[123],"under":[124],"precision-recall":[126],"curve":[127],"(AUPRC)":[128],"by":[129],"as":[130,132],"large":[131],"23%.":[133],"The":[134],"results":[135],"demonstrate":[136],"our":[138],"approach":[139],"using":[140],"GNNs":[141],"can":[142],"successfully":[143],"complicated":[147],"within":[149]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2025-12-25T23:11:45.687758","created_date":"2025-10-10T00:00:00"}
