{"id":"https://openalex.org/W4407390690","doi":"https://doi.org/10.1109/access.2025.3540769","title":"Comparative Analysis of Multi-Omics Integration Using Graph Neural Networks for Cancer Classification","display_name":"Comparative Analysis of Multi-Omics Integration Using Graph Neural Networks for Cancer Classification","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4407390690","doi":"https://doi.org/10.1109/access.2025.3540769","pmid":"https://pubmed.ncbi.nlm.nih.gov/40123934"},"language":"en","primary_location":{"id":"doi:10.1109/access.2025.3540769","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3540769","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1109/access.2025.3540769","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080533728","display_name":"Fadi Alharbi","orcid":null},"institutions":[{"id":"https://openalex.org/I155093810","display_name":"University of Idaho","ror":"https://ror.org/03hbp5t65","country_code":"US","type":"education","lineage":["https://openalex.org/I155093810"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Fadi Alharbi","raw_affiliation_strings":["Department of Computer Science, College of Engineering, University of Idaho, Moscow, ID, USA"],"raw_orcid":"https://orcid.org/0009-0005-1126-4356","affiliations":[{"raw_affiliation_string":"Department of Computer Science, College of Engineering, University of Idaho, Moscow, ID, USA","institution_ids":["https://openalex.org/I155093810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005267824","display_name":"Aleksandar Vakanski","orcid":"https://orcid.org/0000-0003-3365-1291"},"institutions":[{"id":"https://openalex.org/I155093810","display_name":"University of Idaho","ror":"https://ror.org/03hbp5t65","country_code":"US","type":"education","lineage":["https://openalex.org/I155093810"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Aleksandar Vakanski","raw_affiliation_strings":["Department of Computer Science, College of Engineering, University of Idaho, Moscow, ID, USA"],"raw_orcid":"https://orcid.org/0000-0003-3365-1291","affiliations":[{"raw_affiliation_string":"Department of Computer Science, College of Engineering, University of Idaho, Moscow, ID, USA","institution_ids":["https://openalex.org/I155093810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008484378","display_name":"Boyu Zhang","orcid":"https://orcid.org/0000-0002-9401-6163"},"institutions":[{"id":"https://openalex.org/I155093810","display_name":"University of Idaho","ror":"https://ror.org/03hbp5t65","country_code":"US","type":"education","lineage":["https://openalex.org/I155093810"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Boyu Zhang","raw_affiliation_strings":["Department of Computer Science, College of Engineering, University of Idaho, Moscow, ID, USA"],"raw_orcid":"https://orcid.org/0000-0002-9401-6163","affiliations":[{"raw_affiliation_string":"Department of Computer Science, College of Engineering, University of Idaho, Moscow, ID, USA","institution_ids":["https://openalex.org/I155093810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110581810","display_name":"Murtada K. Elbashir","orcid":null},"institutions":[{"id":"https://openalex.org/I199702508","display_name":"Jouf University","ror":"https://ror.org/02zsyt821","country_code":"SA","type":"education","lineage":["https://openalex.org/I199702508"]}],"countries":["SA"],"is_corresponding":false,"raw_author_name":"Murtada K. Elbashir","raw_affiliation_strings":["Department of Information Systems, College of Computer and Information Sciences, Jouf University, Sakaka, Al-Jouf, Saudi Arabia"],"raw_orcid":"https://orcid.org/0000-0003-3431-6604","affiliations":[{"raw_affiliation_string":"Department of Information Systems, College of Computer and Information Sciences, Jouf University, Sakaka, Al-Jouf, Saudi Arabia","institution_ids":["https://openalex.org/I199702508"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058527975","display_name":"Mohanad Mohammed","orcid":"https://orcid.org/0000-0001-5336-0286"},"institutions":[{"id":"https://openalex.org/I95023434","display_name":"University of KwaZulu-Natal","ror":"https://ror.org/04qzfn040","country_code":"ZA","type":"education","lineage":["https://openalex.org/I95023434"]}],"countries":["ZA"],"is_corresponding":false,"raw_author_name":"Mohanad Mohammed","raw_affiliation_strings":["School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematics, Statistics and Computer Science, University of KwaZulu-Natal, Pietermaritzburg, South Africa","institution_ids":["https://openalex.org/I95023434"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5080533728"],"corresponding_institution_ids":["https://openalex.org/I155093810"],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":11.1225,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.98748831,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"13","issue":null,"first_page":"37724","last_page":"37736"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9983999729156494,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9854999780654907,"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":0.6719756722450256},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5302441120147705},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.45514965057373047},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34298771619796753}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6719756722450256},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5302441120147705},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.45514965057373047},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34298771619796753}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1109/access.2025.3540769","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3540769","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmid:40123934","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40123934","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 access : practical innovations, open solutions","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11928009","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11928009","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11928009/pdf/nihms-2062981.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Access","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:1a352378802f4808afa55f1094ff7a1a","is_oa":true,"landing_page_url":"https://doaj.org/article/1a352378802f4808afa55f1094ff7a1a","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Access, Vol 13, Pp 37724-37736 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2025.3540769","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3540769","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3884834885","display_name":null,"funder_award_id":"P20GM104420","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5786885734","display_name":null,"funder_award_id":"P20GM104420","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":61,"referenced_works":["https://openalex.org/W1520812622","https://openalex.org/W1974450480","https://openalex.org/W1977145914","https://openalex.org/W2070494252","https://openalex.org/W2114104545","https://openalex.org/W2119883345","https://openalex.org/W2135046866","https://openalex.org/W2146512944","https://openalex.org/W2158485828","https://openalex.org/W2230320310","https://openalex.org/W2786016794","https://openalex.org/W2899235613","https://openalex.org/W2900569176","https://openalex.org/W2907492528","https://openalex.org/W2911286998","https://openalex.org/W2964015378","https://openalex.org/W2967844557","https://openalex.org/W3014321973","https://openalex.org/W3036962145","https://openalex.org/W3100495486","https://openalex.org/W3107527779","https://openalex.org/W3124379712","https://openalex.org/W3156270925","https://openalex.org/W3163443268","https://openalex.org/W3170986249","https://openalex.org/W3192157621","https://openalex.org/W3206417123","https://openalex.org/W3215765649","https://openalex.org/W3217671853","https://openalex.org/W4210470310","https://openalex.org/W4210912154","https://openalex.org/W4225000950","https://openalex.org/W4226182829","https://openalex.org/W4283785712","https://openalex.org/W4291021611","https://openalex.org/W4297733535","https://openalex.org/W4311959699","https://openalex.org/W4318476344","https://openalex.org/W4367051483","https://openalex.org/W4367299262","https://openalex.org/W4376133438","https://openalex.org/W4380303551","https://openalex.org/W4384928439","https://openalex.org/W4385788329","https://openalex.org/W4386746828","https://openalex.org/W4387805937","https://openalex.org/W4390881001","https://openalex.org/W4390906246","https://openalex.org/W4390992022","https://openalex.org/W4391107757","https://openalex.org/W4391881157","https://openalex.org/W4391969986","https://openalex.org/W4396801956","https://openalex.org/W4399911856","https://openalex.org/W4401657615","https://openalex.org/W4401798479","https://openalex.org/W4402054512","https://openalex.org/W4402192457","https://openalex.org/W6754498612","https://openalex.org/W6767098714","https://openalex.org/W6871280123"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"Recent":[0],"studies":[1],"on":[2,22,93,189],"integrating":[3,58,182],"multiple":[4],"omics":[5,121,191],"data":[6,90,122,184,235],"highlighted":[7],"the":[8,15,52,71,120,128,180,186,196,214,243],"potential":[9],"to":[10,37,40,50,133,217,226],"advance":[11],"our":[12],"understanding":[13],"of":[14,78,159,203],"cancer":[16,34,164],"disease":[17],"process.":[18],"Computational":[19],"models":[20,130,181,187],"based":[21,92],"graph":[23,66,83,211,230],"neural":[24,84],"networks":[25,95,98,102,149],"and":[26,55,100,107,112,124,137,146,166,172,234],"attention-based":[27],"architectures":[28,86],"have":[29],"demonstrated":[30],"promising":[31],"results":[32,177],"for":[33,87,118],"classification":[35],"due":[36],"their":[38],"ability":[39,216],"model":[41],"complex":[42],"relationships":[43],"among":[44],"biological":[45],"entities.":[46],"However,":[47],"challenges":[48],"related":[49],"addressing":[51],"high":[53],"dimensionality":[54,123],"complexity":[56],"in":[57,64,224,237,242],"multi-omics":[59,88,183],"data,":[60,192],"as":[61,63,134],"well":[62],"constructing":[65],"structures":[67,140,212],"that":[68,179,209],"effectively":[69],"capture":[70],"interactions":[72],"between":[73],"nodes,":[74],"remain":[75],"active":[76],"areas":[77],"research.":[79],"This":[80],"study":[81,239],"evaluates":[82],"network":[85],"(MO)":[89],"integration":[91],"graph-convolutional":[94],"(GCN),":[96],"graph-attention":[97],"(GAT),":[99],"graph-transformer":[101],"(GTN).":[103],"Differential":[104],"gene":[105],"expression":[106],"LASSO":[108],"(Least":[109],"Absolute":[110],"Shrinkage":[111],"Selection":[113],"Operator)":[114],"regression":[115],"are":[116,131,150,240],"employed":[117],"reducing":[119],"feature":[125],"selection;":[126],"hence,":[127],"developed":[129],"referred":[132],"LASSO-MOGCN,":[135],"LASSO-MOGAT,":[136],"LASSO-MOGTN.":[138],"Graph":[139],"constructed":[141],"using":[142],"sample":[143],"correlation":[144],"matrices":[145],"protein-protein":[147,227],"interaction":[148,228],"investigated.":[151],"Experimental":[152],"validation":[153],"is":[154],"performed":[155],"with":[156,200],"a":[157],"dataset":[158],"8,464":[160],"samples":[161],"from":[162],"31":[163],"types":[165],"normal":[167],"tissue,":[168],"comprising":[169],"messenger-RNA,":[170],"micro-RNA,":[171],"DNA":[173],"methylation":[174],"data.":[175],"The":[176,205,232],"show":[178],"outperformed":[185],"trained":[188],"single":[190],"where":[193],"LASSO-MOGAT":[194],"achieved":[195],"best":[197],"overall":[198],"performance,":[199],"an":[201],"accuracy":[202],"95.9%.":[204],"findings":[206],"also":[207],"suggest":[208],"correlation-based":[210],"enhance":[213],"models'":[215],"identify":[218],"shared":[219],"cancer-specific":[220],"signatures":[221],"across":[222],"patients":[223],"comparison":[225],"networks-based":[229],"structures.":[231],"code":[233],"used":[236],"this":[238],"available":[241],"link":[244],"(https://github.com/FadiAlharbi2024/Graph_Based_Architecture.git).":[245]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":10}],"updated_date":"2026-05-03T08:25:01.440150","created_date":"2025-10-10T00:00:00"}
