{"id":"https://openalex.org/W7139936937","doi":"https://doi.org/10.1186/s13040-026-00530-8","title":"Profile-guided Hybrid Approach for block-wise missing data handling in multi-omics: a breast cancer case study","display_name":"Profile-guided Hybrid Approach for block-wise missing data handling in multi-omics: a breast cancer case study","publication_year":2026,"publication_date":"2026-03-20","ids":{"openalex":"https://openalex.org/W7139936937","doi":"https://doi.org/10.1186/s13040-026-00530-8","pmid":"https://pubmed.ncbi.nlm.nih.gov/41862959"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-026-00530-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-026-00530-8","pdf_url":null,"source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1186/s13040-026-00530-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036370523","display_name":"Esraa Hamdi Abdelaziz","orcid":"https://orcid.org/0000-0001-6898-864X"},"institutions":[{"id":"https://openalex.org/I107720978","display_name":"Ain Shams University","ror":"https://ror.org/00cb9w016","country_code":"EG","type":"education","lineage":["https://openalex.org/I107720978"]}],"countries":["EG"],"is_corresponding":true,"raw_author_name":"Esraa Hamdi Abdelaziz","raw_affiliation_strings":["Faculty of Computer and Information Sciences, Ain Shams University, Cairo, Egypt. esraahamdiabbas@cis.asu.edu.eg"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer and Information Sciences, Ain Shams University, Cairo, Egypt. esraahamdiabbas@cis.asu.edu.eg","institution_ids":["https://openalex.org/I107720978"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007109525","display_name":"Eman Amin","orcid":null},"institutions":[{"id":"https://openalex.org/I107720978","display_name":"Ain Shams University","ror":"https://ror.org/00cb9w016","country_code":"EG","type":"education","lineage":["https://openalex.org/I107720978"]}],"countries":["EG"],"is_corresponding":false,"raw_author_name":"Eman Amin","raw_affiliation_strings":["Faculty of Computer and Information Sciences, Ain Shams University, Cairo, Egypt"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer and Information Sciences, Ain Shams University, Cairo, Egypt","institution_ids":["https://openalex.org/I107720978"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017124814","display_name":"Rasha M. Ismail","orcid":"https://orcid.org/0000-0003-3581-8112"},"institutions":[{"id":"https://openalex.org/I107720978","display_name":"Ain Shams University","ror":"https://ror.org/00cb9w016","country_code":"EG","type":"education","lineage":["https://openalex.org/I107720978"]}],"countries":["EG"],"is_corresponding":false,"raw_author_name":"Rasha Ismail","raw_affiliation_strings":["Faculty of Computer and Information Sciences, Ain Shams University, Cairo, Egypt"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Computer and Information Sciences, Ain Shams University, Cairo, Egypt","institution_ids":["https://openalex.org/I107720978"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5119885104","display_name":"Mai M. Mabrouk","orcid":null},"institutions":[{"id":"https://openalex.org/I57629906","display_name":"Nile University","ror":"https://ror.org/03cg7cp61","country_code":"EG","type":"education","lineage":["https://openalex.org/I57629906"]}],"countries":["EG"],"is_corresponding":true,"raw_author_name":"Mai Mabrouk","raw_affiliation_strings":["Center for Informatics Science (CIS), School of Information Technology and Computer Science, Nile University, Giza, Egypt. masaid@nu.edu.eg"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Informatics Science (CIS), School of Information Technology and Computer Science, Nile University, Giza, Egypt. masaid@nu.edu.eg","institution_ids":["https://openalex.org/I57629906"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5036370523","https://openalex.org/A5119885104"],"corresponding_institution_ids":["https://openalex.org/I107720978","https://openalex.org/I57629906"],"apc_list":{"value":2490,"currency":"USD","value_usd":2490},"apc_paid":{"value":2490,"currency":"USD","value_usd":2490},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.22672134,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"19","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6509000062942505,"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":0.6509000062942505,"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":0.11630000174045563,"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"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.05040000006556511,"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/missing-data","display_name":"Missing data","score":0.7703999876976013},{"id":"https://openalex.org/keywords/breast-cancer","display_name":"Breast cancer","score":0.5857999920845032},{"id":"https://openalex.org/keywords/group-method-of-data-handling","display_name":"Group method of data handling","score":0.46810001134872437},{"id":"https://openalex.org/keywords/data-collection","display_name":"Data collection","score":0.36079999804496765}],"concepts":[{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.7703999876976013},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6019999980926514},{"id":"https://openalex.org/C530470458","wikidata":"https://www.wikidata.org/wiki/Q128581","display_name":"Breast cancer","level":3,"score":0.5857999920845032},{"id":"https://openalex.org/C13926793","wikidata":"https://www.wikidata.org/wiki/Q3507155","display_name":"Group method of data handling","level":2,"score":0.46810001134872437},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4580000042915344},{"id":"https://openalex.org/C133462117","wikidata":"https://www.wikidata.org/wiki/Q4929239","display_name":"Data collection","level":2,"score":0.36079999804496765},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.36000001430511475},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27810001373291016},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.2718999981880188},{"id":"https://openalex.org/C2779473830","wikidata":"https://www.wikidata.org/wiki/Q1540899","display_name":"MEDLINE","level":2,"score":0.2644999921321869},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.25429999828338623}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13040-026-00530-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-026-00530-8","pdf_url":null,"source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:41862959","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41862959","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":"BioData mining","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13063710","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13063710/","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13063710/pdf/13040_2026_Article_530.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":"BioData Min","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:344a10060b744d76bd9133d638c2b4d7","is_oa":true,"landing_page_url":"https://doaj.org/article/344a10060b744d76bd9133d638c2b4d7","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"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":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Mining, Vol 19, Iss 1 (2026)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13040-026-00530-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-026-00530-8","pdf_url":null,"source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.42773765325546265,"id":"https://metadata.un.org/sdg/5","display_name":"Gender equality"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321119","display_name":"Ain Shams University","ror":"https://ror.org/00cb9w016"},{"id":"https://openalex.org/F4320321655","display_name":"Science and Technology Development Fund","ror":"https://ror.org/044vr6g03"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W2028633780","https://openalex.org/W2064675550","https://openalex.org/W2095377654","https://openalex.org/W2295598076","https://openalex.org/W2771041964","https://openalex.org/W2808076887","https://openalex.org/W2891816174","https://openalex.org/W2911964244","https://openalex.org/W2913840411","https://openalex.org/W2963351448","https://openalex.org/W3015593040","https://openalex.org/W3027051073","https://openalex.org/W3132179307","https://openalex.org/W4319759388","https://openalex.org/W4323294508","https://openalex.org/W4379745448","https://openalex.org/W4400910738","https://openalex.org/W4403052529","https://openalex.org/W4405890571","https://openalex.org/W4407980064","https://openalex.org/W4408924428","https://openalex.org/W4410772492"],"related_works":[],"abstract_inverted_index":{"BACKGROUND:":[0],"Block-wise":[1],"missingness":[2,45,76],"is":[3],"a":[4,62,235,254,268],"common":[5],"challenge":[6],"in":[7],"multi-omics":[8,272],"data,":[9],"hindering":[10],"the":[11,103,136,146,154,174,221,250,277],"development":[12],"of":[13,162,166,171,211,238],"robust":[14,259],"and":[15,57,84,98,102,126,148,168,177,183,200,206,230,257,275,285],"generalizable":[16,269],"machine":[17],"learning":[18,284],"models,":[19],"as":[20],"real-world":[21],"cohorts":[22],"rarely":[23],"contain":[24],"complete":[25,63],"omic":[26],"profiles.":[27],"Many":[28],"current":[29],"methods":[30],"either":[31],"discard":[32],"incomplete":[33],"samples,":[34],"use":[35],"available-case":[36],"models":[37],"that":[38,107,190],"need":[39],"retraining":[40],"when":[41],"faced":[42],"with":[43,111,132,247],"new":[44],"patterns,":[46],"or":[47,179],"depend":[48],"on":[49],"full-dataset":[50],"imputation,":[51],"which":[52],"can":[53],"risk":[54],"biological":[55],"integrity":[56],"model":[58],"stability.":[59,240],"METHODS:":[60],"Using":[61],"four-omics":[64],"breast":[65],"cancer":[66],"dataset":[67],"(705":[68],"patients,":[69],"1,937":[70],"features),":[71],"up":[72],"to":[73,86,153],"60%":[74],"block-wise":[75,262],"was":[77,116],"simulated":[78],"across":[79,128,233],"five":[80],"clinically":[81],"relevant":[82],"scenarios":[83],"used":[85],"compare":[87],"four":[88],"strategies":[89],"for":[90,261,271,279],"handling":[91],"missing":[92,263],"data:":[93],"an":[94,159,207],"Imputation-Based":[95,175],"model,":[96],"Dynamic":[97,182],"Exhaustive":[99,184,222],"Available-Case":[100,185],"approaches,":[101],"proposed":[104],"Hybrid":[105,142,251],"Approach":[106,143,252],"combines":[108],"profile-guided":[109],"modeling":[110],"selective,":[112],"test-time":[113],"imputation.":[114,287],"Performance":[115],"evaluated":[117],"using":[118,135],"accuracy,":[119,123],"F1":[120,164],"score,":[121],"balanced":[122,169],"inference":[124,202],"time,":[125],"variability":[127],"15":[129],"random":[130],"seeds,":[131,234],"significance":[133],"assessed":[134],"Wilcoxon":[137],"signed-rank":[138],"test.":[139],"RESULTS:":[140],"The":[141,195],"consistently":[144],"achieved":[145],"strongest":[147],"most":[149],"stable":[150],"performance.":[151],"Relative":[152],"complete-data":[155],"baseline,":[156],"it":[157],"reached":[158],"average":[160,208],"accuracy":[161,170],"103.7%,":[163],"score":[165],"123.3%,":[167],"104.8%,":[172],"outperforming":[173],"method":[176,196],"matching":[178],"exceeding":[180],"both":[181],"strategies.":[186],"Statistical":[187],"testing":[188],"confirmed":[189],"these":[191],"improvements":[192],"were":[193],"significant.":[194],"also":[197],"demonstrated":[198],"fast":[199],"predictable":[201],"(~":[203,224],"2":[204],"s)":[205],"total":[209],"runtime":[210],"~":[212],"49":[213],"s":[214],"per":[215],"configuration\u2014nearly":[216],"three":[217],"times":[218],"faster":[219],"than":[220],"approach":[223],"124":[225],"s)\u2014while":[226],"maintaining":[227],"high":[228],"reproducibility":[229],"low":[231],"variance":[232],"key":[236],"indicator":[237],"computational":[239],"CONCLUSION:":[241],"By":[242],"selectively":[243],"combining":[244],"lightweight":[245],"imputation":[246],"profile-specific":[248],"modeling,":[249],"provides":[253],"computationally":[255],"efficient":[256],"statistically":[258],"solution":[260],"data.":[264],"This":[265],"framework":[266],"offers":[267],"strategy":[270],"data":[273],"mining,":[274],"lays":[276],"foundation":[278],"future":[280],"systems":[281],"incorporating":[282],"cross-profile":[283],"advanced":[286]},"counts_by_year":[],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2026-03-21T00:00:00"}
