{"id":"https://openalex.org/W4403706042","doi":"https://doi.org/10.1186/s13040-024-00398-6","title":"A regularized Cox hierarchical model for incorporating\u00a0annotation information in predictive omic studies","display_name":"A regularized Cox hierarchical model for incorporating\u00a0annotation information in predictive omic studies","publication_year":2024,"publication_date":"2024-10-24","ids":{"openalex":"https://openalex.org/W4403706042","doi":"https://doi.org/10.1186/s13040-024-00398-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/39449073"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-024-00398-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-024-00398-6","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-024-00398-6","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-024-00398-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023053853","display_name":"D Shen","orcid":"https://orcid.org/0000-0002-2608-2775"},"institutions":[{"id":"https://openalex.org/I4210140816","display_name":"Gilead Sciences (United States)","ror":"https://ror.org/056546b03","country_code":"US","type":"company","lineage":["https://openalex.org/I4210140816"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Dixin Shen","raw_affiliation_strings":["Clinical Data Science, Gilead Sciences, Foster City, USA. dixinshen@gmail.com","Clinical Data Science, Gilead Sciences, Foster City, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Clinical Data Science, Gilead Sciences, Foster City, USA. dixinshen@gmail.com","institution_ids":["https://openalex.org/I4210140816"]},{"raw_affiliation_string":"Clinical Data Science, Gilead Sciences, Foster City, USA","institution_ids":["https://openalex.org/I4210140816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047860888","display_name":"Juan Pablo Lewinger","orcid":"https://orcid.org/0000-0002-0692-2570"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Juan Pablo Lewinger","raw_affiliation_strings":["Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, USA","institution_ids":["https://openalex.org/I1174212"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5047542165","display_name":"Eric S. Kawaguchi","orcid":"https://orcid.org/0000-0003-2014-5023"},"institutions":[{"id":"https://openalex.org/I1174212","display_name":"University of Southern California","ror":"https://ror.org/03taz7m60","country_code":"US","type":"education","lineage":["https://openalex.org/I1174212"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eric Kawaguchi","raw_affiliation_strings":["Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biostatistics, Department of Population and Public Health Sciences, Keck School of Medicine, University of Southern California, Los Angeles, USA","institution_ids":["https://openalex.org/I1174212"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5023053853"],"corresponding_institution_ids":["https://openalex.org/I4210140816"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.2208,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.57801388,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"17","issue":"1","first_page":"44","last_page":"44"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.6593000292778015,"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/T10885","display_name":"Gene expression and cancer classification","score":0.6593000292778015,"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":0.1476999968290329,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.03610000014305115,"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":0.7020882368087769},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5555826425552368},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38470107316970825},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.331637442111969},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.32415810227394104}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7020882368087769},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5555826425552368},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38470107316970825},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.331637442111969},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32415810227394104}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13040-024-00398-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-024-00398-6","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-024-00398-6","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:39449073","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39449073","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":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11515443","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11515443","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11515443/pdf/13040_2024_Article_398.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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BioData Min","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:ec5165fd50414d09aa1521ce72690713","is_oa":true,"landing_page_url":"https://doaj.org/article/ec5165fd50414d09aa1521ce72690713","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":"BioData Mining, Vol 17, Iss 1, Pp 1-20 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13040-024-00398-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-024-00398-6","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/s13040-024-00398-6","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2093246056","display_name":null,"funder_award_id":"P01 CA196569","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2141972424","display_name":null,"funder_award_id":"CA196569","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2790371892","display_name":null,"funder_award_id":"CA196569","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2878536864","display_name":null,"funder_award_id":"R01 CA140561","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G5229491074","display_name":null,"funder_award_id":"P01 CA196569","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G789441714","display_name":null,"funder_award_id":"P01 CA196569, R01 CA140561","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4403706042.pdf"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W1578530776","https://openalex.org/W1881929920","https://openalex.org/W1984246609","https://openalex.org/W1999435920","https://openalex.org/W2005895632","https://openalex.org/W2018107887","https://openalex.org/W2020925091","https://openalex.org/W2044702943","https://openalex.org/W2073184521","https://openalex.org/W2074682976","https://openalex.org/W2082213488","https://openalex.org/W2084139018","https://openalex.org/W2097360283","https://openalex.org/W2112289645","https://openalex.org/W2116815574","https://openalex.org/W2122825543","https://openalex.org/W2130410032","https://openalex.org/W2134752341","https://openalex.org/W2135046866","https://openalex.org/W2136916987","https://openalex.org/W2137089630","https://openalex.org/W2138019504","https://openalex.org/W2157076315","https://openalex.org/W2214074259","https://openalex.org/W2299181842","https://openalex.org/W2568415891","https://openalex.org/W2594836176","https://openalex.org/W2761575992","https://openalex.org/W2912137016","https://openalex.org/W2991758046","https://openalex.org/W3084551437","https://openalex.org/W3147894994","https://openalex.org/W4206252853","https://openalex.org/W4243607236","https://openalex.org/W4294541781"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2358755282","https://openalex.org/W2625833328"],"abstract_inverted_index":{"BACKGROUND:":[0],"Associated":[1],"with":[2,41,51,139,172,228,263],"high-dimensional":[3,77],"omics":[4],"data":[5,78,206],"there":[6],"are":[7,118,214],"often":[8],"\"meta-features\"":[9],"such":[10],"as":[11,70,72,162,164],"biological":[12],"pathways":[13],"and":[14,47,102,144],"functional":[15],"annotations,":[16],"summary":[17],"statistics":[18],"from":[19],"similar":[20],"studies":[21],"that":[22,76,113],"can":[23,79,90,124,246],"be":[24,80,91,248],"informative":[25],"for":[26,38,196],"predicting":[27],"an":[28],"outcome":[29,265],"of":[30,44,97,167,187,235],"interest.":[31],"We":[32,134],"introduce":[33],"a":[34,95,108,269],"regularized":[35,121,131,182,222,230],"hierarchical":[36,56,87,122,181,223],"framework":[37,57],"integrating":[39],"meta-features,":[40,161],"the":[42,67,73,115,120,136,154,165,193,203,211,216,221,236,244,254,264],"goal":[43,256],"improving":[45],"prediction":[46,127,157,200,217],"feature":[48,170],"selection":[49],"performance":[50,128,158,201,218],"time-to-event":[52,197],"outcomes.":[53],"METHODS:":[54],"A":[55],"is":[58,64,207,225,257],"deployed":[59,249],"to":[60,66,141,240,258],"incorporate":[61],"meta-features.":[62],"Regularization":[63],"applied":[65],"omic":[68,169],"features":[69,261],"well":[71,163],"meta-features":[74,117,213],"so":[75],"handled":[81],"at":[82,175],"both":[83],"levels.":[84],"The":[85,179],"proposed":[86,137,180],"Cox":[88,132,231],"model":[89,123,138,184,224,245],"efficiently":[92],"fitted":[93],"by":[94,159],"combination":[96],"iterative":[98],"reweighted":[99],"least":[100],"squares":[101],"cyclic":[103],"coordinate":[104],"descent.":[105],"RESULTS:":[106],"In":[107,238],"simulation":[109],"study":[110],"we":[111],"show":[112,153],"when":[114,202,210],"external":[116,188,204,212],"informative,":[119],"substantially":[125],"improve":[126],"over":[129],"standard":[130,229],"regression.":[133],"illustrate":[135],"applications":[140,252],"breast":[142],"cancer":[143],"melanoma":[145],"survival":[146],"based":[147,219],"on":[148,220,226],"gene":[149],"expression":[150],"profiles,":[151],"which":[152],"improvement":[155],"in":[156,250],"applying":[160],"discovery":[166,251],"important":[168,260],"sets":[171],"sparse":[173],"regularization":[174],"meta-feature":[176,189,205],"level.":[177],"CONCLUSIONS:":[178],"regression":[183],"enables":[185],"integration":[186],"information":[190],"directly":[191],"into":[192],"modeling":[194],"process":[195],"outcomes,":[198],"improves":[199],"informative.":[208],"Importantly,":[209],"uninformative,":[215],"par":[227],"regression,":[232],"indicating":[233],"robustness":[234],"framework.":[237],"addition":[239],"developing":[241,268],"predictive":[242,270],"signatures,":[243],"also":[247],"where":[253],"main":[255],"identify":[259],"associated":[262],"rather":[266],"than":[267],"model.":[271]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}