{"id":"https://openalex.org/W4407895095","doi":"https://doi.org/10.3389/fbinf.2025.1507448","title":"Reliable machine learning models in genomic medicine using conformal prediction","display_name":"Reliable machine learning models in genomic medicine using conformal prediction","publication_year":2025,"publication_date":"2025-02-24","ids":{"openalex":"https://openalex.org/W4407895095","doi":"https://doi.org/10.3389/fbinf.2025.1507448","pmid":"https://pubmed.ncbi.nlm.nih.gov/40066074"},"language":"en","primary_location":{"id":"doi:10.3389/fbinf.2025.1507448","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1507448","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1507448/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1507448/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5106680650","display_name":"Christina Papangelou","orcid":null},"institutions":[{"id":"https://openalex.org/I21370196","display_name":"Aristotle University of Thessaloniki","ror":"https://ror.org/02j61yw88","country_code":"GR","type":"education","lineage":["https://openalex.org/I21370196"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Christina Papangelou","raw_affiliation_strings":["School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece"],"affiliations":[{"raw_affiliation_string":"School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece","institution_ids":["https://openalex.org/I21370196"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049952262","display_name":"Konstantinos Kyriakidis","orcid":"https://orcid.org/0000-0002-1696-4838"},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Konstantinos Kyriakidis","raw_affiliation_strings":["Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States"],"affiliations":[{"raw_affiliation_string":"Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036029445","display_name":"Pantelis Natsiavas","orcid":"https://orcid.org/0000-0002-4061-9815"},"institutions":[{"id":"https://openalex.org/I4210134249","display_name":"Centre for Research and Technology Hellas","ror":"https://ror.org/03bndpq63","country_code":"GR","type":"facility","lineage":["https://openalex.org/I4210134249"]}],"countries":["GR"],"is_corresponding":false,"raw_author_name":"Pantelis Natsiavas","raw_affiliation_strings":["Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece"],"affiliations":[{"raw_affiliation_string":"Institute of Applied Biosciences, Center for Research and Technology Hellas, Thessaloniki, Greece","institution_ids":["https://openalex.org/I4210134249"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078023454","display_name":"Ioanna Chouvarda","orcid":"https://orcid.org/0000-0001-8915-6658"},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ioanna Chouvarda","raw_affiliation_strings":["Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States"],"affiliations":[{"raw_affiliation_string":"Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, United States","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060458297","display_name":"Andigoni Malousi","orcid":"https://orcid.org/0000-0002-1968-7020"},"institutions":[{"id":"https://openalex.org/I21370196","display_name":"Aristotle University of Thessaloniki","ror":"https://ror.org/02j61yw88","country_code":"GR","type":"education","lineage":["https://openalex.org/I21370196"]}],"countries":["GR"],"is_corresponding":true,"raw_author_name":"Andigoni Malousi","raw_affiliation_strings":["GENeTres Research Group, Center for Interdisciplinary Research and Innovation, Thessaloniki, Greece","School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece"],"affiliations":[{"raw_affiliation_string":"GENeTres Research Group, Center for Interdisciplinary Research and Innovation, Thessaloniki, Greece","institution_ids":[]},{"raw_affiliation_string":"School of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece","institution_ids":["https://openalex.org/I21370196"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5060458297"],"corresponding_institution_ids":["https://openalex.org/I21370196"],"apc_list":{"value":1900,"currency":"USD","value_usd":1900},"apc_paid":{"value":1900,"currency":"USD","value_usd":1900},"fwci":3.1375,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.90464818,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"5","issue":null,"first_page":"1507448","last_page":"1507448"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9957000017166138,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9957000017166138,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9908000230789185,"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":0.9825999736785889,"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/precision-medicine","display_name":"Precision medicine","score":0.7193200588226318},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6485635042190552},{"id":"https://openalex.org/keywords/personalized-medicine","display_name":"Personalized medicine","score":0.6064693331718445},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5883880257606506},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5831998586654663},{"id":"https://openalex.org/keywords/predictive-modelling","display_name":"Predictive modelling","score":0.5031194090843201},{"id":"https://openalex.org/keywords/health-care","display_name":"Health care","score":0.48382869362831116},{"id":"https://openalex.org/keywords/subtyping","display_name":"Subtyping","score":0.4621037244796753},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.406652569770813},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.27215564250946045},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.26632896065711975},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09946832060813904}],"concepts":[{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.7193200588226318},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6485635042190552},{"id":"https://openalex.org/C32220436","wikidata":"https://www.wikidata.org/wiki/Q2072214","display_name":"Personalized medicine","level":2,"score":0.6064693331718445},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5883880257606506},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5831998586654663},{"id":"https://openalex.org/C45804977","wikidata":"https://www.wikidata.org/wiki/Q7239673","display_name":"Predictive modelling","level":2,"score":0.5031194090843201},{"id":"https://openalex.org/C160735492","wikidata":"https://www.wikidata.org/wiki/Q31207","display_name":"Health care","level":2,"score":0.48382869362831116},{"id":"https://openalex.org/C83852419","wikidata":"https://www.wikidata.org/wiki/Q2713292","display_name":"Subtyping","level":2,"score":0.4621037244796753},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.406652569770813},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.27215564250946045},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26632896065711975},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09946832060813904},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0},{"id":"https://openalex.org/C50522688","wikidata":"https://www.wikidata.org/wiki/Q189833","display_name":"Economic growth","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3389/fbinf.2025.1507448","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1507448","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1507448/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40066074","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40066074","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":"Frontiers in bioinformatics","raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt37k7k4gs","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/37k7k4gs","pdf_url":"https://escholarship.org/content/qt37k7k4gs/qt37k7k4gs.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"Frontiers in Bioinformatics, vol 5","raw_type":"article"},{"id":"pmh:oai:doaj.org/article:b6241b1f8e314fbdbb09c27df972e64e","is_oa":true,"landing_page_url":"https://doaj.org/article/b6241b1f8e314fbdbb09c27df972e64e","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":"Frontiers in Bioinformatics, Vol 5 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:10703757","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11891349","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3389/fbinf.2025.1507448","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fbinf.2025.1507448","pdf_url":"https://www.frontiersin.org/journals/bioinformatics/articles/10.3389/fbinf.2025.1507448/pdf","source":{"id":"https://openalex.org/S4210219554","display_name":"Frontiers in Bioinformatics","issn_l":"2673-7647","issn":["2673-7647"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.4699999988079071}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4407895095.pdf"},"referenced_works_count":84,"referenced_works":["https://openalex.org/W189742998","https://openalex.org/W352468308","https://openalex.org/W1502318498","https://openalex.org/W1521746852","https://openalex.org/W1553101044","https://openalex.org/W2034998024","https://openalex.org/W2080660780","https://openalex.org/W2100536066","https://openalex.org/W2117112756","https://openalex.org/W2154053567","https://openalex.org/W2160208009","https://openalex.org/W2164943005","https://openalex.org/W2171585602","https://openalex.org/W2225156818","https://openalex.org/W2295598076","https://openalex.org/W2555756618","https://openalex.org/W2576404523","https://openalex.org/W2625952175","https://openalex.org/W2758908936","https://openalex.org/W2773318670","https://openalex.org/W2782259231","https://openalex.org/W2794214436","https://openalex.org/W2885935346","https://openalex.org/W2889664156","https://openalex.org/W2899524971","https://openalex.org/W2902375153","https://openalex.org/W2904422658","https://openalex.org/W2909055772","https://openalex.org/W2963238274","https://openalex.org/W2996167815","https://openalex.org/W3000606108","https://openalex.org/W3006708056","https://openalex.org/W3012464003","https://openalex.org/W3024403430","https://openalex.org/W3026996309","https://openalex.org/W3029598567","https://openalex.org/W3035604179","https://openalex.org/W3093152954","https://openalex.org/W3094111018","https://openalex.org/W3165163721","https://openalex.org/W3172022779","https://openalex.org/W3177828909","https://openalex.org/W3196522557","https://openalex.org/W3198753478","https://openalex.org/W3198774792","https://openalex.org/W3199181458","https://openalex.org/W4206677002","https://openalex.org/W4210545034","https://openalex.org/W4210662307","https://openalex.org/W4210814435","https://openalex.org/W4221140785","https://openalex.org/W4281479607","https://openalex.org/W4283210431","https://openalex.org/W4287075774","https://openalex.org/W4288373770","https://openalex.org/W4306735081","https://openalex.org/W4308773001","https://openalex.org/W4308893993","https://openalex.org/W4311506764","https://openalex.org/W4313270796","https://openalex.org/W4313312731","https://openalex.org/W4321444396","https://openalex.org/W4383180616","https://openalex.org/W4387801342","https://openalex.org/W4387917715","https://openalex.org/W4390707138","https://openalex.org/W4391746981","https://openalex.org/W4392899354","https://openalex.org/W4393200009","https://openalex.org/W4394646487","https://openalex.org/W4399130723","https://openalex.org/W4400129701","https://openalex.org/W4400176958","https://openalex.org/W4402670858","https://openalex.org/W4403090823","https://openalex.org/W4406002868","https://openalex.org/W6607672814","https://openalex.org/W6759230470","https://openalex.org/W6839517006","https://openalex.org/W6854500989","https://openalex.org/W6857101973","https://openalex.org/W6857863506","https://openalex.org/W6860844918","https://openalex.org/W7062342228"],"related_works":["https://openalex.org/W3082935376","https://openalex.org/W4399651953","https://openalex.org/W4386960999","https://openalex.org/W2899657781","https://openalex.org/W4322484660","https://openalex.org/W3193951088","https://openalex.org/W4388011470","https://openalex.org/W4230423494","https://openalex.org/W4403376686","https://openalex.org/W4298001029"],"abstract_inverted_index":{"Machine":[0],"learning":[1,137],"and":[2,22,82,104,138,159],"genomic":[3,80,88,139],"medicine":[4,81,89,140],"are":[5,141],"the":[6,63,84,97,116,149,153],"mainstays":[7],"of":[8,24,65,76,99,118,156],"research":[9],"in":[10,31,48,79,109,123,127],"delivering":[11],"personalized":[12],"healthcare":[13,32,144],"services":[14,33],"for":[15,57],"disease":[16],"diagnosis,":[17],"risk":[18],"stratification,":[19],"tailored":[20],"treatment,":[21],"prediction":[23,29,52,147],"adverse":[25],"effects.":[26],"However,":[27],"potential":[28,74,150],"errors":[30],"can":[34],"have":[35,45],"life-threatening":[36],"impact,":[37],"raising":[38],"reasonable":[39],"skepticism":[40],"about":[41],"whether":[42],"these":[43,59],"applications":[44,75,90,166],"practical":[46],"benefit":[47],"clinical":[49,92,168],"settings.":[50],"Conformal":[51],"offers":[53],"a":[54,100,105,119],"versatile":[55],"framework":[56],"addressing":[58,124],"concerns":[60],"by":[61],"quantifying":[62],"uncertainty":[64],"predictive":[66],"models.":[67],"In":[68],"this":[69],"perspective":[70],"review,":[71],"we":[72],"investigate":[73],"conformalized":[77],"models":[78],"discuss":[83],"challenges":[85],"towards":[86],"bridging":[87],"with":[91],"practice.":[93],"We":[94],"also":[95],"demonstrate":[96],"impact":[98],"binary":[101],"transductive":[102],"model":[103,108],"regression-based":[106],"inductive":[107,121],"predicting":[110],"drug":[111],"response":[112],"as":[113,115,135],"well":[114],"performance":[117],"multi-class":[120],"predictor":[122],"distribution":[125],"shifts":[126],"molecular":[128],"subtyping.":[129],"The":[130],"main":[131],"conclusion":[132],"is":[133],"that":[134],"machine":[136],"increasingly":[142],"infiltrating":[143],"services,":[145],"conformal":[146],"has":[148],"to":[151],"overcome":[152],"safety":[154],"limitations":[155],"current":[157],"methods":[158],"could":[160],"be":[161],"effectively":[162],"integrated":[163],"into":[164],"uncertainty-informed":[165],"within":[167],"environments.":[169]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
