{"id":"https://openalex.org/W4417023081","doi":"https://doi.org/10.1177/15578666251396558","title":"Conformal Prediction with Knowledge Graphs for Reliable Antimicrobial Resistance Detection with MALDI-TOF Mass Spectra","display_name":"Conformal Prediction with Knowledge Graphs for Reliable Antimicrobial Resistance Detection with MALDI-TOF Mass Spectra","publication_year":2025,"publication_date":"2025-12-05","ids":{"openalex":"https://openalex.org/W4417023081","doi":"https://doi.org/10.1177/15578666251396558","pmid":"https://pubmed.ncbi.nlm.nih.gov/41346025"},"language":"en","primary_location":{"id":"doi:10.1177/15578666251396558","is_oa":true,"landing_page_url":"https://doi.org/10.1177/15578666251396558","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1177/15578666251396558","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Nina Corvelo Benz","orcid":null},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I4210121786","display_name":"Max Planck Institute for Software Systems","ror":"https://ror.org/02pe2kf23","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210121786"]}],"countries":["CH","DE"],"is_corresponding":true,"raw_author_name":"Nina Corvelo Benz","raw_affiliation_strings":["Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland","Max Planck Institute for Software Systems, Kaiserslautern, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Max Planck Institute for Software Systems, Kaiserslautern, Germany","institution_ids":["https://openalex.org/I4210121786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085125514","display_name":"Lucas Miranda","orcid":"https://orcid.org/0000-0002-5484-6744"},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Lucas Miranda","raw_affiliation_strings":["Department of Machine Learning and Systems Biology, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Machine Learning and Systems Biology, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085221831","display_name":"Dexiong Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Dexiong Chen","raw_affiliation_strings":["Department of Machine Learning and Systems Biology, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Machine Learning and Systems Biology, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045811468","display_name":"Janko Sattler","orcid":"https://orcid.org/0000-0003-1415-4169"},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Janko Sattler","raw_affiliation_strings":["Department of Machine Learning and Systems Biology, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Machine Learning and Systems Biology, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074540538","display_name":"Karsten Borgwardt","orcid":"https://orcid.org/0000-0001-7221-2393"},"institutions":[{"id":"https://openalex.org/I4210150093","display_name":"Max Planck Institute of Biochemistry","ror":"https://ror.org/04py35477","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210150093"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Karsten Borgwardt","raw_affiliation_strings":["Department of Machine Learning and Systems Biology, Max Planck Institute of Biochemistry, Martinsried, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Machine Learning and Systems Biology, Max Planck Institute of Biochemistry, Martinsried, Germany","institution_ids":["https://openalex.org/I4210150093"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5045811468","https://openalex.org/A5074540538","https://openalex.org/A5085125514"],"corresponding_institution_ids":["https://openalex.org/I35440088","https://openalex.org/I4210121786","https://openalex.org/I4210150093"],"apc_list":null,"apc_paid":null,"fwci":2.4129,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.9042178,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"33","issue":"1","first_page":"19","last_page":"35"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.8934999704360962,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"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/T12167","display_name":"Bacterial Identification and Susceptibility Testing","score":0.8934999704360962,"subfield":{"id":"https://openalex.org/subfields/1308","display_name":"Clinical Biochemistry"},"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.0333000011742115,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10147","display_name":"Antibiotic Resistance in Bacteria","score":0.015599999576807022,"subfield":{"id":"https://openalex.org/subfields/1313","display_name":"Molecular Medicine"},"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/conformal-map","display_name":"Conformal map","score":0.4830999970436096},{"id":"https://openalex.org/keywords/antibiotic-resistance","display_name":"Antibiotic resistance","score":0.46380001306533813},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.43140000104904175},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.4077000021934509},{"id":"https://openalex.org/keywords/repurposing","display_name":"Repurposing","score":0.39890000224113464},{"id":"https://openalex.org/keywords/domain-knowledge","display_name":"Domain knowledge","score":0.33629998564720154},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.3212999999523163}],"concepts":[{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.48539999127388},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4837999939918518},{"id":"https://openalex.org/C98214594","wikidata":"https://www.wikidata.org/wiki/Q850275","display_name":"Conformal map","level":2,"score":0.4830999970436096},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46790000796318054},{"id":"https://openalex.org/C94665300","wikidata":"https://www.wikidata.org/wiki/Q63391344","display_name":"Antibiotic resistance","level":3,"score":0.46380001306533813},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4447999894618988},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.43140000104904175},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.4077000021934509},{"id":"https://openalex.org/C519536355","wikidata":"https://www.wikidata.org/wiki/Q21021151","display_name":"Repurposing","level":2,"score":0.39890000224113464},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.33629998564720154},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.32589998841285706},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.3212999999523163},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.3111000061035156},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.30559998750686646},{"id":"https://openalex.org/C167928553","wikidata":"https://www.wikidata.org/wiki/Q1376021","display_name":"Estimation theory","level":2,"score":0.3028999865055084},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.30160000920295715},{"id":"https://openalex.org/C45804977","wikidata":"https://www.wikidata.org/wiki/Q7239673","display_name":"Predictive modelling","level":2,"score":0.2992999851703644},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2768999934196472},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.2741999924182892},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2639999985694885},{"id":"https://openalex.org/C87007009","wikidata":"https://www.wikidata.org/wiki/Q210832","display_name":"Statistical hypothesis testing","level":2,"score":0.26030001044273376}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000900","descriptor_name":"Anti-Bacterial Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000187","qualifier_name":"drug effects","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008826","descriptor_name":"Microbial Sensitivity Tests","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019032","descriptor_name":"Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D024881","descriptor_name":"Drug Resistance, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1177/15578666251396558","is_oa":true,"landing_page_url":"https://doi.org/10.1177/15578666251396558","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},{"id":"pmid:41346025","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41346025","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":"Journal of computational biology : a journal of computational molecular cell biology","raw_type":null}],"best_oa_location":{"id":"doi:10.1177/15578666251396558","is_oa":true,"landing_page_url":"https://doi.org/10.1177/15578666251396558","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W1895007034","https://openalex.org/W1916459461","https://openalex.org/W2011810147","https://openalex.org/W2027482274","https://openalex.org/W2056317617","https://openalex.org/W2124945254","https://openalex.org/W3009153194","https://openalex.org/W3092024150","https://openalex.org/W4206677002","https://openalex.org/W4226275940","https://openalex.org/W4361012985","https://openalex.org/W4362470865","https://openalex.org/W4365455552","https://openalex.org/W4376108543","https://openalex.org/W4385762558","https://openalex.org/W4388994122","https://openalex.org/W4392910375","https://openalex.org/W4396554694","https://openalex.org/W4401657510","https://openalex.org/W4403132892","https://openalex.org/W6948741583"],"related_works":[],"abstract_inverted_index":{"Bacterial":[0],"antimicrobial":[1,77,106,262],"resistance":[2,31,78,107,128,161,263],"is":[3,32,178],"one":[4],"of":[5,30,90,119,182,195,260,274],"the":[6,214,226,232,258,271],"most":[7],"pressing":[8],"global":[9],"health":[10],"challenges.":[11],"Infections":[12],"with":[13,123],"resistant":[14],"pathogens":[15],"increase":[16],"patient":[17,48],"morbidity":[18],"and":[19,27,87,149,165,190,209,230,251,284],"mortality":[20],"due":[21],"to":[22,51,241],"limited":[23,84],"treatment":[24,288],"options.":[25],"Rapid":[26],"reliable":[28],"identification":[29],"therefore":[33],"crucial.":[34],"However,":[35],"conventional":[36],"culture-based":[37],"diagnostics":[38,277],"are":[39],"slow,":[40],"typically":[41],"requiring":[42],"at":[43],"least":[44],"48":[45],"hours":[46,71],"from":[47,265],"sample":[49],"arrival":[50],"result.":[52],"In":[53],"contrast,":[54],"matrix-assisted":[55],"laser":[56],"desorption/ionization":[57],"time-of-flight":[58],"(MALDI-TOF)":[59],"mass":[60],"spectrometry,":[61],"routinely":[62],"used":[63],"for":[64,76],"species":[65],"identification,":[66],"can":[67],"provide":[68],"data":[69],"24":[70],"earlier.":[72],"Repurposing":[73],"this":[74],"technique":[75],"prediction":[79,116,141],"has":[80],"shown":[81],"promise,":[82],"but":[83],"predictive":[85,253],"performance":[86],"a":[88,111,131,147,183],"lack":[89],"statistically":[91,247],"grounded":[92,248],"uncertainty":[93,249],"estimates":[94,250],"have":[95],"hindered":[96],"clinical":[97,272],"integration.":[98],"To":[99],"address":[100],"these":[101],"issues,":[102],"we":[103],"propose":[104],"an":[105],"detection":[108,129],"framework":[109,201,256],"using":[110,213],"knowledge-graph-enhanced":[112],"conformal":[113,140,222,243],"predictor.":[114],"Conformal":[115],"outputs":[117],"sets":[118],"likely":[120],"effective":[121],"antibiotics":[122],"statistical":[124],"guarantees,":[125],"ensuring":[126],"that":[127,153,186,220,231],"meets":[130],"predefined":[132],"error":[133],"rate.":[134],"Our":[135,217],"approach":[136],"improves":[137],"upon":[138],"standard":[139,242],"by":[142,278],"integrating":[143],"domain":[144],"knowledge":[145,151],"through":[146],"drug-":[148],"species-specific":[150],"graph":[152],"captures":[154],"interdependencies":[155],"between":[156,163],"antibiotics,":[157],"such":[158,275],"as":[159,168,170],"inferable":[160],"patterns":[162,172],"broad-":[164],"narrow-spectrum":[166],"agents,":[167],"well":[169],"co-resistance":[171],"within":[173],"antibiotic":[174],"classes.":[175],"This":[176,268],"predictor":[177,223],"layered":[179],"on":[180,202],"top":[181],"novel":[184],"classifier":[185],"surpasses":[187],"state-of-the-art":[188],"models":[189],"overcomes":[191],"key":[192],"technical":[193],"limitations":[194],"earlier":[196],"approaches.":[197,244],"We":[198],"evaluated":[199],"our":[200,221,255],"two":[203],"clinically":[204],"relevant":[205],"species,":[206],"Klebsiella":[207],"pneumoniae":[208],"Escherichia":[210],"coli":[211],",":[212],"DRIAMS":[215],"dataset.":[216],"results":[218,283],"demonstrate":[219],"consistently":[224],"achieved":[225],"expected":[227],"coverage":[228],"guarantees":[229],"knowledge-graph":[233],"enhancement":[234],"significantly":[235],"reduced":[236],"false":[237],"discovery":[238],"rates":[239],"compared":[240],"By":[245],"adding":[246],"improving":[252],"performance,":[254],"strengthens":[257],"reliability":[259],"early":[261,287],"predictions":[264],"MALDI-TOF":[266],"data.":[267],"could":[269],"support":[270],"integration":[273],"rapid":[276],"increasing":[279],"trust":[280],"in":[281],"their":[282],"enabling":[285],"better-informed":[286],"decisions.":[289],"1":[290]},"counts_by_year":[{"year":2026,"cited_by_count":3}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-12-05T00:00:00"}