{"id":"https://openalex.org/W4414563801","doi":"https://doi.org/10.1109/tbme.2025.3614518","title":"Clinically Explainable Disease Diagnosis Based on Biomarker Activation Map","display_name":"Clinically Explainable Disease Diagnosis Based on Biomarker Activation Map","publication_year":2025,"publication_date":"2025-09-25","ids":{"openalex":"https://openalex.org/W4414563801","doi":"https://doi.org/10.1109/tbme.2025.3614518","pmid":"https://pubmed.ncbi.nlm.nih.gov/40997007"},"language":"en","primary_location":{"id":"doi:10.1109/tbme.2025.3614518","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tbme.2025.3614518","pdf_url":null,"source":{"id":"https://openalex.org/S5240358","display_name":"IEEE Transactions on Biomedical Engineering","issn_l":"0018-9294","issn":["0018-9294","1558-2531"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Biomedical Engineering","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086060762","display_name":"Pengxiao Zang","orcid":"https://orcid.org/0000-0003-1933-8012"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Pengxiao Zang","raw_affiliation_strings":["Casey Eye Institute, Oregon Health and Science University, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Casey Eye Institute, Oregon Health and Science University, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014761203","display_name":"Carol A. Wang","orcid":"https://orcid.org/0000-0002-4301-3974"},"institutions":[{"id":"https://openalex.org/I2799969026","display_name":"Association of Jesuit Colleges and Universities","ror":"https://ror.org/05r1ynr77","country_code":"US","type":"other","lineage":["https://openalex.org/I2799969026"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carol Wang","raw_affiliation_strings":["Jesuit High School, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Jesuit High School, USA","institution_ids":["https://openalex.org/I2799969026"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086120758","display_name":"Tristan T. Hormel","orcid":"https://orcid.org/0000-0002-7242-1934"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tristan T. Hormel","raw_affiliation_strings":["Casey Eye Institute, Oregon Health and Science University, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Casey Eye Institute, Oregon Health and Science University, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084437406","display_name":"Steven T. Bailey","orcid":"https://orcid.org/0000-0003-4949-1464"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven T. Bailey","raw_affiliation_strings":["Casey Eye Institute, Oregon Health and Science University, USA"],"raw_orcid":"https://orcid.org/0000-0003-4949-1464","affiliations":[{"raw_affiliation_string":"Casey Eye Institute, Oregon Health and Science University, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027484815","display_name":"Thomas S. Hwang","orcid":"https://orcid.org/0000-0002-0535-4823"},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas S. Hwang","raw_affiliation_strings":["Casey Eye Institute, Oregon Health and Science University, USA"],"raw_orcid":"https://orcid.org/0000-0002-0535-4823","affiliations":[{"raw_affiliation_string":"Casey Eye Institute, Oregon Health and Science University, USA","institution_ids":["https://openalex.org/I165690674"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100993114","display_name":"Yali Jia","orcid":null},"institutions":[{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yali Jia","raw_affiliation_strings":["Casey Eye Institute, Oregon Health and Science University, Portland, OR, USA"],"raw_orcid":"https://orcid.org/0000-0002-2784-1905","affiliations":[{"raw_affiliation_string":"Casey Eye Institute, Oregon Health and Science University, Portland, OR, USA","institution_ids":["https://openalex.org/I165690674"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5086060762"],"corresponding_institution_ids":["https://openalex.org/I165690674"],"apc_list":null,"apc_paid":null,"fwci":1.0396,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.8059377,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"73","issue":"5","first_page":"1746","last_page":"1757"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11438","display_name":"Retinal Imaging and Analysis","score":0.7585999965667725,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11438","display_name":"Retinal Imaging and Analysis","score":0.7585999965667725,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.0625,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"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/T12026","display_name":"Explainable Artificial Intelligence (XAI)","score":0.05860000103712082,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.6552000045776367},{"id":"https://openalex.org/keywords/biomarker","display_name":"Biomarker","score":0.5760999917984009},{"id":"https://openalex.org/keywords/classifier","display_name":"Classifier (UML)","score":0.54830002784729},{"id":"https://openalex.org/keywords/disease-monitoring","display_name":"Disease monitoring","score":0.3330000042915344},{"id":"https://openalex.org/keywords/clinical-disease","display_name":"Clinical disease","score":0.30149999260902405},{"id":"https://openalex.org/keywords/biomarker-discovery","display_name":"Biomarker discovery","score":0.3001999855041504}],"concepts":[{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.6597999930381775},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.6552000045776367},{"id":"https://openalex.org/C2781197716","wikidata":"https://www.wikidata.org/wiki/Q864574","display_name":"Biomarker","level":2,"score":0.5760999917984009},{"id":"https://openalex.org/C95623464","wikidata":"https://www.wikidata.org/wiki/Q1096149","display_name":"Classifier (UML)","level":2,"score":0.54830002784729},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3677000105381012},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3630000054836273},{"id":"https://openalex.org/C3018877446","wikidata":"https://www.wikidata.org/wiki/Q1421432","display_name":"Disease monitoring","level":3,"score":0.3330000042915344},{"id":"https://openalex.org/C2992264114","wikidata":"https://www.wikidata.org/wiki/Q1394551","display_name":"Clinical disease","level":3,"score":0.30149999260902405},{"id":"https://openalex.org/C124535831","wikidata":"https://www.wikidata.org/wiki/Q4915074","display_name":"Biomarker discovery","level":4,"score":0.3001999855041504},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.29269999265670776},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.28700000047683716},{"id":"https://openalex.org/C31601959","wikidata":"https://www.wikidata.org/wiki/Q931309","display_name":"Medical imaging","level":2,"score":0.27970001101493835},{"id":"https://openalex.org/C3017616150","wikidata":"https://www.wikidata.org/wiki/Q1069330","display_name":"Diagnostic biomarker","level":3,"score":0.27489998936653137},{"id":"https://openalex.org/C2779679900","wikidata":"https://www.wikidata.org/wiki/Q25304431","display_name":"Saliency map","level":3,"score":0.2540999948978424}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001932","descriptor_name":"Brain Neoplasms","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001932","descriptor_name":"Brain Neoplasms","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001932","descriptor_name":"Brain Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001932","descriptor_name":"Brain Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D003930","descriptor_name":"Diabetic Retinopathy","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D003930","descriptor_name":"Diabetic Retinopathy","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D003930","descriptor_name":"Diabetic Retinopathy","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D003930","descriptor_name":"Diabetic Retinopathy","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008268","descriptor_name":"Macular Degeneration","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D008268","descriptor_name":"Macular Degeneration","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D008268","descriptor_name":"Macular Degeneration","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D008268","descriptor_name":"Macular Degeneration","qualifier_ui":"Q000175","qualifier_name":"diagnosis","is_major_topic":false},{"descriptor_ui":"D008279","descriptor_name":"Magnetic Resonance Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D008279","descriptor_name":"Magnetic Resonance Imaging","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D014057","descriptor_name":"Tomography, X-Ray Computed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014057","descriptor_name":"Tomography, X-Ray Computed","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D041623","descriptor_name":"Tomography, Optical Coherence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D041623","descriptor_name":"Tomography, Optical Coherence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tbme.2025.3614518","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tbme.2025.3614518","pdf_url":null,"source":{"id":"https://openalex.org/S5240358","display_name":"IEEE Transactions on Biomedical Engineering","issn_l":"0018-9294","issn":["0018-9294","1558-2531"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Biomedical Engineering","raw_type":"journal-article"},{"id":"pmid:40997007","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40997007","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 transactions on bio-medical engineering","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1859487760","display_name":null,"funder_award_id":"R01 EY035410","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2518674024","display_name":null,"funder_award_id":"R43EY036781","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3962676234","display_name":null,"funder_award_id":"UL1TR002369","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4250101674","display_name":null,"funder_award_id":"R01 EY 036429","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5344252322","display_name":null,"funder_award_id":"R01 EY024544","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G585595255","display_name":null,"funder_award_id":"P30 EY010572","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6447650560","display_name":null,"funder_award_id":"T32 EY023211","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G733164911","display_name":null,"funder_award_id":"R01 EY031394","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G81930060","display_name":null,"funder_award_id":"R01 EY027833","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1901129140","https://openalex.org/W2592929672","https://openalex.org/W2803487511","https://openalex.org/W2906295032","https://openalex.org/W2919115771","https://openalex.org/W2948542848","https://openalex.org/W2962793481","https://openalex.org/W2962858109","https://openalex.org/W2963374347","https://openalex.org/W2964303497","https://openalex.org/W3012430016","https://openalex.org/W3035286874","https://openalex.org/W3116286104","https://openalex.org/W3128220181","https://openalex.org/W3138785910","https://openalex.org/W3164936045","https://openalex.org/W3197217317","https://openalex.org/W3211317523","https://openalex.org/W4225316200","https://openalex.org/W4234165561","https://openalex.org/W4285393401","https://openalex.org/W4292828899","https://openalex.org/W4295939763","https://openalex.org/W4311253153","https://openalex.org/W4312933868","https://openalex.org/W4321350922","https://openalex.org/W4383220215","https://openalex.org/W4384397878","https://openalex.org/W4385245566","https://openalex.org/W4390340600","https://openalex.org/W4395051952","https://openalex.org/W4407192178"],"related_works":[],"abstract_inverted_index":{"OBJECTIVE:":[0],"Artificial":[1],"intelligence":[2],"(AI)-based":[3],"disease":[4,48,74,100,170],"classifiers":[5,19],"have":[6],"achieved":[7],"specialist-level":[8],"performances":[9],"in":[10,147],"several":[11],"diagnostic":[12,184],"tasks.":[13],"However,":[14],"real-world":[15],"adoption":[16],"of":[17,59,72,156,167],"these":[18],"remains":[20],"challenging":[21],"due":[22],"to":[23,45,179],"the":[24,53,57,70,73,81,85,95,148,164,183],"black":[25],"box":[26],"issue.":[27],"Here,":[28],"we":[29],"report":[30],"a":[31,112,122,133],"novel":[32],"biomarker":[33],"activation":[34],"map":[35,83],"(BAM)":[36],"generation":[37],"framework":[38,54],"that":[39,67],"can":[40,162,177],"provide":[41],"clinically":[42],"meaningful":[43],"explainability":[44],"current":[46],"AI-based":[47,169],"classifiers.":[49],"METHODS:":[50],"We":[51,93],"designed":[52],"based":[55,108,116,126,137],"on":[56,97,109,117,127,138],"concept":[58],"residual":[60],"counterfactual":[61,65,86],"explanation":[62],"by":[63,172],"generating":[64],"outputs":[66],"could":[68],"reverse":[69],"decision-making":[71],"classifier.":[75],"The":[76,144,160],"BAM":[77,96,149,161],"was":[78],"generated":[79],"as":[80],"difference":[82],"between":[84],"output":[87,175],"and":[88,132,181],"original":[89],"input":[90],"with":[91,152],"postprocessing.":[92],"evaluated":[94],"four":[98],"different":[99],"classifiers,":[101],"including":[102],"an":[103,168],"age-related":[104],"macular":[105],"degeneration":[106],"classier":[107],"fundus":[110],"photography,":[111],"diabetic":[113],"retinopathy":[114],"classifier":[115,125,136,171],"optical":[118],"coherence":[119],"tomography":[120,140],"angiography,":[121],"brain":[123],"tumor":[124],"magnetic":[128],"resonance":[129],"imaging":[130],"(MRI),":[131],"breast":[134],"cancer":[135],"computerized":[139],"(CT)":[141],"scans.":[142],"RESULTS:":[143],"highlighted":[145],"regions":[146],"correlated":[150],"highly":[151],"manually":[153],"demarcated":[154],"biomarkers":[155],"each":[157],"disease.":[158],"CONCLUSION/SIGNIFICANCE:":[159],"improve":[163],"clinical":[165],"applicability":[166],"providing":[173],"intuitive":[174],"clinicians":[176],"use":[178],"understand":[180],"verify":[182],"decision.":[185]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-06-06T09:05:17.133730","created_date":"2025-10-10T00:00:00"}
