{"id":"https://openalex.org/W4293217185","doi":"https://doi.org/10.1016/j.jpi.2022.100066","title":"USING PROGRESSIVE CONTEXT ENCODERS FOR ANOMALY DETECTION IN DIGITAL PATHOLOGY IMAGES","display_name":"USING PROGRESSIVE CONTEXT ENCODERS FOR ANOMALY DETECTION IN DIGITAL PATHOLOGY IMAGES","publication_year":2022,"publication_date":"2022-01-01","ids":{"openalex":"https://openalex.org/W4293217185","doi":"https://doi.org/10.1016/j.jpi.2022.100066"},"language":"en","primary_location":{"id":"doi:10.1016/j.jpi.2022.100066","doi":"https://doi.org/10.1016/j.jpi.2022.100066","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.jpi.2022.100066","pdf_url":"https://www.sciencedirect.com/science/article/pii/S2153353922000669/pdf","source":{"id":"https://openalex.org/S4210177785","display_name":"Journal of Pathology Informatics","issn_l":"2153-3539","issn":["2153-3539","2229-5089"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","doyens","jufo-1","ki-jl-1","norway-1","oarl","poland-70"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"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":"Journal of Pathology Informatics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.sciencedirect.com/science/article/pii/S2153353922000669/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091072367","display_name":"Ryan Gillard","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ryan Gillard","raw_affiliation_strings":["Google, Cloud Professional Services, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Google, Cloud Professional Services, United States","institution_ids":["https://openalex.org/I1291425158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015018740","display_name":"Chady Meroueh","orcid":"https://orcid.org/0000-0003-2352-4336","observed_orcids":["https://orcid.org/0000-0003-2352-4336"]},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chady Meroueh","raw_affiliation_strings":["Mayo Clinic, Laboratory Medicine and Pathology, Rochester, MN, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Laboratory Medicine and Pathology, Rochester, MN, United States","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038851501","display_name":"Qiangqiang Gu","orcid":"https://orcid.org/0000-0003-3258-3557","observed_orcids":["https://orcid.org/0000-0003-3258-3557"]},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Qiangqiang Gu","raw_affiliation_strings":["Mayo Clinic, Laboratory Medicine and Pathology, Rochester, MN, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Laboratory Medicine and Pathology, Rochester, MN, United States","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068134362","display_name":"Naresh Prodduturi","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Naresh Prodduturi","raw_affiliation_strings":["Mayo Clinic, Laboratory Medicine and Pathology, Rochester, MN, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Laboratory Medicine and Pathology, Rochester, MN, United States","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112493980","display_name":"Sandhya Patil","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I1291425158","display_name":"Google (United States)","ror":"https://ror.org/00njsd438","country_code":"US","type":"company","lineage":["https://openalex.org/I1291425158","https://openalex.org/I4210128969"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sandhya Patil","raw_affiliation_strings":["Google, Cloud Professional Services, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Google, Cloud Professional Services, United States","institution_ids":["https://openalex.org/I1291425158"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010963221","display_name":"Thomas James Flotte","orcid":"https://orcid.org/0000-0001-5691-8249","observed_orcids":["https://orcid.org/0000-0001-5691-8249"]},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas Flotte","raw_affiliation_strings":["Mayo Clinic, Laboratory Medicine and Pathology, Rochester, MN, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Laboratory Medicine and Pathology, Rochester, MN, United States","institution_ids":["https://openalex.org/I1330342723"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085507659","display_name":"Steven N. Hart","orcid":"https://orcid.org/0000-0001-7714-2734","observed_orcids":["https://orcid.org/0000-0001-7714-2734"]},"institutions":[{"id":"https://openalex.org/I1330342723","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Steven N. Hart","raw_affiliation_strings":["Mayo Clinic, Laboratory Medicine and Pathology, Rochester, MN, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mayo Clinic, Laboratory Medicine and Pathology, Rochester, MN, United States","institution_ids":["https://openalex.org/I1330342723"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5038851501"],"corresponding_institution_ids":["https://openalex.org/I1330342723"],"apc_list":{"value":1400,"currency":"USD","value_usd":1400},"apc_paid":{"value":1400,"currency":"USD","value_usd":1400},"fwci":0.2129,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.45976067,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"13","issue":null,"first_page":"100066","last_page":"100066"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.9976000189781189,"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"}},"topics":[{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.9976000189781189,"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/T11512","display_name":"Anomaly Detection Techniques and Applications","score":0.0007999999797903001,"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/T12422","display_name":"Radiomics and Machine Learning in Medical Imaging","score":0.00019999999494757503,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/anomaly-detection","display_name":"anomaly detection","score":0.7770000100135803},{"id":"https://openalex.org/keywords/digital-pathology-images","display_name":"digital pathology images","score":0.8980000019073486},{"id":"https://openalex.org/keywords/weakly-supervised-learning","display_name":"weakly supervised learning","score":0.5879999995231628},{"id":"https://openalex.org/keywords/semantic-encoding","display_name":"semantic encoding","score":0.46799999475479126},{"id":"https://openalex.org/keywords/the-cancer-genome-atlas","display_name":"TCGA","score":0.6340000033378601},{"id":"https://openalex.org/keywords/densenet-201","display_name":"DenseNet201","score":0.9290000200271606},{"id":"https://openalex.org/keywords/transfer-learning","display_name":"transfer learning","score":0.9039999842643738},{"id":"https://openalex.org/keywords/whole-slide-images","display_name":"whole slide images","score":0.5569999814033508},{"id":"https://openalex.org/keywords/lung-squamous-cell-carcinoma","display_name":"lung squamous cell carcinoma","score":0.7789999842643738},{"id":"https://openalex.org/keywords/lung-adenocarcinoma","display_name":"lung adenocarcinoma","score":0.9980000257492065},{"id":"https://openalex.org/keywords/adrenocortical-carcinoma","display_name":"adrenocortical carcinoma","score":0.9950000047683716},{"id":"https://openalex.org/keywords/clear-cell-renal-cell-carcinoma","display_name":"clear cell renal cell carcinoma","score":0.996999979019165},{"id":"https://openalex.org/keywords/seminoma","display_name":"seminoma","score":0.8730000257492065},{"id":"https://openalex.org/keywords/testicular-cancer","display_name":"testicular cancer","score":0.5529999732971191},{"id":"https://openalex.org/keywords/tumor-classification","display_name":"tumor classification","score":0.4560000002384186}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7755168676376343},{"id":"https://openalex.org/C2777522853","wikidata":"https://www.wikidata.org/wiki/Q5276128","display_name":"Digital pathology","level":2,"score":0.717857301235199},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6895947456359863},{"id":"https://openalex.org/C739882","wikidata":"https://www.wikidata.org/wiki/Q3560506","display_name":"Anomaly detection","level":2,"score":0.6518045663833618},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.4719713628292084},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3878825604915619},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3671247065067291},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.32186782360076904},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.195978045463562},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10492175817489624},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1016/j.jpi.2022.100066","doi":"https://doi.org/10.1016/j.jpi.2022.100066","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.jpi.2022.100066","pdf_url":"https://www.sciencedirect.com/science/article/pii/S2153353922000669/pdf","source":{"id":"https://openalex.org/S4210177785","display_name":"Journal of Pathology Informatics","issn_l":"2153-3539","issn":["2153-3539","2229-5089"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","doyens","jufo-1","ki-jl-1","norway-1","oarl","poland-70"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"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":"Journal of Pathology Informatics","raw_type":"journal-article"},{"id":"doi:10.1101/2021.07.02.450957","doi":"https://doi.org/10.1101/2021.07.02.450957","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2021.07.02.450957","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2021/07/04/2021.07.02.450957.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmh:oai:doaj.org/article:a5dac4d5807340c6a2dd477a533fbaaf","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/a5dac4d5807340c6a2dd477a533fbaaf","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,"listed_in":[],"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":"Journal of Pathology Informatics, Vol 13, Iss , Pp 100066- (2022)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1016/j.jpi.2022.100066","doi":"https://doi.org/10.1016/j.jpi.2022.100066","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.jpi.2022.100066","pdf_url":"https://www.sciencedirect.com/science/article/pii/S2153353922000669/pdf","source":{"id":"https://openalex.org/S4210177785","display_name":"Journal of Pathology Informatics","issn_l":"2153-3539","issn":["2153-3539","2229-5089"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","doyens","jufo-1","ki-jl-1","norway-1","oarl","poland-70"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"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":"Journal of Pathology Informatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.5683000087738037,"display_name":"Good health and well-being"}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306143","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03"},{"id":"https://openalex.org/F4320313748","display_name":"Leon Lowenstein Foundation","ror":"https://ror.org/04q350418"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4293217185.pdf","grobid_xml":"https://content.openalex.org/works/W4293217185.grobid-xml"},"referenced_works_count":30,"referenced_works":["https://openalex.org/W1593832246","https://openalex.org/W2006410648","https://openalex.org/W2040414046","https://openalex.org/W2066020421","https://openalex.org/W2098336507","https://openalex.org/W2103676924","https://openalex.org/W2115328641","https://openalex.org/W2122538988","https://openalex.org/W2342877626","https://openalex.org/W2460896619","https://openalex.org/W2504150216","https://openalex.org/W2557414982","https://openalex.org/W2599354622","https://openalex.org/W2760354783","https://openalex.org/W2787947370","https://openalex.org/W2906774465","https://openalex.org/W2914570111","https://openalex.org/W2915860004","https://openalex.org/W2945626616","https://openalex.org/W2946576587","https://openalex.org/W2950237263","https://openalex.org/W2952481429","https://openalex.org/W2954278343","https://openalex.org/W2962760235","https://openalex.org/W2962879692","https://openalex.org/W2963045681","https://openalex.org/W2967444033","https://openalex.org/W3006244628","https://openalex.org/W3015236565","https://openalex.org/W3038022805"],"related_works":["https://openalex.org/W4293217022","https://openalex.org/W4393574639","https://openalex.org/W7155387043","https://openalex.org/W7213218116","https://openalex.org/W7148316164","https://openalex.org/W2914955798","https://openalex.org/W296380546","https://openalex.org/W7117240468","https://openalex.org/W4281562763","https://openalex.org/W7160180975"],"abstract_inverted_index":{"ABSTRACT":[0],"Whole":[1],"slide":[2],"imaging":[3],"(WSI)":[4],"is":[5,104,158,176],"transforming":[6],"the":[7,53,71,93,122],"practice":[8],"of":[9,66,120,125,127,146],"pathology,":[10],"converting":[11],"a":[12,16,40,79,114,159],"qualitative":[13],"discipline":[14],"into":[15],"quantitative":[17],"one.":[18],"However,":[19],"one":[20],"must":[21],"exercise":[22],"caution":[23],"in":[24,29],"interpreting":[25],"algorithm":[26,54],"assertions,":[27],"particularly":[28],"pathology":[30],"where":[31],"an":[32,67,102],"incorrect":[33],"classification":[34],"could":[35],"have":[36,49],"profound":[37],"impacts":[38],"on":[39],"patient,":[41],"and":[42,97,135],"rare":[43],"classes":[44],"exist":[45],"that":[46,152],"may":[47],"not":[48],"been":[50],"seen":[51],"by":[52,172],"during":[55],"training.":[56],"A":[57],"more":[58],"robust":[59],"approach":[60,103,142],"would":[61,86],"be":[62,87],"to":[63,77],"identify":[64],"areas":[65],"image":[68],"for":[69,89,148,162],"which":[70],"pathologist":[72],"should":[73],"concentrate":[74],"their":[75],"effort":[76],"make":[78],"final":[80],"diagnosis.":[81],"This":[82],"anomaly":[83,138,155],"detection":[84,139,156],"strategy":[85,161],"ideal":[88],"WSI,":[90],"but":[91],"given":[92],"extremely":[94,132],"high":[95,133,164],"resolution":[96,134],"large":[98],"file":[99],"sizes,":[100],"such":[101],"difficult.":[105],"Here,":[106],"we":[107],"combine":[108],"progressive":[109],"generative":[110],"adversarial":[111,116],"networks":[112],"with":[113],"flexible":[115],"autoencoder":[117],"architecture":[118],"capable":[119],"learning":[121],"\u201cnormal":[123],"distribution\u201d":[124],"WSIs":[126],"normal":[128],"skin":[129],"tissue":[130],"at":[131,179],"demonstrate":[136],"its":[137],"performance.":[140],"Our":[141],"yielded":[143],"pixel-level":[144],"accuracy":[145],"89%":[147],"identifying":[149],"melanoma,":[150],"suggesting":[151],"our":[153],"label-free":[154],"pipeline":[157],"viable":[160],"generating":[163],"quality":[165],"annotations":[166],"-":[167],"without":[168],"tedious":[169],"manual":[170],"segmentation":[171],"pathologists.":[173],"The":[174],"code":[175],"publicly":[177],"available":[178],"https://github.com/Steven-N-Hart/P-CEAD":[180],".":[181]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2}],"updated_date":"2026-11-03T10:50:19.383937","created_date":"2022-08-27T00:00:00"}