{"id":"https://openalex.org/W4379377108","doi":"https://doi.org/10.1016/j.cmpb.2023.107631","title":"ChampKit: A framework for rapid evaluation of deep neural networks for patch-based histopathology classification","display_name":"ChampKit: A framework for rapid evaluation of deep neural networks for patch-based histopathology classification","publication_year":2023,"publication_date":"2023-05-30","ids":{"openalex":"https://openalex.org/W4379377108","doi":"https://doi.org/10.1016/j.cmpb.2023.107631","pmid":"https://pubmed.ncbi.nlm.nih.gov/37271050"},"language":"en","primary_location":{"id":"doi:10.1016/j.cmpb.2023.107631","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.cmpb.2023.107631","pdf_url":null,"source":{"id":"https://openalex.org/S138959710","display_name":"Computer Methods and Programs in Biomedicine","issn_l":"0169-2607","issn":["0169-2607","1872-7565"],"is_oa":false,"is_in_doaj":false,"is_core":true,"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":"Computer Methods and Programs in Biomedicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1016/j.cmpb.2023.107631","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071516360","display_name":"Jakub Kaczmarzyk","orcid":"https://orcid.org/0000-0002-5544-7577"},"institutions":[{"id":"https://openalex.org/I4210102711","display_name":"Stony Brook Medicine","ror":"https://ror.org/01882y777","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210102711"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jakub R. Kaczmarzyk","raw_affiliation_strings":["Department of Biomedical Informatics, Stony Brook Medicine, 101 Nicolls Rd, Stony Brook, 11794, NY, USA; Simons Center for Quantitative Biology, 1 Bungtown Rd, Cold Spring Harbor, 11724, NY, USA. Electronic address: jakub.kaczmarzyk@stonybrookmedicine.edu","Department of Biomedical Informatics, Stony Brook Medicine, 101 Nicolls Rd, Stony Brook, 11794, NY, USA","Simons Center for Quantitative Biology, 1 Bungtown Rd, Cold Spring Harbor, 11724, NY, USA"],"raw_orcid":"https://orcid.org/0000-0002-5544-7577","affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Stony Brook Medicine, 101 Nicolls Rd, Stony Brook, 11794, NY, USA; Simons Center for Quantitative Biology, 1 Bungtown Rd, Cold Spring Harbor, 11724, NY, USA. Electronic address: jakub.kaczmarzyk@stonybrookmedicine.edu","institution_ids":["https://openalex.org/I4210102711"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Stony Brook Medicine, 101 Nicolls Rd, Stony Brook, 11794, NY, USA","institution_ids":["https://openalex.org/I4210102711"]},{"raw_affiliation_string":"Simons Center for Quantitative Biology, 1 Bungtown Rd, Cold Spring Harbor, 11724, NY, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062591338","display_name":"Rajarsi Gupta","orcid":"https://orcid.org/0000-0002-1577-8718"},"institutions":[{"id":"https://openalex.org/I4210102711","display_name":"Stony Brook Medicine","ror":"https://ror.org/01882y777","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210102711"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rajarsi Gupta","raw_affiliation_strings":["Department of Biomedical Informatics, Stony Brook Medicine, 101 Nicolls Rd, Stony Brook, 11794, NY, USA"],"raw_orcid":"https://orcid.org/0000-0002-1577-8718","affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Stony Brook Medicine, 101 Nicolls Rd, Stony Brook, 11794, NY, USA","institution_ids":["https://openalex.org/I4210102711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037383891","display_name":"Tahsin Kur\u00e7","orcid":"https://orcid.org/0000-0001-9237-4306"},"institutions":[{"id":"https://openalex.org/I4210102711","display_name":"Stony Brook Medicine","ror":"https://ror.org/01882y777","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210102711"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tahsin M. Kurc","raw_affiliation_strings":["Department of Biomedical Informatics, Stony Brook Medicine, 101 Nicolls Rd, Stony Brook, 11794, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Stony Brook Medicine, 101 Nicolls Rd, Stony Brook, 11794, NY, USA","institution_ids":["https://openalex.org/I4210102711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023386865","display_name":"Shahira Abousamra","orcid":"https://orcid.org/0000-0001-6214-1923"},"institutions":[{"id":"https://openalex.org/I59553526","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33","country_code":"US","type":"education","lineage":["https://openalex.org/I59553526"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shahira Abousamra","raw_affiliation_strings":["Department of Computer Science, Stony Brook University, Stony Brook, NY, USA"],"raw_orcid":"https://orcid.org/0000-0001-6214-1923","affiliations":[{"raw_affiliation_string":"Department of Computer Science, Stony Brook University, Stony Brook, NY, USA","institution_ids":["https://openalex.org/I59553526"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072946826","display_name":"Joel Saltz","orcid":"https://orcid.org/0000-0002-3451-2165"},"institutions":[{"id":"https://openalex.org/I4210087560","display_name":"Stony Brook School","ror":"https://ror.org/003wx9n05","country_code":"US","type":"education","lineage":["https://openalex.org/I4210087560"]},{"id":"https://openalex.org/I4210102711","display_name":"Stony Brook Medicine","ror":"https://ror.org/01882y777","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210102711"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joel H. Saltz","raw_affiliation_strings":["Department of Biomedical Informatics, Stony Brook Medicine, 101 Nicolls Rd, Stony Brook, 11794, NY, USA. Electronic address: joel.saltz@stonybrookmedicine.edu","Department of Biomedical Informatics, Stony Brook Medicine, 101 Nicolls Rd, Stony Brook, 11794, NY, USA"],"raw_orcid":"https://orcid.org/0000-0002-3451-2165","affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, Stony Brook Medicine, 101 Nicolls Rd, Stony Brook, 11794, NY, USA. Electronic address: joel.saltz@stonybrookmedicine.edu","institution_ids":["https://openalex.org/I4210102711","https://openalex.org/I4210087560"]},{"raw_affiliation_string":"Department of Biomedical Informatics, Stony Brook Medicine, 101 Nicolls Rd, Stony Brook, 11794, NY, USA","institution_ids":["https://openalex.org/I4210102711"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060820355","display_name":"Peter K. Koo","orcid":"https://orcid.org/0000-0001-8722-0038"},"institutions":[{"id":"https://openalex.org/I2750212522","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2750212522"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Peter K. Koo","raw_affiliation_strings":["Simons Center for Quantitative Biology, 1 Bungtown Rd, Cold Spring Harbor, 11724, NY, USA. Electronic address: koo@cshl.edu","Simons Center for Quantitative Biology, 1 Bungtown Rd, Cold Spring Harbor, 11724, NY, USA"],"raw_orcid":"https://orcid.org/0000-0001-8722-0038","affiliations":[{"raw_affiliation_string":"Simons Center for Quantitative Biology, 1 Bungtown Rd, Cold Spring Harbor, 11724, NY, USA. Electronic address: koo@cshl.edu","institution_ids":["https://openalex.org/I2750212522"]},{"raw_affiliation_string":"Simons Center for Quantitative Biology, 1 Bungtown Rd, Cold Spring Harbor, 11724, NY, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5071516360"],"corresponding_institution_ids":["https://openalex.org/I4210102711"],"apc_list":{"value":2880,"currency":"USD","value_usd":2880},"apc_paid":{"value":2880,"currency":"USD","value_usd":2880},"fwci":2.6858,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.91837286,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"239","issue":null,"first_page":"107631","last_page":"107631"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10862","display_name":"AI in cancer detection","score":0.9678000211715698,"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":0.9678000211715698,"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/T12874","display_name":"Digital Imaging for Blood Diseases","score":0.018699999898672104,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.0017999999690800905,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.8041768074035645},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6900648474693298},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.6859909296035767},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5885778665542603},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5769088864326477},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.5266202092170715},{"id":"https://openalex.org/keywords/coding","display_name":"Coding (social sciences)","score":0.4548533260822296},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4469428062438965},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08504635095596313}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8041768074035645},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6900648474693298},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.6859909296035767},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5885778665542603},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5769088864326477},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.5266202092170715},{"id":"https://openalex.org/C179518139","wikidata":"https://www.wikidata.org/wiki/Q5140297","display_name":"Coding (social sciences)","level":2,"score":0.4548533260822296},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4469428062438965},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08504635095596313},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"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":"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":"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":"D006652","descriptor_name":"Histological Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006652","descriptor_name":"Histological Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006652","descriptor_name":"Histological Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006652","descriptor_name":"Histological Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006652","descriptor_name":"Histological Techniques","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006652","descriptor_name":"Histological Techniques","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":"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":"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1016/j.cmpb.2023.107631","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.cmpb.2023.107631","pdf_url":null,"source":{"id":"https://openalex.org/S138959710","display_name":"Computer Methods and Programs in Biomedicine","issn_l":"0169-2607","issn":["0169-2607","1872-7565"],"is_oa":false,"is_in_doaj":false,"is_core":true,"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":"Computer Methods and Programs in Biomedicine","raw_type":"journal-article"},{"id":"pmid:37271050","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37271050","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":"Computer methods and programs in biomedicine","raw_type":null},{"id":"pmh:oai:repository.cshl.edu:41034","is_oa":true,"landing_page_url":null,"pdf_url":"https://repository.cshl.edu/id/eprint/41034/1/2023_Kaczmarzyk_ChampKit_A_framework_for_rapid.pdf","source":{"id":"https://openalex.org/S4306402288","display_name":"Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"PeerReviewed"},{"id":"pmh:oai:pubmedcentral.nih.gov:11093625","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11093625","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11093625/pdf/nihms-1991817.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-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Comput Methods Programs Biomed","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1016/j.cmpb.2023.107631","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.cmpb.2023.107631","pdf_url":null,"source":{"id":"https://openalex.org/S138959710","display_name":"Computer Methods and Programs in Biomedicine","issn_l":"0169-2607","issn":["0169-2607","1872-7565"],"is_oa":false,"is_in_doaj":false,"is_core":true,"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":"Computer Methods and Programs in Biomedicine","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1056770891","display_name":null,"funder_award_id":"U24CA215109","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2528306368","display_name":null,"funder_award_id":"S10OD028632-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4275513708","display_name":null,"funder_award_id":"5P30CA045508","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4373432326","display_name":null,"funder_award_id":"5P30CA045508","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4653000387","display_name":null,"funder_award_id":"UH3CA225021","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G5753238768","display_name":null,"funder_award_id":"5P30CA045508","funder_id":"https://openalex.org/F4320314202","funder_display_name":"Cold Spring Harbor Laboratory"},{"id":"https://openalex.org/G5841191496","display_name":null,"funder_award_id":"S10OD028632","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G666509988","display_name":null,"funder_award_id":"T32GM008444","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G823988569","display_name":null,"funder_award_id":"R01HG012131","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G8829570253","display_name":null,"funder_award_id":"T32GM008444","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320314202","display_name":"Cold Spring Harbor Laboratory","ror":"https://ror.org/02qz8b764"},{"id":"https://openalex.org/F4320331904","display_name":"Stony Brook University","ror":"https://ror.org/05qghxh33"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334591","display_name":"Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory","ror":null},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":122,"referenced_works":["https://openalex.org/W1504535992","https://openalex.org/W1977653087","https://openalex.org/W2032983127","https://openalex.org/W2033689666","https://openalex.org/W2066549535","https://openalex.org/W2091877475","https://openalex.org/W2097998348","https://openalex.org/W2117539524","https://openalex.org/W2120431466","https://openalex.org/W2302501749","https://openalex.org/W2324712956","https://openalex.org/W2474421929","https://openalex.org/W2593345132","https://openalex.org/W2594760301","https://openalex.org/W2760946358","https://openalex.org/W2770647635","https://openalex.org/W2772723798","https://openalex.org/W2794622599","https://openalex.org/W2796153844","https://openalex.org/W2796409016","https://openalex.org/W2802206159","https://openalex.org/W2806857275","https://openalex.org/W2902947426","https://openalex.org/W2905022081","https://openalex.org/W2908510526","https://openalex.org/W2914836117","https://openalex.org/W2944675676","https://openalex.org/W2945092046","https://openalex.org/W2947706148","https://openalex.org/W2948930564","https://openalex.org/W2952481429","https://openalex.org/W2964611302","https://openalex.org/W2973237362","https://openalex.org/W2981841914","https://openalex.org/W3004016611","https://openalex.org/W3008826523","https://openalex.org/W3014157798","https://openalex.org/W3016045558","https://openalex.org/W3019938913","https://openalex.org/W3025630280","https://openalex.org/W3027417966","https://openalex.org/W3030889987","https://openalex.org/W3033828193","https://openalex.org/W3036122989","https://openalex.org/W3040734937","https://openalex.org/W3046154346","https://openalex.org/W3081081614","https://openalex.org/W3084161163","https://openalex.org/W3089090082","https://openalex.org/W3094502228","https://openalex.org/W3096715224","https://openalex.org/W3099794024","https://openalex.org/W3112737733","https://openalex.org/W3115168802","https://openalex.org/W3125924492","https://openalex.org/W3130681742","https://openalex.org/W3141984075","https://openalex.org/W3147456160","https://openalex.org/W3155701827","https://openalex.org/W3160261825","https://openalex.org/W3172957366","https://openalex.org/W3186721627","https://openalex.org/W3192919049","https://openalex.org/W3195171687","https://openalex.org/W3197433610","https://openalex.org/W3209295695","https://openalex.org/W3212889265","https://openalex.org/W3215385221","https://openalex.org/W4200217763","https://openalex.org/W4205566005","https://openalex.org/W4205900565","https://openalex.org/W4206041598","https://openalex.org/W4206244272","https://openalex.org/W4207048774","https://openalex.org/W4207066074","https://openalex.org/W4210984894","https://openalex.org/W4212774754","https://openalex.org/W4213294068","https://openalex.org/W4214901231","https://openalex.org/W4220801231","https://openalex.org/W4224295454","https://openalex.org/W4225009193","https://openalex.org/W4225864685","https://openalex.org/W4226139415","https://openalex.org/W4229049871","https://openalex.org/W4234552385","https://openalex.org/W4236072661","https://openalex.org/W4247237676","https://openalex.org/W4281562603","https://openalex.org/W4281732693","https://openalex.org/W4286859131","https://openalex.org/W4288809219","https://openalex.org/W4298161330","https://openalex.org/W4306173528","https://openalex.org/W4307229392","https://openalex.org/W4308016413","https://openalex.org/W4312566606","https://openalex.org/W6674385629","https://openalex.org/W6687483927","https://openalex.org/W6721136770","https://openalex.org/W6734147758","https://openalex.org/W6749127402","https://openalex.org/W6751806240","https://openalex.org/W6751925790","https://openalex.org/W6752381671","https://openalex.org/W6752412184","https://openalex.org/W6756054304","https://openalex.org/W6757817989","https://openalex.org/W6763301180","https://openalex.org/W6766978945","https://openalex.org/W6768133545","https://openalex.org/W6769086501","https://openalex.org/W6784333009","https://openalex.org/W6786010316","https://openalex.org/W6789961193","https://openalex.org/W6794172776","https://openalex.org/W6796379873","https://openalex.org/W6799372920","https://openalex.org/W6804280552","https://openalex.org/W6805446335","https://openalex.org/W6810965135","https://openalex.org/W6848565453"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W4287027380","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W3193760048","https://openalex.org/W4285822516","https://openalex.org/W2551200859"],"abstract_inverted_index":{"BACKGROUND":[0],"AND":[1],"OBJECTIVE:":[2],"Histopathology":[3,116],"is":[4,74,129,290,352,371],"the":[5,23,32,58,64,162,166,190,209,215,291,314,327,362,384,406],"gold":[6],"standard":[7],"for":[8,28,51,93,103,139,168,223,365,405],"diagnosis":[9],"of":[10,25,34,60,66,89,118,147,155,192,217,226,287,316,357,386,388,398],"many":[11,29],"cancers.":[12],"Recent":[13],"advances":[14],"in":[15,71,96,98,326],"computer":[16,358],"vision,":[17],"specifically":[18],"deep":[19,136,198,239,392],"learning,":[20],"have":[21],"facilitated":[22],"analysis":[24],"histopathology":[26,53],"images":[27],"tasks,":[30],"including":[31],"detection":[33],"immune":[35],"cells":[36],"and":[37,48,63,84,107,134,153,182,194,197,245,403],"microsatellite":[38],"instability.":[39],"However,":[40],"it":[41,205],"remains":[42],"difficult":[43],"to":[44,57,75,132,170,208,299,336,354,378],"identify":[45],"optimal":[46],"models":[47,92,156,175,196,228,394],"training":[49,152],"configurations":[50],"different":[52],"classification":[54,95],"tasks":[55],"due":[56],"abundance":[59],"available":[61],"architectures":[62,200],"lack":[65],"systematic":[67,87],"evaluations.":[68],"Our":[69],"objective":[70],"this":[72,82,288,380],"work":[73],"present":[76,113],"a":[77,99,130,144,179,186,224,247,279,366,375,396],"software":[78],"tool":[79,377,407],"that":[80,128,229,342],"addresses":[81],"need":[83,167],"enables":[85,151],"robust,":[86],"evaluation":[88,126,154,191,385],"neural":[90,137,303],"network":[91],"patch":[94,140],"histology":[97],"light-weight,":[100],"easy-to-use":[101],"package":[102],"both":[104],"algorithm":[105],"developers":[106],"biomedical":[108],"researchers.":[109],"METHODS:":[110],"Here":[111],"we":[112,219,253,273,296,340],"ChampKit":[114,142,292,373],"(Comprehensive":[115],"Assessment":[117],"Model":[119],"Predictions":[120],"toolKit):":[121],"an":[122],"extensible,":[123],"fully":[124],"reproducible":[125],"toolkit":[127],"one-stop-shop":[131],"train":[133],"evaluate":[135,301],"networks":[138,304],"classification.":[141],"curates":[143],"broad":[145],"range":[146],"public":[148],"datasets.":[149,307],"It":[150],"supported":[157],"by":[158,382],"timm":[159],"directly":[160],"from":[161,259,267,278,345],"command":[163],"line,":[164],"without":[165],"users":[169],"write":[171],"any":[172],"code.":[173],"External":[174],"are":[176,408],"enabled":[177],"through":[178],"straightforward":[180],"API":[181],"minimal":[183],"coding.":[184],"As":[185],"result,":[187],"Champkit":[188],"facilitates":[189],"existing":[193,389],"new":[195],"learning":[199,240,266,277,333,344,393],"on":[201,236],"pathology":[202,369,399],"datasets,":[203],"making":[204],"more":[206],"accessible":[207,410],"broader":[210],"scientific":[211],"community.":[212],"To":[213],"demonstrate":[214],"utility":[216],"ChampKit,":[218,234,295],"establish":[220],"baseline":[221],"performance":[222],"subset":[225],"possible":[227],"could":[230],"be":[231,337],"employed":[232],"with":[233,264,321],"focusing":[235],"several":[237],"popular":[238],"models,":[241],"namely":[242],"ResNet18,":[243,272],"ResNet50,":[244],"R26-ViT,":[246],"hybrid":[248],"vision":[249],"transformer.":[250],"In":[251],"addition,":[252],"compare":[254],"each":[255],"model":[256,364],"trained":[257],"either":[258],"random":[260,319],"weight":[261],"initialization":[262],"or":[263],"transfer":[265,276,332,343],"ImageNet":[268],"pretrained":[269,281],"models.":[270],"For":[271],"also":[274],"consider":[275],"self-supervised":[280,346],"model.":[282],"RESULTS:":[283],"The":[284],"main":[285],"result":[286],"paper":[289],"software.":[293],"Using":[294],"were":[297],"able":[298],"systemically":[300],"multiple":[302],"across":[305,395],"six":[306],"We":[308],"observed":[309],"mixed":[310],"results":[311],"when":[312],"evaluating":[313],"benefits":[315],"pretraining":[317],"versus":[318],"intialization,":[320],"no":[322],"clear":[323],"benefit":[324],"except":[325],"low":[328],"data":[329,404],"regime,":[330],"where":[331],"was":[334],"found":[335,341],"beneficial.":[338],"Surprisingly,":[339],"weights":[347],"rarely":[348],"improved":[349],"performance,":[350],"which":[351],"counter":[353],"other":[355],"areas":[356],"vision.":[359],"CONCLUSIONS:":[360],"Choosing":[361],"right":[363],"given":[367],"digital":[368],"dataset":[370],"nontrivial.":[372],"provides":[374],"valuable":[376],"fill":[379],"gap":[381],"enabling":[383],"hundreds":[387],"(or":[390],"user-defined)":[391],"variety":[397],"tasks.":[400],"Source":[401],"code":[402],"freely":[409],"at":[411],"https://github.com/SBU-BMI/champkit.":[412]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":8}],"updated_date":"2026-05-08T15:41:06.802602","created_date":"2025-10-10T00:00:00"}
