{"id":"https://openalex.org/W4200506499","doi":"https://doi.org/10.1109/embc46164.2021.9629898","title":"Learning Cellular Phenotypes through Supervision","display_name":"Learning Cellular Phenotypes through Supervision","publication_year":2021,"publication_date":"2021-11-01","ids":{"openalex":"https://openalex.org/W4200506499","doi":"https://doi.org/10.1109/embc46164.2021.9629898","pmid":"https://pubmed.ncbi.nlm.nih.gov/34892015"},"language":"en","primary_location":{"id":"doi:10.1109/embc46164.2021.9629898","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc46164.2021.9629898","pdf_url":null,"source":{"id":"https://openalex.org/S4363607750","display_name":"2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)","raw_type":"proceedings-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/A5010258369","display_name":"Helen Theissen","orcid":"https://orcid.org/0000-0002-4628-9722"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Helen Theissen","raw_affiliation_strings":["Dept. of Engineering Science, Institute of Biomedical Engineering (IBME) and the Big Data Institute (BDI), University of Oxford, Oxford, UK"],"affiliations":[{"raw_affiliation_string":"Dept. of Engineering Science, Institute of Biomedical Engineering (IBME) and the Big Data Institute (BDI), University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049571472","display_name":"Tapabrata Chakraborti","orcid":"https://orcid.org/0000-0002-5597-908X"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Tapabrata Chakraborti","raw_affiliation_strings":["Dept. of Engineering Science, Institute of Biomedical Engineering (IBME) and the Big Data Institute (BDI), University of Oxford, Oxford, UK"],"affiliations":[{"raw_affiliation_string":"Dept. of Engineering Science, Institute of Biomedical Engineering (IBME) and the Big Data Institute (BDI), University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082807892","display_name":"Stefano Malacrino","orcid":"https://orcid.org/0000-0003-1237-8572"},"institutions":[{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Stefano Malacrino","raw_affiliation_strings":["Dept. of Engineering Science, Institute of Biomedical Engineering (IBME) and the Big Data Institute (BDI), University of Oxford, Oxford, UK"],"affiliations":[{"raw_affiliation_string":"Dept. of Engineering Science, Institute of Biomedical Engineering (IBME) and the Big Data Institute (BDI), University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037405971","display_name":"Korsuk Sirinukunwattana","orcid":"https://orcid.org/0000-0002-3603-4435"},"institutions":[{"id":"https://openalex.org/I4210146357","display_name":"Oxford BioMedica (United Kingdom)","ror":"https://ror.org/03dp0vf82","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210146357"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Korsuk Sirinukunwattana","raw_affiliation_strings":["Dept. of Engineering Science, Institute of Biomedical Engineering (IBME) and the Big Data Institute (BDI), University of Oxford, Oxford, UK","NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK"],"affiliations":[{"raw_affiliation_string":"Dept. of Engineering Science, Institute of Biomedical Engineering (IBME) and the Big Data Institute (BDI), University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK","institution_ids":["https://openalex.org/I4210146357","https://openalex.org/I40120149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023326852","display_name":"Daniel Royston","orcid":"https://orcid.org/0000-0002-5151-2378"},"institutions":[{"id":"https://openalex.org/I4210146357","display_name":"Oxford BioMedica (United Kingdom)","ror":"https://ror.org/03dp0vf82","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210146357"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]},{"id":"https://openalex.org/I2802742124","display_name":"John Radcliffe Hospital","ror":"https://ror.org/0080acb59","country_code":"GB","type":"healthcare","lineage":["https://openalex.org/I2802742124","https://openalex.org/I4210127145","https://openalex.org/I4210147381"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Daniel Royston","raw_affiliation_strings":["Department of Cellular Pathology, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, United Kingdom","NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK"],"affiliations":[{"raw_affiliation_string":"Department of Cellular Pathology, John Radcliffe Hospital, Oxford University NHS Foundation Trust, Oxford, United Kingdom","institution_ids":["https://openalex.org/I2802742124","https://openalex.org/I40120149"]},{"raw_affiliation_string":"NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK","institution_ids":["https://openalex.org/I4210146357","https://openalex.org/I40120149"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027416348","display_name":"Jens Rittscher","orcid":"https://orcid.org/0000-0002-8528-8298"},"institutions":[{"id":"https://openalex.org/I4210146357","display_name":"Oxford BioMedica (United Kingdom)","ror":"https://ror.org/03dp0vf82","country_code":"GB","type":"company","lineage":["https://openalex.org/I4210146357"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jens Rittscher","raw_affiliation_strings":["Dept. of Engineering Science, Institute of Biomedical Engineering (IBME) and the Big Data Institute (BDI), University of Oxford, Oxford, UK","NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK"],"affiliations":[{"raw_affiliation_string":"Dept. of Engineering Science, Institute of Biomedical Engineering (IBME) and the Big Data Institute (BDI), University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK","institution_ids":["https://openalex.org/I4210146357","https://openalex.org/I40120149"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5010258369"],"corresponding_institution_ids":["https://openalex.org/I40120149"],"apc_list":null,"apc_paid":null,"fwci":0.2614,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.64962558,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"16","issue":null,"first_page":"3592","last_page":"3595"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12874","display_name":"Digital Imaging for Blood Diseases","score":0.9775999784469604,"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"}},"topics":[{"id":"https://openalex.org/T12874","display_name":"Digital Imaging for Blood Diseases","score":0.9775999784469604,"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/T11503","display_name":"Cytokine Signaling Pathways and Interactions","score":0.921500027179718,"subfield":{"id":"https://openalex.org/subfields/2730","display_name":"Oncology"},"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.9160000085830688,"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":0.6289831399917603},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.545910120010376},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5248361229896545},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5063036680221558},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.5057189464569092},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.4972887337207794},{"id":"https://openalex.org/keywords/relevance","display_name":"Relevance (law)","score":0.4641730785369873},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4540201425552368},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.4423828721046448},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.43730786442756653},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38664132356643677},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3381883502006531},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19067281484603882}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6289831399917603},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.545910120010376},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5248361229896545},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5063036680221558},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.5057189464569092},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.4972887337207794},{"id":"https://openalex.org/C158154518","wikidata":"https://www.wikidata.org/wiki/Q7310970","display_name":"Relevance (law)","level":2,"score":0.4641730785369873},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4540201425552368},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.4423828721046448},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.43730786442756653},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38664132356643677},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3381883502006531},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19067281484603882},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/embc46164.2021.9629898","is_oa":false,"landing_page_url":"https://doi.org/10.1109/embc46164.2021.9629898","pdf_url":null,"source":{"id":"https://openalex.org/S4363607750","display_name":"2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 43rd Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC)","raw_type":"proceedings-article"},{"id":"pmid:34892015","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34892015","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":"Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320335087","display_name":"Innovate UK","ror":"https://ror.org/05ar5fy68"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1983421266","https://openalex.org/W2008970948","https://openalex.org/W2126438085","https://openalex.org/W2749512402","https://openalex.org/W2781229448","https://openalex.org/W2797060364","https://openalex.org/W2892741787","https://openalex.org/W2903685163","https://openalex.org/W2962862931","https://openalex.org/W2974146427","https://openalex.org/W3044964811","https://openalex.org/W3092633470","https://openalex.org/W3120345372","https://openalex.org/W6737947904","https://openalex.org/W6750672517"],"related_works":["https://openalex.org/W3176621072","https://openalex.org/W2085384747","https://openalex.org/W2088166309","https://openalex.org/W1891216533","https://openalex.org/W2106071040","https://openalex.org/W4312133475","https://openalex.org/W4238976562","https://openalex.org/W2276587472","https://openalex.org/W4248323080","https://openalex.org/W20047544"],"abstract_inverted_index":{"Image-based":[0],"cell":[1,20,118,123],"phenotyping":[2],"is":[3,125,129],"an":[4,132,145],"important":[5],"and":[6,30,33,43,60,73,103],"open":[7],"problem":[8],"in":[9,107,150],"computational":[10],"pathology.":[11],"The":[12,134],"two":[13],"principal":[14],"challenges":[15],"are:":[16],"1)":[17],"making":[18],"the":[19,37,53,56,68,71,80,110,160],"cluster":[21],"properties":[22],"insensitive":[23],"to":[24,79,96],"experimental":[25],"settings":[26],"(like":[27],"seed":[28],"point":[29],"feature":[31,75],"selection)":[32],"2)":[34],"ensuring":[35],"that":[36],"phenotypes":[38,57,102,157],"emerging":[39],"are":[40],"biologically":[41],"relevant":[42,100],"support":[44],"clinical":[45,81],"reporting.":[46],"To":[47],"gauge":[48],"robustness,":[49],"we":[50,66,85,88],"first":[51],"compare":[52],"consistency":[54],"of":[55,70,109,126,140,147],"using":[58,155],"self-supervised":[59,72],"supervised":[61,74,161],"features.":[62],"Through":[63],"case":[64,153],"classification,":[65],"analyse":[67],"relevance":[69,128],"sets":[76],"with":[77],"respect":[78],"diagnosis.":[82],"In":[83],"addition,":[84],"demonstrate":[86,144],"how":[87],"can":[89],"add":[90],"model":[91],"explainability":[92],"through":[93],"Shapley":[94],"values":[95],"identify":[97],"more":[98],"disease":[99],"cellular":[101,156],"measure":[104],"their":[105],"importance":[106],"context":[108],"disease.":[111],"Here,":[112],"myeloproliferative":[113],"neoplasms,":[114],"a":[115,138],"haematopoietic":[116],"stem":[117],"disorder,":[119],"where":[120],"one":[121],"particular":[122],"type":[124],"diagnostic":[127],"used":[130],"as":[131],"exemplar.":[133],"experiments":[135],"conducted":[136],"on":[137],"set":[139],"bone":[141],"marrow":[142],"trephines":[143],"improvement":[146],"7.4":[148],"%":[149],"accuracy":[151],"for":[152],"classification":[154],"derived":[158],"from":[159],"scenario.":[162]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}