{"id":"https://openalex.org/W4402401769","doi":"https://doi.org/10.1109/tvcg.2024.3456370","title":"A General Framework for Comparing Embedding Visualizations Across Class-Label Hierarchies","display_name":"A General Framework for Comparing Embedding Visualizations Across Class-Label Hierarchies","publication_year":2024,"publication_date":"2024-09-10","ids":{"openalex":"https://openalex.org/W4402401769","doi":"https://doi.org/10.1109/tvcg.2024.3456370","pmid":"https://pubmed.ncbi.nlm.nih.gov/39255153"},"language":"en","primary_location":{"id":"doi:10.1109/tvcg.2024.3456370","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tvcg.2024.3456370","pdf_url":null,"source":{"id":"https://openalex.org/S84775595","display_name":"IEEE Transactions on Visualization and Computer Graphics","issn_l":"1077-2626","issn":["1077-2626","1941-0506","2160-9306"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Visualization and Computer Graphics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1109/tvcg.2024.3456370","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057253726","display_name":"Trevor Manz","orcid":"https://orcid.org/0000-0001-7694-5164"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Trevor Manz","raw_affiliation_strings":["Harvard Medical School, USA"],"raw_orcid":"https://orcid.org/0000-0001-7694-5164","affiliations":[{"raw_affiliation_string":"Harvard Medical School, USA","institution_ids":["https://openalex.org/I136199984"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038027438","display_name":"Fritz Lekschas","orcid":"https://orcid.org/0000-0001-8432-4835"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fritz Lekschas","raw_affiliation_strings":["Ozette Technologies, Canada"],"raw_orcid":"https://orcid.org/0000-0001-8432-4835","affiliations":[{"raw_affiliation_string":"Ozette Technologies, Canada","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057193188","display_name":"Evan Greene","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Evan Greene","raw_affiliation_strings":["Ozette Technologies, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ozette Technologies, Canada","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069196767","display_name":"Greg Finak","orcid":"https://orcid.org/0000-0003-4341-9090"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Greg Finak","raw_affiliation_strings":["Ozette Technologies, Canada"],"raw_orcid":"https://orcid.org/0000-0003-4341-9090","affiliations":[{"raw_affiliation_string":"Ozette Technologies, Canada","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066335313","display_name":"Nils Gehlenborg","orcid":"https://orcid.org/0000-0003-0327-8297"},"institutions":[{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nils Gehlenborg","raw_affiliation_strings":["Harvard Medical School, USA"],"raw_orcid":"https://orcid.org/0000-0003-0327-8297","affiliations":[{"raw_affiliation_string":"Harvard Medical School, USA","institution_ids":["https://openalex.org/I136199984"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.6445,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.69355506,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"31","issue":"1","first_page":"283","last_page":"293"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10799","display_name":"Data Visualization and Analytics","score":0.977400004863739,"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/T10799","display_name":"Data Visualization and Analytics","score":0.977400004863739,"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/T13083","display_name":"Advanced Text Analysis Techniques","score":0.9717000126838684,"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/T10260","display_name":"Software Engineering Research","score":0.9229000210762024,"subfield":{"id":"https://openalex.org/subfields/1710","display_name":"Information Systems"},"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/computer-science","display_name":"Computer science","score":0.8145155906677246},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6833031177520752},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.6639100909233093},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6583291292190552},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.5331021547317505},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.45247000455856323},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3666929602622986},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3587934970855713},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.32394564151763916}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8145155906677246},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6833031177520752},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.6639100909233093},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6583291292190552},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.5331021547317505},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.45247000455856323},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3666929602622986},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3587934970855713},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.32394564151763916}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/tvcg.2024.3456370","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tvcg.2024.3456370","pdf_url":null,"source":{"id":"https://openalex.org/S84775595","display_name":"IEEE Transactions on Visualization and Computer Graphics","issn_l":"1077-2626","issn":["1077-2626","1941-0506","2160-9306"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Visualization and Computer Graphics","raw_type":"journal-article"},{"id":"pmid:39255153","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39255153","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 visualization and computer graphics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11875997","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11875997","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11875997/pdf/nihms-2039886.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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Trans Vis Comput Graph","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1109/tvcg.2024.3456370","is_oa":true,"landing_page_url":"https://doi.org/10.1109/tvcg.2024.3456370","pdf_url":null,"source":{"id":"https://openalex.org/S84775595","display_name":"IEEE Transactions on Visualization and Computer Graphics","issn_l":"1077-2626","issn":["1077-2626","1941-0506","2160-9306"],"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Visualization and Computer Graphics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities","score":0.47999998927116394}],"awards":[{"id":"https://openalex.org/G1527859589","display_name":null,"funder_award_id":"OT2 OD033758","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2292794843","display_name":null,"funder_award_id":"R33 CA263666","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G3937140210","display_name":null,"funder_award_id":"R33CA263666","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5090901529","display_name":null,"funder_award_id":"OT2OD033758","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6988551844","display_name":null,"funder_award_id":"UM1HG011536","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8017732303","display_name":null,"funder_award_id":"UM1 HG011536","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":62,"referenced_works":["https://openalex.org/W1553862741","https://openalex.org/W1861492603","https://openalex.org/W1927933524","https://openalex.org/W1987971958","https://openalex.org/W1997780235","https://openalex.org/W2001917229","https://openalex.org/W2007339694","https://openalex.org/W2015755066","https://openalex.org/W2047752105","https://openalex.org/W2063295648","https://openalex.org/W2079272025","https://openalex.org/W2087016914","https://openalex.org/W2088323702","https://openalex.org/W2113586398","https://openalex.org/W2144764737","https://openalex.org/W2157379557","https://openalex.org/W2158019369","https://openalex.org/W2162825485","https://openalex.org/W2163825541","https://openalex.org/W2163965546","https://openalex.org/W2323909273","https://openalex.org/W2346476940","https://openalex.org/W2395274837","https://openalex.org/W2484828460","https://openalex.org/W2542768043","https://openalex.org/W2752662042","https://openalex.org/W2807795618","https://openalex.org/W2900144939","https://openalex.org/W2902652978","https://openalex.org/W2960826148","https://openalex.org/W2975605169","https://openalex.org/W2984472267","https://openalex.org/W2986308225","https://openalex.org/W2995755016","https://openalex.org/W3009872610","https://openalex.org/W3028131613","https://openalex.org/W3039222472","https://openalex.org/W3163414494","https://openalex.org/W3178561764","https://openalex.org/W3186838184","https://openalex.org/W3196650609","https://openalex.org/W3210362879","https://openalex.org/W4220910651","https://openalex.org/W4220975008","https://openalex.org/W4280605846","https://openalex.org/W4283687643","https://openalex.org/W4287714414","https://openalex.org/W4297094730","https://openalex.org/W4297461125","https://openalex.org/W4312765319","https://openalex.org/W4364360177","https://openalex.org/W4385571801","https://openalex.org/W4388286222","https://openalex.org/W4389988539","https://openalex.org/W4402405762","https://openalex.org/W4403120618","https://openalex.org/W4403665808","https://openalex.org/W6675807900","https://openalex.org/W6685053522","https://openalex.org/W6712062058","https://openalex.org/W6730169232","https://openalex.org/W6780022514"],"related_works":["https://openalex.org/W2013728941","https://openalex.org/W4225274103","https://openalex.org/W2579659702","https://openalex.org/W2154046714","https://openalex.org/W1965329638","https://openalex.org/W1574055964","https://openalex.org/W2923661510","https://openalex.org/W2189613078","https://openalex.org/W2586219255","https://openalex.org/W2547096368"],"abstract_inverted_index":{"Projecting":[0],"high-dimensional":[1],"vectors":[2],"into":[3,90],"two":[4,48],"dimensions":[5],"for":[6,73],"visualization,":[7,11],"known":[8],"as":[9,47],"embedding":[10,19,75],"facilitates":[12],"perceptual":[13,118],"reasoning":[14],"and":[15,54,99,104,125,145,176,183,190,201],"interpretation.":[16],"Comparing":[17],"multiple":[18],"visualizations":[20,76],"drives":[21],"decision-making":[22],"in":[23,205],"many":[24],"domains,":[25],"but":[26],"traditional":[27],"comparison":[28],"methods":[29],"are":[30],"limited":[31],"by":[32,108],"a":[33,70,109],"reliance":[34],"on":[35,78],"direct":[36],"point":[37,44,62],"correspondences.":[38],"This":[39],"requirement":[40],"precludes":[41],"comparisons":[42,155,197],"without":[43],"correspondences,":[45],"such":[46],"different":[49],"datasets":[50],"of":[51,136,163],"annotated":[52],"images,":[53],"fails":[55],"to":[56,93,121,128,152],"capture":[57],"meaningful":[58],"higher-level":[59],"relationships":[60],"among":[61],"groups.":[63],"To":[64,159],"address":[65],"these":[66,123],"shortcomings,":[67],"we":[68,113,166],"propose":[69],"general":[71],"framework":[72,116,138],"comparing":[74],"based":[77],"shared":[79],"class":[80,96],"labels":[81],"rather":[82],"than":[83],"individual":[84],"points.":[85],"Our":[86,192],"approach":[87],"partitions":[88],"points":[89],"regions":[91,124],"corresponding":[92],"three":[94],"key":[95],"concepts-confusion,":[97],"neighborhood,":[98],"relative":[100],"size-to":[101],"characterize":[102],"intra-":[103],"inter-class":[105],"relationships.":[106],"Informed":[107],"preliminary":[110],"user":[111],"study,":[112],"implemented":[114],"our":[115,137,149,164],"using":[117,180],"neighborhood":[119],"graphs":[120],"define":[122],"introduced":[126],"metrics":[127,193],"quantify":[129],"each":[130],"concept.":[131],"We":[132],"demonstrate":[133],"the":[134,161],"generality":[135],"with":[139,171,187],"usage":[140],"scenarios":[141],"from":[142],"machine":[143,173],"learning":[144,174],"single-cell":[146,178],"biology,":[147],"highlighting":[148],"metrics'":[150],"ability":[151],"draw":[153],"insightful":[154],"across":[156],"label":[157],"hierarchies.":[158],"assess":[160],"effectiveness":[162],"approach,":[165],"conducted":[167],"an":[168,181],"evaluation":[169],"study":[170],"five":[172],"researchers":[175],"six":[177],"biologists":[179],"interactive":[182],"scalable":[184],"prototype":[185],"built":[186],"Python,":[188],"JavaScript,":[189],"Rust.":[191],"enable":[194],"more":[195],"structured":[196],"through":[198],"visual":[199],"guidance":[200],"increased":[202],"participants'":[203],"confidence":[204],"their":[206],"findings.":[207]},"counts_by_year":[{"year":2025,"cited_by_count":3}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
