{"id":"https://openalex.org/W3193698651","doi":"https://doi.org/10.1093/bib/bbab314","title":"A systematic comparison of data- and knowledge-driven approaches to disease subtype discovery","display_name":"A systematic comparison of data- and knowledge-driven approaches to disease subtype discovery","publication_year":2021,"publication_date":"2021-08-11","ids":{"openalex":"https://openalex.org/W3193698651","doi":"https://doi.org/10.1093/bib/bbab314","mag":"3193698651","pmid":"https://pubmed.ncbi.nlm.nih.gov/34396389"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbab314","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab314","pdf_url":"https://academic.oup.com/bib/article-pdf/22/6/bbab314/41089595/bbab314.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/22/6/bbab314/41089595/bbab314.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004153233","display_name":"Teemu Rintala","orcid":"https://orcid.org/0000-0003-1849-235X"},"institutions":[{"id":"https://openalex.org/I175532246","display_name":"University of Eastern Finland","ror":"https://ror.org/00cyydd11","country_code":"FI","type":"education","lineage":["https://openalex.org/I175532246"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Teemu J Rintala","raw_affiliation_strings":["Institute of Biomedicine University of Eastern Finland, Yliopistonranta 1 E, 70210 Kuopio, Finland"],"affiliations":[{"raw_affiliation_string":"Institute of Biomedicine University of Eastern Finland, Yliopistonranta 1 E, 70210 Kuopio, Finland","institution_ids":["https://openalex.org/I175532246"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101807666","display_name":"Antonio Federico","orcid":"https://orcid.org/0000-0003-2554-9879"},"institutions":[{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Antonio Federico","raw_affiliation_strings":["BioMediTech Institute Tampere University, Kalevantie 4, 33100 Tampere, Finland","Faculty of Medicine and Health Technology Tampere University, Kalevantie, 4 33100 Tampere, Finland"],"affiliations":[{"raw_affiliation_string":"BioMediTech Institute Tampere University, Kalevantie 4, 33100 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Faculty of Medicine and Health Technology Tampere University, Kalevantie, 4 33100 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003926457","display_name":"Leena Latonen","orcid":"https://orcid.org/0000-0003-4502-2193"},"institutions":[{"id":"https://openalex.org/I175532246","display_name":"University of Eastern Finland","ror":"https://ror.org/00cyydd11","country_code":"FI","type":"education","lineage":["https://openalex.org/I175532246"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Leena Latonen","raw_affiliation_strings":["Institute of Biomedicine University of Eastern Finland, Yliopistonranta 1 E, 70210 Kuopio, Finland"],"affiliations":[{"raw_affiliation_string":"Institute of Biomedicine University of Eastern Finland, Yliopistonranta 1 E, 70210 Kuopio, Finland","institution_ids":["https://openalex.org/I175532246"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028682033","display_name":"Dario Greco","orcid":"https://orcid.org/0000-0001-9195-9003"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]},{"id":"https://openalex.org/I166825849","display_name":"Tampere University","ror":"https://ror.org/033003e23","country_code":"FI","type":"education","lineage":["https://openalex.org/I166825849"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Dario Greco","raw_affiliation_strings":["BioMediTech Institute Tampere University, Kalevantie 4, 33100 Tampere, Finland","Faculty of Medicine and Health Technology Tampere University, Kalevantie, 4 33100 Tampere, Finland","Institute of Biotechnology University of Helsinki, Viikinkaari 5d, 00014 Helsinki, Finland"],"affiliations":[{"raw_affiliation_string":"BioMediTech Institute Tampere University, Kalevantie 4, 33100 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Faculty of Medicine and Health Technology Tampere University, Kalevantie, 4 33100 Tampere, Finland","institution_ids":["https://openalex.org/I166825849"]},{"raw_affiliation_string":"Institute of Biotechnology University of Helsinki, Viikinkaari 5d, 00014 Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011752174","display_name":"Vittorio Fortino","orcid":"https://orcid.org/0000-0001-8693-5285"},"institutions":[{"id":"https://openalex.org/I175532246","display_name":"University of Eastern Finland","ror":"https://ror.org/00cyydd11","country_code":"FI","type":"education","lineage":["https://openalex.org/I175532246"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Vittorio Fortino","raw_affiliation_strings":["Institute of Biomedicine University of Eastern Finland, Yliopistonranta 1 E, 70210 Kuopio, Finland"],"affiliations":[{"raw_affiliation_string":"Institute of Biomedicine University of Eastern Finland, Yliopistonranta 1 E, 70210 Kuopio, Finland","institution_ids":["https://openalex.org/I175532246"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5011752174"],"corresponding_institution_ids":["https://openalex.org/I175532246"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.4869,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.62118318,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"22","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"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"}},{"id":"https://openalex.org/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.9883999824523926,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"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/cluster-analysis","display_name":"Cluster analysis","score":0.817762017250061},{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.7642143368721008},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6321610808372498},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5804365873336792},{"id":"https://openalex.org/keywords/benchmarking","display_name":"Benchmarking","score":0.57831209897995},{"id":"https://openalex.org/keywords/dimensionality-reduction","display_name":"Dimensionality reduction","score":0.5323716998100281},{"id":"https://openalex.org/keywords/consensus-clustering","display_name":"Consensus clustering","score":0.5121669769287109},{"id":"https://openalex.org/keywords/robustness","display_name":"Robustness (evolution)","score":0.4999227523803711},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.46862438321113586},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.43134114146232605},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.40085840225219727},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.36082351207733154},{"id":"https://openalex.org/keywords/fuzzy-clustering","display_name":"Fuzzy clustering","score":0.26068031787872314},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19931456446647644},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18774810433387756},{"id":"https://openalex.org/keywords/cure-data-clustering-algorithm","display_name":"CURE data clustering algorithm","score":0.1821857988834381},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10556736588478088}],"concepts":[{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.817762017250061},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.7642143368721008},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6321610808372498},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5804365873336792},{"id":"https://openalex.org/C86251818","wikidata":"https://www.wikidata.org/wiki/Q816754","display_name":"Benchmarking","level":2,"score":0.57831209897995},{"id":"https://openalex.org/C70518039","wikidata":"https://www.wikidata.org/wiki/Q16000077","display_name":"Dimensionality reduction","level":2,"score":0.5323716998100281},{"id":"https://openalex.org/C186767784","wikidata":"https://www.wikidata.org/wiki/Q5162841","display_name":"Consensus clustering","level":5,"score":0.5121669769287109},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.4999227523803711},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.46862438321113586},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.43134114146232605},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40085840225219727},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.36082351207733154},{"id":"https://openalex.org/C17212007","wikidata":"https://www.wikidata.org/wiki/Q5511111","display_name":"Fuzzy clustering","level":3,"score":0.26068031787872314},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19931456446647644},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18774810433387756},{"id":"https://openalex.org/C33704608","wikidata":"https://www.wikidata.org/wiki/Q5014717","display_name":"CURE data clustering algorithm","level":4,"score":0.1821857988834381},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10556736588478088},{"id":"https://openalex.org/C144133560","wikidata":"https://www.wikidata.org/wiki/Q4830453","display_name":"Business","level":0,"score":0.0},{"id":"https://openalex.org/C162853370","wikidata":"https://www.wikidata.org/wiki/Q39809","display_name":"Marketing","level":1,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","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":"D004198","descriptor_name":"Disease Susceptibility","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004198","descriptor_name":"Disease Susceptibility","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004198","descriptor_name":"Disease Susceptibility","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011379","descriptor_name":"Prognosis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015415","descriptor_name":"Biomarkers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016019","descriptor_name":"Survival Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016019","descriptor_name":"Survival Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016019","descriptor_name":"Survival Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020022","descriptor_name":"Genetic Predisposition to Disease","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":6,"locations":[{"id":"doi:10.1093/bib/bbab314","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab314","pdf_url":"https://academic.oup.com/bib/article-pdf/22/6/bbab314/41089595/bbab314.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34396389","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34396389","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:7467718","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8575038","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:helda.helsinki.fi:10138/355140","is_oa":true,"landing_page_url":"http://hdl.handle.net/10138/355140","pdf_url":null,"source":{"id":"https://openalex.org/S4210213322","display_name":"Ty\u00f6v\u00e4entutkimus Vuosikirja","issn_l":"0784-1272","issn":["0784-1272","1459-7780"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8575038","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8575038","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"},{"id":"pmh:oai:trepo.tuni.fi:10024/220276","is_oa":true,"landing_page_url":"https://trepo.tuni.fi/handle/10024/220276","pdf_url":null,"source":{"id":"https://openalex.org/S7407055260","display_name":"Trepo - Institutional Repository of Tampere University","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":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbab314","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbab314","pdf_url":"https://academic.oup.com/bib/article-pdf/22/6/bbab314/41089595/bbab314.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4615739710","display_name":null,"funder_award_id":"336275","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G5262436819","display_name":null,"funder_award_id":"317871","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G7014781287","display_name":"Biomarker Discovery for Precision Medicine: an Artificial Intelligence based approach.","funder_award_id":"332510","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G7306447382","display_name":null,"funder_award_id":"332510","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"}],"funders":[{"id":"https://openalex.org/F4320317353","display_name":"Finnish Cancer Institute","ror":null},{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"},{"id":"https://openalex.org/F4320323824","display_name":"Sy\u00f6p\u00e4j\u00e4rjest\u00f6t","ror":"https://ror.org/05pgg4z49"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3193698651.pdf","grobid_xml":"https://content.openalex.org/works/W3193698651.grobid-xml"},"referenced_works_count":79,"referenced_works":["https://openalex.org/W1493454437","https://openalex.org/W1950829641","https://openalex.org/W1959608418","https://openalex.org/W1966327575","https://openalex.org/W1989277387","https://openalex.org/W1999574084","https://openalex.org/W2008327230","https://openalex.org/W2015887370","https://openalex.org/W2016381774","https://openalex.org/W2023826235","https://openalex.org/W2044702943","https://openalex.org/W2060516118","https://openalex.org/W2073459066","https://openalex.org/W2090247362","https://openalex.org/W2096283457","https://openalex.org/W2103017472","https://openalex.org/W2105776484","https://openalex.org/W2107363136","https://openalex.org/W2110065044","https://openalex.org/W2123402141","https://openalex.org/W2132619562","https://openalex.org/W2142635246","https://openalex.org/W2145290999","https://openalex.org/W2154941270","https://openalex.org/W2159482845","https://openalex.org/W2159707944","https://openalex.org/W2161112598","https://openalex.org/W2168175751","https://openalex.org/W2169101662","https://openalex.org/W2187089797","https://openalex.org/W2214074259","https://openalex.org/W2230320310","https://openalex.org/W2294798173","https://openalex.org/W2309067861","https://openalex.org/W2315322086","https://openalex.org/W2319660501","https://openalex.org/W2395887422","https://openalex.org/W2472544934","https://openalex.org/W2519132385","https://openalex.org/W2536515765","https://openalex.org/W2557530941","https://openalex.org/W2560367415","https://openalex.org/W2566814726","https://openalex.org/W2601262142","https://openalex.org/W2608513795","https://openalex.org/W2733047156","https://openalex.org/W2791063392","https://openalex.org/W2795441251","https://openalex.org/W2806412533","https://openalex.org/W2902652978","https://openalex.org/W2912792455","https://openalex.org/W2913710075","https://openalex.org/W2918849193","https://openalex.org/W2922229918","https://openalex.org/W2951029718","https://openalex.org/W2951880440","https://openalex.org/W2952768699","https://openalex.org/W2954650112","https://openalex.org/W2956953160","https://openalex.org/W2991920366","https://openalex.org/W3005127469","https://openalex.org/W3041242936","https://openalex.org/W3095200063","https://openalex.org/W3147894994","https://openalex.org/W4231254854","https://openalex.org/W4231665431","https://openalex.org/W4235169531","https://openalex.org/W4294216483","https://openalex.org/W4294329053","https://openalex.org/W4399570638","https://openalex.org/W6640963894","https://openalex.org/W6668990524","https://openalex.org/W6675966139","https://openalex.org/W6678914141","https://openalex.org/W6698498768","https://openalex.org/W6720512875","https://openalex.org/W6741091983","https://openalex.org/W6742297177","https://openalex.org/W6813094581"],"related_works":["https://openalex.org/W4238897586","https://openalex.org/W2905433371","https://openalex.org/W435179959","https://openalex.org/W2619091065","https://openalex.org/W2059640416","https://openalex.org/W1490753184","https://openalex.org/W2284465472","https://openalex.org/W2291782699","https://openalex.org/W2803139007","https://openalex.org/W2088647418"],"abstract_inverted_index":{"Typical":[0],"clustering":[1,15,46,68,129,185,216],"analysis":[2,116,127,160],"for":[3,103,125],"large-scale":[4],"genomics":[5],"data":[6,225],"combines":[7,146],"two":[8],"unsupervised":[9],"learning":[10],"techniques:":[11],"dimensionality":[12],"reduction":[13],"and":[14,33,95,109,135,156,178,196,245],"(DR-CL)":[16],"methods.":[17,65,137],"It":[18],"has":[19],"been":[20],"demonstrated":[21,220],"that":[22,91,106,145,237],"transforming":[23],"gene":[24,157,223],"expression":[25,224],"to":[26,42,53,75,161,170,183],"pathway-level":[27,164],"information":[28],"can":[29,234],"improve":[30],"the":[31,77,83,114,172,211,231],"robustness":[32],"interpretability":[34],"of":[35,56,85,117,128,149,202],"disease":[36,89,150,197],"grouping":[37,173],"results.":[38],"This":[39],"approach,":[40,48],"referred":[41],"as":[43],"biological":[44,94,108],"knowledge-driven":[45],"(BK-CL)":[47],"is":[49,100],"often":[50],"neglected,":[51],"due":[52],"a":[54,101,122,141],"lack":[55],"tools":[57],"enabling":[58],"systematic":[59,115],"comparisons":[60],"with":[61,181,189,193],"more":[62],"established":[63],"DR-based":[64],"Moreover,":[66,138],"classic":[67],"metrics":[69,105],"based":[70],"on":[71,222],"group":[72],"separability":[73],"tend":[74],"favor":[76],"DR-CL":[78,134,177],"paradigm,":[79],"which":[80],"may":[81],"increase":[82],"risk":[84],"identifying":[86],"less":[87],"actionable":[88],"subtypes":[90],"have":[92],"ambiguous":[93],"clinical":[96,110,194],"explanations.":[97],"Hence,":[98],"there":[99],"need":[102],"developing":[104],"assess":[107],"relevance.":[111],"To":[112],"facilitate":[113],"BK-CL":[118,136,143,179,232],"methods,":[119],"we":[120,139,219],"propose":[121,140],"computational":[123],"protocol":[124],"quantitative":[126],"results":[130,174],"derived":[131,227],"from":[132,175,228],"both":[133,243],"new":[142],"method":[144],"prior":[147],"knowledge":[148],"relevant":[151],"genes,":[152],"network":[153],"diffusion":[154],"algorithms":[155],"set":[158],"enrichment":[159],"generate":[162],"robust":[163],"information.":[165],"Benchmarking":[166],"studies":[167],"were":[168],"conducted":[169],"compare":[171],"different":[176],"approaches":[180],"respect":[182],"standard":[184],"evaluation":[186,214],"metrics,":[187],"concordance":[188],"known":[190],"subtypes,":[191],"association":[192],"outcomes":[195],"modules":[198],"in":[199,215,242],"co-expression":[200],"networks":[201],"genes.":[203],"No":[204],"single":[205],"approach":[206,233],"dominated":[207],"every":[208],"metric,":[209],"showing":[210],"importance":[212],"multi-objective":[213],"analysis.":[217],"However,":[218],"that,":[221],"sets":[226],"TCGA":[229],"samples,":[230],"find":[235],"groupings":[236],"provide":[238],"significant":[239],"prognostic":[240],"value":[241],"breast":[244],"prostate":[246],"cancers.":[247]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}