{"id":"https://openalex.org/W4382630944","doi":"https://doi.org/10.1093/bioinformatics/btad204","title":"COmic: convolutional kernel networks for interpretable end-to-end learning on (multi-)omics data","display_name":"COmic: convolutional kernel networks for interpretable end-to-end learning on (multi-)omics data","publication_year":2023,"publication_date":"2023-06-01","ids":{"openalex":"https://openalex.org/W4382630944","doi":"https://doi.org/10.1093/bioinformatics/btad204","pmid":"https://pubmed.ncbi.nlm.nih.gov/37387152"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad204","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad204","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i76/50741537/btad204.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i76/50741537/btad204.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5081565721","display_name":"Jonas C. Ditz","orcid":"https://orcid.org/0000-0002-4561-1900"},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Jonas C Ditz","raw_affiliation_strings":["Methods in Medical Informatics, Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen 72076, Germany"],"affiliations":[{"raw_affiliation_string":"Methods in Medical Informatics, Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen 72076, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056688592","display_name":"Bernhard Reuter","orcid":null},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bernhard Reuter","raw_affiliation_strings":["Methods in Medical Informatics, Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen 72076, Germany"],"affiliations":[{"raw_affiliation_string":"Methods in Medical Informatics, Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen 72076, Germany","institution_ids":["https://openalex.org/I8087733"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076705834","display_name":"Nico Pfeifer","orcid":"https://orcid.org/0000-0002-4647-8566"},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Nico Pfeifer","raw_affiliation_strings":["Methods in Medical Informatics, Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen 72076, Germany"],"affiliations":[{"raw_affiliation_string":"Methods in Medical Informatics, Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen 72076, Germany","institution_ids":["https://openalex.org/I8087733"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5081565721"],"corresponding_institution_ids":["https://openalex.org/I8087733"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4568,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.6677293,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"39","issue":"Supplement_1","first_page":"i76","last_page":"i85"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","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"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","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/T10885","display_name":"Gene expression and cancer classification","score":0.9988999962806702,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9919999837875366,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6818349957466125},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.667992115020752},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5411632657051086},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5175570845603943},{"id":"https://openalex.org/keywords/comics","display_name":"Comics","score":0.4969649612903595},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.49672895669937134},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.492771178483963},{"id":"https://openalex.org/keywords/omics","display_name":"Omics","score":0.43522581458091736},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.34283727407455444},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2223922610282898},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10816085338592529},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.08951354026794434}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6818349957466125},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.667992115020752},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5411632657051086},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5175570845603943},{"id":"https://openalex.org/C529099274","wikidata":"https://www.wikidata.org/wiki/Q1004","display_name":"Comics","level":2,"score":0.4969649612903595},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.49672895669937134},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.492771178483963},{"id":"https://openalex.org/C157585117","wikidata":"https://www.wikidata.org/wiki/Q158666","display_name":"Omics","level":2,"score":0.43522581458091736},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34283727407455444},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2223922610282898},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10816085338592529},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.08951354026794434}],"mesh":[{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","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":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad204","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad204","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i76/50741537/btad204.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37387152","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37387152","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10311322","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10311322","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10311322/pdf/btad204.pdf","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad204","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad204","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/Supplement_1/i76/50741537/btad204.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2011604621","display_name":null,"funder_award_id":"IS18039A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G233922387","display_name":null,"funder_award_id":"EXC number 2064/1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G352791218","display_name":null,"funder_award_id":"(BMBF)","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G5106512922","display_name":null,"funder_award_id":"Deutsche Forschungsgemeinschaft (DFG","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5168466499","display_name":null,"funder_award_id":"Project","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G5415233182","display_name":null,"funder_award_id":"01IS18039A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G6955755495","display_name":null,"funder_award_id":"Germany","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G7225624288","display_name":null,"funder_award_id":"This work was","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G762232396","display_name":null,"funder_award_id":"Project","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G7907426250","display_name":null,"funder_award_id":"390727645","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G802091010","display_name":null,"funder_award_id":"01IS18039","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8330397625","display_name":null,"funder_award_id":"Funding","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G8413167928","display_name":null,"funder_award_id":"Excellence Strategy","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G864726782","display_name":null,"funder_award_id":"FKZ: 01IS18039A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G8915364236","display_name":null,"funder_award_id":"2064/1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4382630944.pdf"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1906461790","https://openalex.org/W1976173969","https://openalex.org/W1983876698","https://openalex.org/W1992045522","https://openalex.org/W2005895632","https://openalex.org/W2062725167","https://openalex.org/W2065341127","https://openalex.org/W2079105722","https://openalex.org/W2088160256","https://openalex.org/W2096079397","https://openalex.org/W2097926631","https://openalex.org/W2099401974","https://openalex.org/W2107725114","https://openalex.org/W2110119381","https://openalex.org/W2110520112","https://openalex.org/W2115580179","https://openalex.org/W2118413367","https://openalex.org/W2123734813","https://openalex.org/W2128689695","https://openalex.org/W2132914434","https://openalex.org/W2143426320","https://openalex.org/W2150671673","https://openalex.org/W2154318594","https://openalex.org/W2163563958","https://openalex.org/W2167608136","https://openalex.org/W2168264491","https://openalex.org/W2195388612","https://openalex.org/W2198606573","https://openalex.org/W2345512687","https://openalex.org/W2404901863","https://openalex.org/W2467496703","https://openalex.org/W2504431993","https://openalex.org/W2516519427","https://openalex.org/W2531897166","https://openalex.org/W2795123374","https://openalex.org/W2806834952","https://openalex.org/W2886281300","https://openalex.org/W2901830477","https://openalex.org/W2913783817","https://openalex.org/W2936379053","https://openalex.org/W2945976633","https://openalex.org/W2947996805","https://openalex.org/W2948216679","https://openalex.org/W2949578333","https://openalex.org/W2950695830","https://openalex.org/W2963766931","https://openalex.org/W2999362542","https://openalex.org/W3011358689","https://openalex.org/W3048513378","https://openalex.org/W3088181395","https://openalex.org/W3104974184","https://openalex.org/W3125997628","https://openalex.org/W3138819813","https://openalex.org/W6676068203","https://openalex.org/W6678131844","https://openalex.org/W6683033130","https://openalex.org/W6684918892","https://openalex.org/W6712094938","https://openalex.org/W6763206878","https://openalex.org/W6775014351"],"related_works":["https://openalex.org/W3201315974","https://openalex.org/W3015688758","https://openalex.org/W3171682447","https://openalex.org/W3216780987","https://openalex.org/W4226493464","https://openalex.org/W4312417841","https://openalex.org/W3193565141","https://openalex.org/W3133861977","https://openalex.org/W3167935049","https://openalex.org/W3029198973"],"abstract_inverted_index":{"Datasets,":[0],"labels,":[1],"and":[2,18,56],"pathway-induced":[3],"graph":[4,19],"Laplacians":[5,20],"used":[6],"for":[7,21],"the":[8,22,29,33,54],"single-omics":[9],"tasks":[10],"can":[11,25],"be":[12,26,37],"downloaded":[13,27,38],"at":[14,41,61],"https://ibm.ent.box.com/s/ac2ilhyn7xjj27r0xiwtom4crccuobst/folder/48027287036.":[15],"While":[16],"datasets":[17],"METABRIC":[23],"cohort":[24],"from":[28,39],"above":[30],"mentioned":[31],"repository,":[32],"labels":[34],"have":[35],"to":[36,52],"cBioPortal":[40],"https://www.cbioportal.org/study/clinicalData?id=brca\\_metabric.":[42],"COmic":[43],"source":[44],"code":[45],"as":[46,48],"well":[47],"all":[49],"scripts":[50],"necessary":[51],"reproduce":[53],"experiments":[55],"analysis":[57],"are":[58],"publicly":[59],"available":[60],"https://github.com/jditz/comics.":[62]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
