{"id":"https://openalex.org/W4200253510","doi":"https://doi.org/10.1093/bioinformatics/btab830","title":"Unsupervised construction of computational graphs for gene expression data with explicit structural inductive biases","display_name":"Unsupervised construction of computational graphs for gene expression data with explicit structural inductive biases","publication_year":2021,"publication_date":"2021-12-03","ids":{"openalex":"https://openalex.org/W4200253510","doi":"https://doi.org/10.1093/bioinformatics/btab830","pmid":"https://pubmed.ncbi.nlm.nih.gov/34888618"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab830","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab830","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/5/1320/42419841/btab830.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/38/5/1320/42419841/btab830.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5073085630","display_name":"Paul Scherer","orcid":"https://orcid.org/0000-0002-2240-7501"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Paul Scherer","raw_affiliation_strings":["Department of Computer Science and Technology, University of Cambridge , Cambridge, CB3 0FD, UK"],"raw_orcid":"https://orcid.org/0000-0002-2240-7501","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, University of Cambridge , Cambridge, CB3 0FD, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033339425","display_name":"Maja Tr\u0119bacz","orcid":null},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Maja Tr\u0119bacz","raw_affiliation_strings":["Department of Computer Science and Technology, University of Cambridge , Cambridge, CB3 0FD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, University of Cambridge , Cambridge, CB3 0FD, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003682166","display_name":"Nikola Simidjievski","orcid":"https://orcid.org/0000-0003-3948-6370"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Nikola Simidjievski","raw_affiliation_strings":["Department of Computer Science and Technology, University of Cambridge , Cambridge, CB3 0FD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, University of Cambridge , Cambridge, CB3 0FD, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055834118","display_name":"Ram\u00f3n Vi\u00f1as","orcid":"https://orcid.org/0000-0003-2411-4478"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ramon Vi\u00f1as","raw_affiliation_strings":["Department of Computer Science and Technology, University of Cambridge , Cambridge, CB3 0FD, UK"],"raw_orcid":"https://orcid.org/0000-0003-2411-4478","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, University of Cambridge , Cambridge, CB3 0FD, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082391822","display_name":"Zohreh Shams","orcid":"https://orcid.org/0000-0002-0143-798X"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Zohreh Shams","raw_affiliation_strings":["Department of Computer Science and Technology, University of Cambridge , Cambridge, CB3 0FD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, University of Cambridge , Cambridge, CB3 0FD, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075286523","display_name":"Helena Andr\u00e9s-Terr\u00e9","orcid":"https://orcid.org/0000-0001-7199-7897"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Helena Andres Terre","raw_affiliation_strings":["Department of Computer Science and Technology, University of Cambridge , Cambridge, CB3 0FD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, University of Cambridge , Cambridge, CB3 0FD, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036018012","display_name":"Mateja Jamnik","orcid":"https://orcid.org/0000-0003-2772-2532"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mateja Jamnik","raw_affiliation_strings":["Department of Computer Science and Technology, University of Cambridge , Cambridge, CB3 0FD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, University of Cambridge , Cambridge, CB3 0FD, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5056748708","display_name":"P\u00edetro Li\u00f3","orcid":"https://orcid.org/0000-0002-0540-5053"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Pietro Li\u00f2","raw_affiliation_strings":["Department of Computer Science and Technology, University of Cambridge , Cambridge, CB3 0FD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, University of Cambridge , Cambridge, CB3 0FD, UK","institution_ids":["https://openalex.org/I241749"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5073085630"],"corresponding_institution_ids":["https://openalex.org/I241749"],"apc_list":{"value":3478,"currency":"USD","value_usd":3478},"apc_paid":{"value":3478,"currency":"USD","value_usd":3478},"fwci":0.1492,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.46588863,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"38","issue":"5","first_page":"1320","last_page":"1327"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9056000113487244,"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":0.9056000113487244,"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":0.031300000846385956,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.01730000041425228,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6023167967796326},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.5491233468055725},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.46884122490882874},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.429370254278183},{"id":"https://openalex.org/keywords/inductive-bias","display_name":"Inductive bias","score":0.42505279183387756},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41580480337142944},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.39568179845809937},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.37617766857147217},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2647242546081543},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24573475122451782},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12727683782577515}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6023167967796326},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5491233468055725},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.46884122490882874},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.429370254278183},{"id":"https://openalex.org/C197352929","wikidata":"https://www.wikidata.org/wiki/Q1074074","display_name":"Inductive bias","level":4,"score":0.42505279183387756},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41580480337142944},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.39568179845809937},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.37617766857147217},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2647242546081543},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24573475122451782},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12727683782577515},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","level":1,"score":0.0},{"id":"https://openalex.org/C28006648","wikidata":"https://www.wikidata.org/wiki/Q6934509","display_name":"Multi-task learning","level":3,"score":0.0},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"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":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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015870","descriptor_name":"Gene Expression","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015982","descriptor_name":"Bias","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015982","descriptor_name":"Bias","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015982","descriptor_name":"Bias","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":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":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}],"locations_count":6,"locations":[{"id":"doi:10.1093/bioinformatics/btab830","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab830","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/5/1320/42419841/btab830.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34888618","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34888618","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":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8826027","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8826027","pdf_url":null,"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":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:iris.uniroma1.it:11573/1723940","is_oa":false,"landing_page_url":"https://hdl.handle.net/11573/1723940","pdf_url":null,"source":{"id":"https://openalex.org/S4377196107","display_name":"IRIS Research product catalog (Sapienza University of Rome)","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:www.repository.cam.ac.uk:1810/331638","is_oa":true,"landing_page_url":"https://www.repository.cam.ac.uk/handle/1810/331638","pdf_url":null,"source":{"id":"https://openalex.org/S4306401777","display_name":"Apollo (University of Cambridge)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I241749","host_organization_name":"University of Cambridge","host_organization_lineage":["https://openalex.org/I241749"],"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"},{"id":"doi:10.17863/cam.79090","is_oa":true,"landing_page_url":"https://doi.org/10.17863/cam.79090","pdf_url":null,"source":{"id":"https://openalex.org/S7407050737","display_name":"Apollo","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":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"JournalArticle"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab830","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab830","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/38/5/1320/42419841/btab830.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G242731019","display_name":null,"funder_award_id":"C9685/A25177","funder_id":"https://openalex.org/F4320315143","funder_display_name":"Mark Foundation For Cancer Research"},{"id":"https://openalex.org/G510844398","display_name":null,"funder_award_id":"C9685","funder_id":"https://openalex.org/F4320315143","funder_display_name":"Mark Foundation For Cancer Research"},{"id":"https://openalex.org/G5167650663","display_name":null,"funder_award_id":"A25177","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G5495922725","display_name":null,"funder_award_id":"C9685/A25177","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G6052482428","display_name":null,"funder_award_id":"C96/A25177","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G7782972677","display_name":null,"funder_award_id":"C9685","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"}],"funders":[{"id":"https://openalex.org/F4320315143","display_name":"Mark Foundation For Cancer Research","ror":"https://ror.org/00v7th354"},{"id":"https://openalex.org/F4320319985","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67"},{"id":"https://openalex.org/F4320320273","display_name":"University of Cambridge","ror":"https://ror.org/013meh722"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4200253510.pdf","grobid_xml":"https://content.openalex.org/works/W4200253510.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1485582261","https://openalex.org/W1493357981","https://openalex.org/W1533861849","https://openalex.org/W1986214964","https://openalex.org/W1986241711","https://openalex.org/W1993528080","https://openalex.org/W2005895632","https://openalex.org/W2090422756","https://openalex.org/W2106292881","https://openalex.org/W2114382052","https://openalex.org/W2116063398","https://openalex.org/W2136850043","https://openalex.org/W2143426320","https://openalex.org/W2144073719","https://openalex.org/W2594633041","https://openalex.org/W2624021832","https://openalex.org/W2739852640","https://openalex.org/W2900569176","https://openalex.org/W2904997892","https://openalex.org/W2905810301","https://openalex.org/W2912083425","https://openalex.org/W2944308937","https://openalex.org/W2952540014","https://openalex.org/W2963627083","https://openalex.org/W2981626361","https://openalex.org/W2981806891","https://openalex.org/W2996227376","https://openalex.org/W3047163763","https://openalex.org/W3113128075","https://openalex.org/W4295728955","https://openalex.org/W4301186107","https://openalex.org/W6631943919","https://openalex.org/W6718343364","https://openalex.org/W6734194636","https://openalex.org/W6762376150","https://openalex.org/W6769669728","https://openalex.org/W6769896426","https://openalex.org/W6779733120","https://openalex.org/W6787680825"],"related_works":["https://openalex.org/W1810370127","https://openalex.org/W1594946127","https://openalex.org/W4312273141","https://openalex.org/W4310274968","https://openalex.org/W3040224948","https://openalex.org/W1587378402","https://openalex.org/W4382318988","https://openalex.org/W3011040805","https://openalex.org/W175299670","https://openalex.org/W2392243736"],"abstract_inverted_index":{"MOTIVATION:":[0],"Gene":[1,119],"expression":[2,35,53,137],"data":[3,36,54,138,332],"are":[4,55,140,171,333],"commonly":[5],"used":[6,325],"at":[7,315,335],"the":[8,20,45,111,179,197,200,240,295,322],"intersection":[9],"of":[10,19,23,67,99,113,131,146,196,216,220,242,251,265,321],"cancer":[11,164,266],"research":[12,190],"and":[13,43,61,81,213,245,281],"machine":[14],"learning":[15,27,74],"for":[16,33,47,73,128,135,230,298,308],"better":[17],"understanding":[18],"molecular":[21],"status":[22],"tumour":[24],"tissue.":[25],"Deep":[26],"predictive":[28,114,235],"models":[29,76,134],"have":[30],"been":[31],"employed":[32],"gene":[34,52,100,136,147,253],"due":[37],"to":[38,41,83,109,257],"their":[39],"ability":[40],"scale":[42],"remove":[44],"need":[46],"manual":[48],"feature":[49],"engineering.":[50],"However,":[51],"often":[56,77,271],"very":[57],"high":[58],"dimensional,":[59],"noisy":[60],"presented":[62],"with":[63,255,306],"a":[64,155,160,221,226,263,304],"low":[65],"number":[66,241],"samples.":[68],"This":[69,224,317],"poses":[70],"significant":[71],"problems":[72],"algorithms:":[75],"overfit,":[78],"learn":[79],"noise":[80],"struggle":[82],"capture":[84],"biologically":[85,227],"relevant":[86,228],"information.":[87],"In":[88],"this":[89,152,327],"article,":[90],"we":[91],"utilize":[92],"external":[93],"biological":[94,205],"knowledge":[95,145],"embedded":[96],"within":[97,312],"structures":[98],"interaction":[101,106,148],"graphs":[102,170],"such":[103,207],"as":[104,208],"protein-protein":[105],"(PPI)":[107],"networks":[108,181,314],"guide":[110],"construction":[112,130],"models.":[115],"RESULTS:":[116],"We":[117,150,301],"present":[118],"Interaction":[120],"Network":[121],"Constrained":[122],"Construction":[123],"(GINCCo),":[124],"an":[125],"unsupervised":[126],"method":[127],"automated":[129],"computational":[132,169,202],"graph":[133,203],"that":[139,269],"structurally":[141,172],"constrained":[142],"by":[143],"prior":[144],"networks.":[149],"employ":[151],"methodology":[153],"in":[154,163,199,326],"case":[156],"study":[157],"on":[158,178,191],"incorporating":[159],"PPI":[161,180,313],"network":[162,188],"phenotype":[165],"prediction":[166],"tasks.":[167],"Our":[168,260],"constructed":[173],"using":[174],"topological":[175],"clustering":[176,323],"algorithms":[177,307,324],"which":[182],"incorporate":[183],"inductive":[184],"biases":[185],"stemming":[186],"from":[187],"biology":[189],"protein":[192,211,309],"complex":[193,310],"discovery.":[194],"Each":[195],"entities":[198,206],"GINCCo":[201,270],"represents":[204],"genes,":[209],"candidate":[210],"complexes":[212],"phenotypes":[214,267],"instead":[215],"arbitrary":[217],"hidden":[218],"nodes":[219],"neural":[222],"network.":[223],"provides":[225],"mechanism":[229],"model":[231,243,288],"regularization":[232],"yielding":[233],"strong":[234],"performance":[236],"while":[237],"drastically":[238],"reducing":[239],"parameters":[244],"enabling":[246],"guided":[247],"post-hoc":[248],"enrichment":[249],"analyses":[250],"influential":[252],"sets":[254],"respect":[256],"target":[258],"phenotypes.":[259],"experiments":[261],"analysing":[262],"variety":[264],"show":[268],"outperforms":[272],"support":[273],"vector":[274],"machine,":[275],"Fully":[276],"Connected":[277,283],"Multi-layer":[278],"Perceptrons":[279],"(MLP)":[280],"Randomly":[282],"MLPs":[284],"despite":[285],"greatly":[286],"reduced":[287],"complexity.":[289],"AVAILABILITY":[290],"AND":[291],"IMPLEMENTATION:":[292],"https://github.com/paulmorio/gincco":[293],"contains":[294,319],"source":[296],"code":[297],"our":[299],"approach.":[300],"also":[302],"release":[303],"library":[305],"discovery":[311],"https://github.com/paulmorio/protclus.":[316],"repository":[318],"implementations":[320],"article.":[328],"SUPPLEMENTARY":[329],"INFORMATION:":[330],"Supplementary":[331],"available":[334],"Bioinformatics":[336],"online.":[337]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}
