{"id":"https://openalex.org/W2512331153","doi":"https://doi.org/10.1186/s13040-016-0106-4","title":"Functional networks inference from rule-based machine learning models","display_name":"Functional networks inference from rule-based machine learning models","publication_year":2016,"publication_date":"2016-09-05","ids":{"openalex":"https://openalex.org/W2512331153","doi":"https://doi.org/10.1186/s13040-016-0106-4","mag":"2512331153","pmid":"https://pubmed.ncbi.nlm.nih.gov/27597880"},"language":"en","primary_location":{"id":"doi:10.1186/s13040-016-0106-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-016-0106-4","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-016-0106-4","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-016-0106-4","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062947296","display_name":"Nicola Lazzarini","orcid":"https://orcid.org/0000-0003-1783-5488"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Nicola Lazzarini","raw_affiliation_strings":["Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091154883","display_name":"Pawe\u0142 Widera","orcid":"https://orcid.org/0000-0003-4955-3653"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Pawe\u0142 Widera","raw_affiliation_strings":["Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033882151","display_name":"Stuart C. Williamson","orcid":"https://orcid.org/0000-0002-5209-4796"},"institutions":[{"id":"https://openalex.org/I4210129527","display_name":"Cancer Research UK Manchester Institute","ror":"https://ror.org/037405c78","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2801316944","https://openalex.org/I4210129527"]},{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Stuart Williamson","raw_affiliation_strings":["Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Clinical and Experimental Pharmacology Group, Cancer Research UK Manchester Institute, University of Manchester, Manchester, UK","institution_ids":["https://openalex.org/I4210129527","https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081651099","display_name":"Rakesh Heer","orcid":"https://orcid.org/0000-0003-1952-7462"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Rakesh Heer","raw_affiliation_strings":["Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Northern Institute for Cancer Research, Medical School, Newcastle University, Newcastle upon Tyne, UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043620976","display_name":"Natalio Krasnogor","orcid":"https://orcid.org/0000-0002-2651-4320"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Natalio Krasnogor","raw_affiliation_strings":["Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, UK","institution_ids":["https://openalex.org/I84884186"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012372361","display_name":"Jaume Bacardit","orcid":"https://orcid.org/0000-0002-2692-7205"},"institutions":[{"id":"https://openalex.org/I84884186","display_name":"Newcastle University","ror":"https://ror.org/01kj2bm70","country_code":"GB","type":"education","lineage":["https://openalex.org/I84884186"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jaume Bacardit","raw_affiliation_strings":["Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Interdisciplinary Computing and Complex BioSystems (ICOS) research group, School of Computing Science, Newcastle University, Newcastle upon Tyne, UK","institution_ids":["https://openalex.org/I84884186"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5062947296"],"corresponding_institution_ids":["https://openalex.org/I84884186"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1768,"currency":"EUR","value_usd":1906},"fwci":0.6963,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.74569529,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"9","issue":"1","first_page":"28","last_page":"28"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9592000246047974,"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":0.9592000246047974,"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":0.017100000753998756,"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/T11303","display_name":"Bayesian Modeling and Causal Inference","score":0.002400000113993883,"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":0.7407064437866211},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.7179566025733948},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5663050413131714},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.551973283290863},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32801443338394165}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7407064437866211},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7179566025733948},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5663050413131714},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.551973283290863},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32801443338394165}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/s13040-016-0106-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-016-0106-4","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-016-0106-4","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:27597880","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27597880","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":"BioData mining","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5011349","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5011349","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":"BioData Min","raw_type":"Text"},{"id":"pmh:oai:pure.atira.dk:openaire_cris_publications/72551501-de1f-45ce-881c-33f40b94277a","is_oa":true,"landing_page_url":"https://research.manchester.ac.uk/en/publications/72551501-de1f-45ce-881c-33f40b94277a","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"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":"Lazzarini, N, Widera, P, Williamson, S, Heer, R, Krasnogor, N & Bacardit, J 2016, 'Functional networks inference from rule-based machine learning models', BioData Mining, vol. 9, no. 1, 28. https://doi.org/10.1186/s13040-016-0106-4","raw_type":"article"},{"id":"pmh:oai:pure.atira.dk:publications/72551501-de1f-45ce-881c-33f40b94277a","is_oa":true,"landing_page_url":"http://www.scopus.com/inward/record.url?scp=84984903728&partnerID=8YFLogxK","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"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":"Lazzarini, N, Widera, P, Williamson, S, Heer, R, Krasnogor, N & Bacardit, J 2016, 'Functional networks inference from rule-based machine learning models', BioData Mining, vol. 9, no. 1, 28. https://doi.org/10.1186/s13040-016-0106-4","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1186/s13040-016-0106-4","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13040-016-0106-4","pdf_url":"https://biodatamining.biomedcentral.com/track/pdf/10.1186/s13040-016-0106-4","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1192083291","display_name":"TAURUS: Towards an Audacious Universal Constructor","funder_award_id":"EP/L001489/2","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G3063934243","display_name":null,"funder_award_id":"EP/K000225","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G3639414224","display_name":null,"funder_award_id":"I031642","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G3930798712","display_name":null,"funder_award_id":"L001489/2","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G4475059929","display_name":"Synthetic Portabolomics: Leading the way at the crossroads of the Digital and the Bio Economies","funder_award_id":"EP/N031962/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G4773421476","display_name":null,"funder_award_id":"MR/N005872/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G5010676993","display_name":null,"funder_award_id":"K000225","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G502459198","display_name":null,"funder_award_id":"EP/I031642/2","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G5104852140","display_name":"Towards a Universal Biological-Cell Operating System (AUdACiOuS)","funder_award_id":"EP/J004111/2","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G5140230474","display_name":null,"funder_award_id":"EP/J004111/2","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G6253955250","display_name":null,"funder_award_id":"EP/L001489/2","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G7133998767","display_name":null,"funder_award_id":"EP/K000225/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G7274221867","display_name":"E-Infrastructure Interconnectivity EPSRC - Chris Taylor","funder_award_id":"EP/K000225/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G8035887905","display_name":null,"funder_award_id":"EP/N031962/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G8699219344","display_name":null,"funder_award_id":"N031962","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G939259430","display_name":"ROADBLOCK: Towards Programmable Defensive Bacterial Coatings &amp; Skins","funder_award_id":"EP/I031642/2","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G998543061","display_name":null,"funder_award_id":"J004111","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2512331153.pdf","grobid_xml":"https://content.openalex.org/works/W2512331153.grobid-xml"},"referenced_works_count":70,"referenced_works":["https://openalex.org/W1979377971","https://openalex.org/W1990123231","https://openalex.org/W1992442866","https://openalex.org/W1993217610","https://openalex.org/W2000771269","https://openalex.org/W2001903569","https://openalex.org/W2004859816","https://openalex.org/W2008719690","https://openalex.org/W2020852864","https://openalex.org/W2022133687","https://openalex.org/W2029368184","https://openalex.org/W2030455922","https://openalex.org/W2030623929","https://openalex.org/W2038082731","https://openalex.org/W2045413197","https://openalex.org/W2045761815","https://openalex.org/W2047992209","https://openalex.org/W2053299445","https://openalex.org/W2060071214","https://openalex.org/W2064208261","https://openalex.org/W2067559668","https://openalex.org/W2067811518","https://openalex.org/W2070837962","https://openalex.org/W2076513103","https://openalex.org/W2080271888","https://openalex.org/W2088213532","https://openalex.org/W2088851040","https://openalex.org/W2097150876","https://openalex.org/W2097532544","https://openalex.org/W2098425296","https://openalex.org/W2099407139","https://openalex.org/W2100526049","https://openalex.org/W2107498970","https://openalex.org/W2107633226","https://openalex.org/W2109363337","https://openalex.org/W2115108153","https://openalex.org/W2116172285","https://openalex.org/W2119412782","https://openalex.org/W2120286360","https://openalex.org/W2125698969","https://openalex.org/W2126964466","https://openalex.org/W2129560785","https://openalex.org/W2129794000","https://openalex.org/W2130253098","https://openalex.org/W2137304236","https://openalex.org/W2139997707","https://openalex.org/W2141097399","https://openalex.org/W2143426320","https://openalex.org/W2144101487","https://openalex.org/W2144169031","https://openalex.org/W2147649238","https://openalex.org/W2147710851","https://openalex.org/W2148078825","https://openalex.org/W2148499186","https://openalex.org/W2149441684","https://openalex.org/W2155330008","https://openalex.org/W2159400887","https://openalex.org/W2159438835","https://openalex.org/W2161868542","https://openalex.org/W2163296115","https://openalex.org/W2165700458","https://openalex.org/W2167689714","https://openalex.org/W2171115585","https://openalex.org/W2249366592","https://openalex.org/W2282660342","https://openalex.org/W2319197375","https://openalex.org/W2472285172","https://openalex.org/W3099289621","https://openalex.org/W4285719527","https://openalex.org/W6773842061"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W4313488044","https://openalex.org/W3209574120","https://openalex.org/W4312192474","https://openalex.org/W4210805261"],"abstract_inverted_index":{"BACKGROUND:":[0],"Functional":[1],"networks":[2,19,104,160,171,234],"play":[3],"an":[4,25,288],"important":[5],"role":[6],"in":[7,196,209,235,293],"the":[8,32,41,67,72,93,125,163,192,197,203,213,220,224,228,232,253,268,278,283,294],"analysis":[9],"of":[10,17,27,69,74,151,172,188,199,212,227,252,300],"biological":[11,134,194,221,269],"processes":[12],"and":[13,144,202,223,240,280,286],"systems.":[14],"The":[15,136,159,180,216,298],"inference":[16,34,68,295,303],"these":[18],"from":[20,71,105,162,184],"high-throughput":[21],"(-omics)":[22],"data":[23,165],"is":[24,66,138,182,275,305],"area":[26],"intense":[28],"research.":[29],"So":[30],"far,":[31],"similarity-based":[33,94,238],"paradigm":[35,65],"(e.g.":[36],"gene":[37,169],"co-expression)":[38],"has":[39],"been":[40],"most":[42],"popular":[43],"approach.":[44],"It":[45,111],"assumes":[46],"a":[47,99,118,133,148,210,257,262],"functional":[48,103],"relationship":[49],"between":[50,86,205],"genes":[51,114,208],"which":[52],"are":[53,80,90,166],"expressed":[54],"at":[55,132],"similar":[56],"levels":[57],"across":[58],"different":[59,178,186],"samples.":[60],"An":[61],"alternative":[62],"to":[63,82,92,101,123,156,237,244,277],"this":[64],"relationships":[70,85,204],"structure":[73],"machine":[75,106,120],"learning":[76,107,121],"models.":[77],"These":[78],"models":[79],"able":[81],"capture":[83],"complex":[84],"variables,":[87],"that":[88,113,267],"often":[89],"different/complementary":[91],"methods.":[95,179],"RESULTS:":[96],"We":[97,190],"propose":[98],"protocol":[100,137,304],"infer":[102],"models,":[108],"called":[109],"FuNeL.":[110],"assumes,":[112],"used":[115,292],"together":[116],"within":[117],"rule-based":[119],"model":[122],"classify":[124],"samples,":[126],"might":[127],"also":[128],"be":[129],"functionally":[130],"related":[131,155],"level.":[135],"first":[139],"tested":[140],"on":[141,147],"synthetic":[142],"datasets":[143,154],"then":[145],"evaluated":[146],"test":[149],"suite":[150],"8":[152],"real-world":[153,164],"human":[157],"cancer.":[158],"inferred":[161],"compared":[167],"against":[168],"co-expression":[170],"equal":[173],"size,":[174],"generated":[175],"with":[176,282,287],"3":[177],"comparison":[181,217],"performed":[183],"two":[185],"points":[187],"view.":[189],"analyse":[191],"enriched":[193],"terms":[195],"set":[198],"network":[200,214,302],"nodes":[201],"known":[206,246],"disease-associated":[207],"context":[211],"topology.":[215],"confirms":[218],"both":[219],"relevance":[222],"complementary":[225],"character":[226],"knowledge":[229,270],"captured":[230,271],"by":[231,272],"FuNeL":[233],"relation":[236],"methods":[239],"demonstrates":[241],"its":[242],"potential":[243],"identify":[245],"disease":[247,279],"associations":[248],"as":[249,261],"core":[250],"elements":[251],"network.":[254],"Finally,":[255],"using":[256],"prostate":[258],"cancer":[259],"dataset":[260,290],"case":[263],"study,":[264],"we":[265],"confirm":[266],"our":[273,301],"method":[274],"relevant":[276],"consistent":[281],"specialised":[284],"literature":[285],"independent":[289],"not":[291],"process.":[296],"AVAILABILITY:":[297],"implementation":[299],"available":[306],"at:":[307],"http://ico2s.org/software/funel.html.":[308]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}
