{"id":"https://openalex.org/W2953378632","doi":"https://doi.org/10.1093/bib/bby095","title":"Algebraic shortcuts for leave-one-out cross-validation in supervised network inference","display_name":"Algebraic shortcuts for leave-one-out cross-validation in supervised network inference","publication_year":2018,"publication_date":"2018-09-10","ids":{"openalex":"https://openalex.org/W2953378632","doi":"https://doi.org/10.1093/bib/bby095","mag":"2953378632","pmid":"https://pubmed.ncbi.nlm.nih.gov/30329015"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bby095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bby095","pdf_url":"https://academic.oup.com/bib/article-pdf/21/1/262/32376187/bby095.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":null,"license_id":null,"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":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/21/1/262/32376187/bby095.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079406761","display_name":"Michiel Stock","orcid":"https://orcid.org/0000-0003-0903-6061"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Michiel Stock","raw_affiliation_strings":["Department of Data Analysis and Mathematical Modelling, Ghent University, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Data Analysis and Mathematical Modelling, Ghent University, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021993986","display_name":"Tapio Pahikkala","orcid":"https://orcid.org/0000-0003-4183-2455"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Tapio Pahikkala","raw_affiliation_strings":["Department of Future Technologies, University of Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Future Technologies, University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084144711","display_name":"Antti Airola","orcid":"https://orcid.org/0000-0002-1010-4386"},"institutions":[{"id":"https://openalex.org/I155660961","display_name":"University of Turku","ror":"https://ror.org/05vghhr25","country_code":"FI","type":"education","lineage":["https://openalex.org/I155660961"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Antti Airola","raw_affiliation_strings":["Department of Future Technologies, University of Turku, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Future Technologies, University of Turku, Finland","institution_ids":["https://openalex.org/I155660961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028945060","display_name":"Willem Waegeman","orcid":"https://orcid.org/0000-0002-5950-3003"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Willem Waegeman","raw_affiliation_strings":["Department of Data Analysis and Mathematical Modelling, Ghent University, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Data Analysis and Mathematical Modelling, Ghent University, Belgium","institution_ids":["https://openalex.org/I32597200"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012437460","display_name":"Bernard De Baets","orcid":"https://orcid.org/0000-0002-3876-620X"},"institutions":[{"id":"https://openalex.org/I32597200","display_name":"Ghent University","ror":"https://ror.org/00cv9y106","country_code":"BE","type":"education","lineage":["https://openalex.org/I32597200"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Bernard De Baets","raw_affiliation_strings":["Department of Data Analysis and Mathematical Modelling, Ghent University, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Data Analysis and Mathematical Modelling, Ghent University, Belgium","institution_ids":["https://openalex.org/I32597200"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5079406761"],"corresponding_institution_ids":["https://openalex.org/I32597200"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.9022,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.74488334,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"21","issue":"1","first_page":"262","last_page":"271"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9962999820709229,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9961000084877014,"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":0.7756190896034241},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.715262770652771},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6204583644866943},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.61363685131073},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5724483132362366},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.5165544748306274},{"id":"https://openalex.org/keywords/cross-validation","display_name":"Cross-validation","score":0.4876374304294586},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4290408492088318},{"id":"https://openalex.org/keywords/linear-model","display_name":"Linear model","score":0.4264419674873352},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.09852820634841919}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7756190896034241},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.715262770652771},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6204583644866943},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.61363685131073},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5724483132362366},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.5165544748306274},{"id":"https://openalex.org/C27181475","wikidata":"https://www.wikidata.org/wiki/Q541014","display_name":"Cross-validation","level":2,"score":0.4876374304294586},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4290408492088318},{"id":"https://openalex.org/C163175372","wikidata":"https://www.wikidata.org/wiki/Q3339222","display_name":"Linear model","level":2,"score":0.4264419674873352},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.09852820634841919},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bby095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bby095","pdf_url":"https://academic.oup.com/bib/article-pdf/21/1/262/32376187/bby095.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30329015","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30329015","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:archive.ugent.be:8655765","is_oa":false,"landing_page_url":"http://hdl.handle.net/1854/LU-8655765","pdf_url":null,"source":{"id":"https://openalex.org/S4306400478","display_name":"Ghent University Academic Bibliography (Ghent University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I32597200","host_organization_name":"Ghent University","host_organization_lineage":["https://openalex.org/I32597200"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ISSN: 1477-4054","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bib/bby095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bby095","pdf_url":"https://academic.oup.com/bib/article-pdf/21/1/262/32376187/bby095.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":null,"license_id":null,"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/G1781988190","display_name":null,"funder_award_id":"313266","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G5091040182","display_name":null,"funder_award_id":"311273","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G7148818622","display_name":"Understanding, predicting and controlling community ecosystems by means of machine learning methods","funder_award_id":"FWO17/PDO/067","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"},{"id":"https://openalex.org/F4320321730","display_name":"Fonds Wetenschappelijk Onderzoek","ror":"https://ror.org/03qtxy027"},{"id":"https://openalex.org/F4320327336","display_name":"Vlaamse regering","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2953378632.pdf","grobid_xml":"https://content.openalex.org/works/W2953378632.grobid-xml"},"referenced_works_count":74,"referenced_works":["https://openalex.org/W252473821","https://openalex.org/W652269744","https://openalex.org/W1019830208","https://openalex.org/W1506859583","https://openalex.org/W1510073064","https://openalex.org/W1542652324","https://openalex.org/W1668147540","https://openalex.org/W1867746808","https://openalex.org/W1973714307","https://openalex.org/W1979537657","https://openalex.org/W2008840001","https://openalex.org/W2009313526","https://openalex.org/W2010890545","https://openalex.org/W2026738983","https://openalex.org/W2047606947","https://openalex.org/W2063492450","https://openalex.org/W2067833766","https://openalex.org/W2073685065","https://openalex.org/W2074110893","https://openalex.org/W2074888914","https://openalex.org/W2076513103","https://openalex.org/W2082360590","https://openalex.org/W2087064593","https://openalex.org/W2099862356","https://openalex.org/W2100672820","https://openalex.org/W2101029276","https://openalex.org/W2104360366","https://openalex.org/W2106029302","https://openalex.org/W2108069034","https://openalex.org/W2108933868","https://openalex.org/W2109384743","https://openalex.org/W2109991441","https://openalex.org/W2121569737","https://openalex.org/W2121971770","https://openalex.org/W2122617678","https://openalex.org/W2123958887","https://openalex.org/W2128817214","https://openalex.org/W2135007932","https://openalex.org/W2139736926","https://openalex.org/W2140922100","https://openalex.org/W2141007997","https://openalex.org/W2144000913","https://openalex.org/W2146766088","https://openalex.org/W2148145769","https://openalex.org/W2153838454","https://openalex.org/W2161922860","https://openalex.org/W2162422091","https://openalex.org/W2165674132","https://openalex.org/W2167212630","https://openalex.org/W2167821759","https://openalex.org/W2169053773","https://openalex.org/W2177411254","https://openalex.org/W2230403050","https://openalex.org/W2243910093","https://openalex.org/W2309916540","https://openalex.org/W2560136348","https://openalex.org/W2580767461","https://openalex.org/W2580903965","https://openalex.org/W2605169404","https://openalex.org/W2616038372","https://openalex.org/W2787640683","https://openalex.org/W2913059114","https://openalex.org/W2963091287","https://openalex.org/W3100984977","https://openalex.org/W3119651796","https://openalex.org/W4298876635","https://openalex.org/W6637436264","https://openalex.org/W6662383355","https://openalex.org/W6669019322","https://openalex.org/W6678151125","https://openalex.org/W6680972884","https://openalex.org/W6685350579","https://openalex.org/W6732280925","https://openalex.org/W6736200421"],"related_works":["https://openalex.org/W2487162673","https://openalex.org/W2942366970","https://openalex.org/W2793211469","https://openalex.org/W2949152769","https://openalex.org/W4372354731","https://openalex.org/W2562400057","https://openalex.org/W1692008701","https://openalex.org/W2597588799","https://openalex.org/W4360593462","https://openalex.org/W2012255351"],"abstract_inverted_index":{"Supervised":[0],"machine":[1,215],"learning":[2,216],"techniques":[3,25,217],"have":[4],"traditionally":[5],"been":[6,45],"very":[7],"successful":[8],"at":[9],"reconstructing":[10],"biological":[11],"networks,":[12],"such":[13,52,131],"as":[14],"protein-ligand":[15],"interaction,":[16],"protein-protein":[17],"interaction":[18],"and":[19,101],"gene":[20],"regulatory":[21],"networks.":[22],"Many":[23],"supervised":[24,53],"for":[26,77,196],"network":[27,72,143,199],"prediction":[28,99,133,200],"use":[29],"linear":[30],"models":[31],"on":[32,47,114],"a":[33,62,70,78,140,162,182],"possibly":[34],"nonlinear":[35],"pairwise":[36],"feature":[37],"representation":[38],"of":[39,51,117,169,175,184,211],"edges.":[40,176],"Recently,":[41],"much":[42],"emphasis":[43],"has":[44],"placed":[46],"the":[48,84,92,98,104,109,115,128,167,173,193,209,219,225],"correct":[49],"evaluation":[50],"models.":[54,213],"It":[55],"is":[56],"vital":[57],"to":[58,64,74,107,123,126,181,190,206],"distinguish":[59],"between":[60,97],"using":[61],"model":[63,105,112,156,194],"either":[65],"predict":[66,75],"new":[67,79],"interactions":[68,76],"in":[69,83,130,224],"given":[71],"or":[73],"vertex":[80],"not":[81],"present":[82],"original":[85],"network.":[86],"This":[87,202],"distinction":[88],"matters":[89],"because":[90],"(i)":[91],"performance":[93,129,195],"might":[94],"dramatically":[95],"differ":[96],"settings":[100],"(ii)":[102],"tuning":[103],"hyperparameters":[106],"obtain":[108],"best":[110],"possible":[111],"depends":[113],"setting":[116],"interest.":[118],"Specific":[119],"cross-validation":[120,185],"schemes":[121],"need":[122],"be":[124,158],"used":[125],"assess":[127,208],"different":[132],"settings.":[134],"In":[135],"this":[136,154,178],"work":[137],"we":[138],"discuss":[139],"state-of-the-art":[141],"kernel-based":[142],"inference":[144],"technique":[145],"called":[146],"two-step":[147],"kernel":[148],"ridge":[149],"regression.":[150],"We":[151],"show":[152],"that":[153,187],"regression":[155],"can":[157],"trained":[159],"efficiently,":[160],"with":[161,166,218],"time":[163],"complexity":[164],"scaling":[165],"number":[168,174],"vertices":[170],"rather":[171],"than":[172],"Furthermore,":[177],"framework":[179],"leads":[180],"series":[183],"shortcuts":[186,221],"allow":[188],"one":[189],"rapidly":[191],"estimate":[192],"any":[197],"relevant":[198],"setting.":[201],"allows":[203],"computational":[204],"biologists":[205],"fully":[207],"capabilities":[210],"their":[212],"The":[214],"algebraic":[220],"are":[222],"implemented":[223],"RLScore":[226],"software":[227],"package:":[228],"https://github.com/aatapa/RLScore.":[229]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
