{"id":"https://openalex.org/W2620912394","doi":"https://doi.org/10.1371/journal.pcbi.1005466","title":"A review of active learning approaches to experimental design for uncovering biological networks","display_name":"A review of active learning approaches to experimental design for uncovering biological networks","publication_year":2017,"publication_date":"2017-06-01","ids":{"openalex":"https://openalex.org/W2620912394","doi":"https://doi.org/10.1371/journal.pcbi.1005466","mag":"2620912394","pmid":"https://pubmed.ncbi.nlm.nih.gov/28570593"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1005466","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005466","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005466&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005466&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5023716437","display_name":"Yuriy Sverchkov","orcid":"https://orcid.org/0000-0002-9851-8582"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yuriy Sverchkov","raw_affiliation_strings":["Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-9851-8582","affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071722704","display_name":"Mark Craven","orcid":"https://orcid.org/0000-0002-8917-7464"},"institutions":[{"id":"https://openalex.org/I135310074","display_name":"University of Wisconsin\u2013Madison","ror":"https://ror.org/01y2jtd41","country_code":"US","type":"education","lineage":["https://openalex.org/I135310074"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark Craven","raw_affiliation_strings":["Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-8917-7464","affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]},{"raw_affiliation_string":"Department of Biostatistics and Medical Informatics, University of Wisconsin\u2013Madison, Madison, Wisconsin, United States of America","institution_ids":["https://openalex.org/I135310074"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5023716437"],"corresponding_institution_ids":["https://openalex.org/I135310074"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":3.1433,"has_fulltext":true,"cited_by_count":77,"citation_normalized_percentile":{"value":0.92773152,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"13","issue":"6","first_page":"e1005466","last_page":"e1005466"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9993000030517578,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9993000030517578,"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/T11178","display_name":"Receptor Mechanisms and Signaling","score":0.9936000108718872,"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":0.9911999702453613,"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":0.7096522450447083},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.652269721031189},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6056420803070068},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5964648127555847},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.5839658379554749},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.5223858952522278},{"id":"https://openalex.org/keywords/model-selection","display_name":"Model selection","score":0.46283650398254395},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.43382522463798523},{"id":"https://openalex.org/keywords/active-learning","display_name":"Active learning (machine learning)","score":0.4332071542739868},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.35142800211906433},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.17557784914970398},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13312086462974548}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7096522450447083},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.652269721031189},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6056420803070068},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5964648127555847},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.5839658379554749},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.5223858952522278},{"id":"https://openalex.org/C93959086","wikidata":"https://www.wikidata.org/wiki/Q6888345","display_name":"Model selection","level":2,"score":0.46283650398254395},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.43382522463798523},{"id":"https://openalex.org/C77967617","wikidata":"https://www.wikidata.org/wiki/Q4677561","display_name":"Active learning (machine learning)","level":2,"score":0.4332071542739868},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.35142800211906433},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.17557784914970398},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13312086462974548},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","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":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012107","descriptor_name":"Research Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1005466","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005466","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005466&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:28570593","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28570593","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1005466","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005466","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:doaj.org/article:a9e108e4220f49bb908b36cf82b87815","is_oa":true,"landing_page_url":"https://doaj.org/article/a9e108e4220f49bb908b36cf82b87815","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 13, Iss 6, p e1005466 (2017)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4316069","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5453429","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1005466","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1005466","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005466&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1455390755","display_name":null,"funder_award_id":"U54 AI117924","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1536938475","display_name":null,"funder_award_id":"U54AI117924","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G1668283625","display_name":null,"funder_award_id":"T15 LM007359","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2890725500","display_name":"RI: Small: Active Learning with Rich Query Types on Networks and Trees","funder_award_id":"1218880","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4338327699","display_name":null,"funder_award_id":"T15LM007359","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"},{"id":"https://openalex.org/G7939070741","display_name":null,"funder_award_id":"LM007359","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7952862298","display_name":null,"funder_award_id":"AI117924","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2620912394.pdf","grobid_xml":"https://content.openalex.org/works/W2620912394.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W284239745","https://openalex.org/W1481635749","https://openalex.org/W1541824660","https://openalex.org/W1543507677","https://openalex.org/W1623155147","https://openalex.org/W1645969895","https://openalex.org/W1965555277","https://openalex.org/W1971266246","https://openalex.org/W1972129511","https://openalex.org/W1972764318","https://openalex.org/W1982189144","https://openalex.org/W1986177561","https://openalex.org/W1990930479","https://openalex.org/W1995875735","https://openalex.org/W2010507548","https://openalex.org/W2011173182","https://openalex.org/W2110266641","https://openalex.org/W2112407533","https://openalex.org/W2114804859","https://openalex.org/W2126602684","https://openalex.org/W2129632913","https://openalex.org/W2132582966","https://openalex.org/W2136636278","https://openalex.org/W2137813581","https://openalex.org/W2139417466","https://openalex.org/W2142170851","https://openalex.org/W2142901992","https://openalex.org/W2145899141","https://openalex.org/W2146206618","https://openalex.org/W2149992463","https://openalex.org/W2159638256","https://openalex.org/W2162690533","https://openalex.org/W2163076211","https://openalex.org/W2171620180","https://openalex.org/W2172049947","https://openalex.org/W2175406438","https://openalex.org/W6632450347","https://openalex.org/W7075292137"],"related_works":["https://openalex.org/W2155492529","https://openalex.org/W4252504573","https://openalex.org/W4385510321","https://openalex.org/W2101315668","https://openalex.org/W15348386","https://openalex.org/W4381571012","https://openalex.org/W2314128295","https://openalex.org/W1509942269","https://openalex.org/W4287026692","https://openalex.org/W2770735656"],"abstract_inverted_index":{"Various":[0],"types":[1],"of":[2,7,18,30,65,143],"biological":[3],"knowledge":[4,25],"describe":[5],"networks":[6,16,32],"interactions":[8,19],"among":[9,20,137],"elementary":[10],"entities.":[11],"For":[12],"example,":[13],"transcriptional":[14],"regulatory":[15],"consist":[17],"proteins":[21],"and":[22,36,100,124,134,139,146],"genes.":[23],"Current":[24],"about":[26,49],"the":[27,41,94,101,111,116,129,150],"exact":[28],"structure":[29],"such":[31],"is":[33,78,86,107],"highly":[34],"incomplete,":[35],"laboratory":[37],"experiments":[38,102],"that":[39,106],"manipulate":[40],"entities":[42],"involved":[43],"are":[44,91],"conducted":[45],"to":[46,58,96,109],"test":[47],"hypotheses":[48,90],"these":[50,66],"networks.":[51],"In":[52],"recent":[53],"years,":[54],"various":[55,117],"automated":[56],"approaches":[57,67],"experiment":[59,119],"selection":[60,120],"have":[61],"been":[62],"proposed.":[63],"Many":[64],"can":[68],"be":[69],"characterized":[70],"as":[71],"active":[72],"machine":[73],"learning":[74,77],"algorithms.":[75],"Active":[76],"an":[79],"iterative":[80],"process":[81],"in":[82,128,149],"which":[83],"a":[84],"model":[85,95],"learned":[87],"from":[88,93],"data,":[89],"generated":[92],"propose":[97],"informative":[98],"experiments,":[99],"yield":[103],"new":[104],"data":[105],"used":[108],"update":[110],"model.":[112],"This":[113],"review":[114],"describes":[115],"models,":[118],"strategies,":[121],"validation":[122],"techniques,":[123],"successful":[125],"applications":[126],"described":[127],"literature;":[130],"highlights":[131],"common":[132],"themes":[133],"notable":[135],"distinctions":[136],"methods;":[138],"identifies":[140],"likely":[141],"directions":[142],"future":[144],"research":[145],"open":[147],"problems":[148],"area.":[151]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
