{"id":"https://openalex.org/W4415706823","doi":"https://doi.org/10.1371/journal.pcbi.1013614","title":"HMFGraph: Novel Bayesian approach for recovering biological networks","display_name":"HMFGraph: Novel Bayesian approach for recovering biological networks","publication_year":2025,"publication_date":"2025-10-30","ids":{"openalex":"https://openalex.org/W4415706823","doi":"https://doi.org/10.1371/journal.pcbi.1013614","pmid":"https://pubmed.ncbi.nlm.nih.gov/41166379"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013614","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013614","pdf_url":null,"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://doi.org/10.1371/journal.pcbi.1013614","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040854564","display_name":"Anna-Leena Korhonen","orcid":"https://orcid.org/0009-0007-6156-3121"},"institutions":[{"id":"https://openalex.org/I98381234","display_name":"University of Oulu","ror":"https://ror.org/03yj89h83","country_code":"FI","type":"education","lineage":["https://openalex.org/I98381234"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Aapo E. Korhonen","raw_affiliation_strings":["Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland"],"raw_orcid":"https://orcid.org/0009-0007-6156-3121","affiliations":[{"raw_affiliation_string":"Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland","institution_ids":["https://openalex.org/I98381234"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079867160","display_name":"Olli Sarala","orcid":"https://orcid.org/0000-0002-7330-3577"},"institutions":[{"id":"https://openalex.org/I98381234","display_name":"University of Oulu","ror":"https://ror.org/03yj89h83","country_code":"FI","type":"education","lineage":["https://openalex.org/I98381234"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Olli Sarala","raw_affiliation_strings":["Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland","institution_ids":["https://openalex.org/I98381234"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5120192511","display_name":"Tuomas Hautam\u00e4ki","orcid":null},"institutions":[{"id":"https://openalex.org/I98381234","display_name":"University of Oulu","ror":"https://ror.org/03yj89h83","country_code":"FI","type":"education","lineage":["https://openalex.org/I98381234"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Tuomas Hautam\u00e4ki","raw_affiliation_strings":["Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland"],"raw_orcid":"https://orcid.org/0009-0004-4641-3828","affiliations":[{"raw_affiliation_string":"Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland","institution_ids":["https://openalex.org/I98381234"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001036744","display_name":"Markku Kuismin","orcid":"https://orcid.org/0000-0001-9074-7420"},"institutions":[{"id":"https://openalex.org/I98381234","display_name":"University of Oulu","ror":"https://ror.org/03yj89h83","country_code":"FI","type":"education","lineage":["https://openalex.org/I98381234"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Markku Kuismin","raw_affiliation_strings":["Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland","institution_ids":["https://openalex.org/I98381234"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5055050168","display_name":"Mikko J. Sillanp\u00e4\u00e4","orcid":"https://orcid.org/0000-0003-2808-2768"},"institutions":[{"id":"https://openalex.org/I98381234","display_name":"University of Oulu","ror":"https://ror.org/03yj89h83","country_code":"FI","type":"education","lineage":["https://openalex.org/I98381234"]}],"countries":["FI"],"is_corresponding":true,"raw_author_name":"Mikko J. Sillanp\u00e4\u00e4","raw_affiliation_strings":["Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland"],"raw_orcid":"https://orcid.org/0000-0003-2808-2768","affiliations":[{"raw_affiliation_string":"Research Unit of Mathematical Sciences, University of Oulu, Oulu, Finland","institution_ids":["https://openalex.org/I98381234"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5001036744","https://openalex.org/A5040854564","https://openalex.org/A5055050168","https://openalex.org/A5079867160","https://openalex.org/A5120192511"],"corresponding_institution_ids":["https://openalex.org/I98381234"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.6255,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.73437806,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"21","issue":"10","first_page":"e1013614","last_page":"e1013614"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.35100001096725464,"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":0.35100001096725464,"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":0.29679998755455017,"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"}},{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.04960000142455101,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/hyperparameter","display_name":"Hyperparameter","score":0.8285999894142151},{"id":"https://openalex.org/keywords/markov-chain-monte-carlo","display_name":"Markov chain Monte Carlo","score":0.6341000199317932},{"id":"https://openalex.org/keywords/bayesian-network","display_name":"Bayesian network","score":0.5515999794006348},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5450999736785889},{"id":"https://openalex.org/keywords/graphical-model","display_name":"Graphical model","score":0.5329999923706055},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5187000036239624},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.44290000200271606},{"id":"https://openalex.org/keywords/gaussian","display_name":"Gaussian","score":0.4300999939441681},{"id":"https://openalex.org/keywords/hyperparameter-optimization","display_name":"Hyperparameter optimization","score":0.4090999960899353}],"concepts":[{"id":"https://openalex.org/C8642999","wikidata":"https://www.wikidata.org/wiki/Q4171168","display_name":"Hyperparameter","level":2,"score":0.8285999894142151},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7002999782562256},{"id":"https://openalex.org/C111350023","wikidata":"https://www.wikidata.org/wiki/Q1191869","display_name":"Markov chain Monte Carlo","level":3,"score":0.6341000199317932},{"id":"https://openalex.org/C33724603","wikidata":"https://www.wikidata.org/wiki/Q812540","display_name":"Bayesian network","level":2,"score":0.5515999794006348},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5450999736785889},{"id":"https://openalex.org/C155846161","wikidata":"https://www.wikidata.org/wiki/Q1143367","display_name":"Graphical model","level":2,"score":0.5329999923706055},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5187000036239624},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.46480000019073486},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.44290000200271606},{"id":"https://openalex.org/C163716315","wikidata":"https://www.wikidata.org/wiki/Q901177","display_name":"Gaussian","level":2,"score":0.4300999939441681},{"id":"https://openalex.org/C10485038","wikidata":"https://www.wikidata.org/wiki/Q48996162","display_name":"Hyperparameter optimization","level":3,"score":0.4090999960899353},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.39340001344680786},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.390500009059906},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.38190001249313354},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.35429999232292175},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.34470000863075256},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.3400999903678894},{"id":"https://openalex.org/C162307627","wikidata":"https://www.wikidata.org/wiki/Q204833","display_name":"Enhanced Data Rates for GSM Evolution","level":2,"score":0.3346000015735626},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.3319999873638153},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.3188999891281128},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.31310001015663147},{"id":"https://openalex.org/C61326573","wikidata":"https://www.wikidata.org/wiki/Q1496376","display_name":"Gaussian process","level":3,"score":0.29989999532699585},{"id":"https://openalex.org/C71983512","wikidata":"https://www.wikidata.org/wiki/Q7915687","display_name":"Variable-order Bayesian network","level":4,"score":0.288100004196167},{"id":"https://openalex.org/C61224824","wikidata":"https://www.wikidata.org/wiki/Q2260434","display_name":"Mixture model","level":2,"score":0.25850000977516174},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.2556999921798706},{"id":"https://openalex.org/C2778049539","wikidata":"https://www.wikidata.org/wiki/Q17002908","display_name":"Bayesian optimization","level":2,"score":0.25130000710487366}],"mesh":[{"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":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016011","descriptor_name":"Normal Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016011","descriptor_name":"Normal Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016011","descriptor_name":"Normal Distribution","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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1013614","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013614","pdf_url":null,"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:41166379","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41166379","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:doaj.org/article:50a52dd393e2405d8aa0a294b5fba5c3","is_oa":true,"landing_page_url":"https://doaj.org/article/50a52dd393e2405d8aa0a294b5fba5c3","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 21, Iss 10, p e1013614 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11399122","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12591435","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.1013614","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013614","pdf_url":null,"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/G1519898314","display_name":null,"funder_award_id":"349393","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G6217888606","display_name":"Future Methods for Identifying Interacting Genes using Dynamic Gene Network Inference","funder_award_id":"349393","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"},{"id":"https://openalex.org/G8539607782","display_name":null,"funder_award_id":"329439","funder_id":"https://openalex.org/F4320321108","funder_display_name":"Academy of Finland"}],"funders":[{"id":"https://openalex.org/F4320321108","display_name":"Academy of Finland","ror":"https://ror.org/05k73zm37"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W1524469599","https://openalex.org/W1547176439","https://openalex.org/W1741702827","https://openalex.org/W1864161604","https://openalex.org/W1959730594","https://openalex.org/W1967639437","https://openalex.org/W1968634476","https://openalex.org/W2010824638","https://openalex.org/W2039256638","https://openalex.org/W2062125287","https://openalex.org/W2065808340","https://openalex.org/W2099978770","https://openalex.org/W2110065044","https://openalex.org/W2132555912","https://openalex.org/W2138307025","https://openalex.org/W2138477261","https://openalex.org/W2142972916","https://openalex.org/W2147566730","https://openalex.org/W2160299056","https://openalex.org/W2162193517","https://openalex.org/W2163480486","https://openalex.org/W2163738067","https://openalex.org/W2272700822","https://openalex.org/W2479782352","https://openalex.org/W2535502084","https://openalex.org/W2558664061","https://openalex.org/W2567948266","https://openalex.org/W2782670000","https://openalex.org/W2794407684","https://openalex.org/W2795304539","https://openalex.org/W2907862584","https://openalex.org/W2950483248","https://openalex.org/W2963330637","https://openalex.org/W2963819041","https://openalex.org/W2964033684","https://openalex.org/W2996000760","https://openalex.org/W2996717677","https://openalex.org/W3006757787","https://openalex.org/W3044795635","https://openalex.org/W3083170245","https://openalex.org/W3090988770","https://openalex.org/W3094555844","https://openalex.org/W3124158341","https://openalex.org/W3126232929","https://openalex.org/W3138406337","https://openalex.org/W3145918735","https://openalex.org/W3167389373","https://openalex.org/W4200306155","https://openalex.org/W4212908912","https://openalex.org/W4225598392","https://openalex.org/W4388323202","https://openalex.org/W4392349056","https://openalex.org/W4399649090","https://openalex.org/W4402043754","https://openalex.org/W4404511387","https://openalex.org/W4406234938","https://openalex.org/W4406610060","https://openalex.org/W4410077367","https://openalex.org/W4411006704"],"related_works":[],"abstract_inverted_index":{"Gaussian":[0],"graphical":[1],"models":[2],"(GGM)":[3],"are":[4,223],"powerful":[5],"tools":[6],"to":[7,103,219],"examine":[8],"partial":[9],"correlation":[10,17],"structures":[11],"in":[12,207],"high-dimensional":[13],"omics":[14],"datasets.":[15],"Partial":[16],"networks":[18],"can":[19,171],"explain":[20],"complex":[21],"relationships":[22],"between":[23],"genes":[24],"or":[25],"other":[26],"biological":[27,91],"variables.":[28],"Bayesian":[29,64,74,193],"implementations":[30,45],"of":[31,43,118,128,169],"GGMs":[32],"have":[33],"recently":[34],"received":[35],"more":[36],"attention.":[37],"Usually,":[38],"the":[39,60,120,125,129,148,173,208,221],"most":[40],"demanding":[41],"parts":[42],"GGM":[44,75,194],"are:":[46],"(i)":[47],"hyperparameter":[48,122,170],"tuning,":[49],"(ii)":[50],"edge":[51,134],"selection,":[52,135],"(iii)":[53],"scalability":[54],"for":[55,63,109,178],"large":[56],"datasets,":[57],"and":[58,90,106,180],"(iv)":[59],"prior":[61,80,96,175],"choice":[62,168],"GGM.":[65],"To":[66],"address":[67],"these":[68],"limitations,":[69],"we":[70,136],"introduce":[71],"a":[72,77,82,115,166,186],"novel":[73],"using":[76,138],"hierarchical":[78],"matrix-F":[79],"with":[81,87,185],"fast":[83],"implementation.":[84],"We":[85,113],"show,":[86],"extensive":[88],"simulations":[89],"example":[92],"analyses,":[93],"that":[94,196],"this":[95],"has":[97],"competitive":[98],"network":[99],"recovery":[100],"capabilities":[101],"compared":[102],"state-of-the-art":[104],"approaches":[105,195],"good":[107],"properties":[108],"recovering":[110],"meaningful":[111],"networks.":[112],"present":[114],"new":[116],"way":[117],"tuning":[119],"shrinkage":[121],"by":[123,147,157],"constraining":[124],"condition":[126],"number":[127],"estimated":[130,160],"precision":[131],"matrix.":[132],"For":[133],"propose":[137],"approximated":[139],"credible":[140],"intervals":[141],"(CI)":[142],"whose":[143],"width":[144],"is":[145,155,205],"controlled":[146],"false":[149],"discovery":[150],"rate.":[151],"An":[152],"optimal":[153],"CI":[154],"selected":[156],"maximizing":[158],"an":[159],"F1-score":[161],"via":[162],"permutations.":[163],"In":[164],"addition,":[165],"specific":[167],"make":[172],"proposed":[174],"better":[176],"suited":[177],"clustering":[179],"community":[181],"detection.":[182],"Our":[183],"method,":[184],"generalized":[187],"expectation-maximization":[188],"algorithm,":[189],"computationally":[190],"outperforms":[191],"existing":[192],"use":[197],"Markov":[198],"chain":[199],"Monte":[200],"Carlo":[201],"algorithms.":[202],"The":[203],"method":[204],"implemented":[206],"R":[209],"package":[210],"HMFGraph,":[211],"found":[212,224],"on":[213,225],"GitHub":[214,226],"at":[215,227],"https://github.com/AapoKorhonen/HMFGraph.":[216],"All":[217],"codes":[218],"reproduce":[220],"results":[222],"https://github.com/AapoKorhonen/HMFGraph-Supplementary.":[228]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-30T00:00:00"}
