{"id":"https://openalex.org/W4386615124","doi":"https://doi.org/10.1371/journal.pcbi.1011444","title":"iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease","display_name":"iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease","publication_year":2023,"publication_date":"2023-09-11","ids":{"openalex":"https://openalex.org/W4386615124","doi":"https://doi.org/10.1371/journal.pcbi.1011444","pmid":"https://pubmed.ncbi.nlm.nih.gov/37695793"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011444","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011444","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011444&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.1011444&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052582390","display_name":"Ziheng Duan","orcid":"https://orcid.org/0000-0003-4696-0042"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ziheng Duan","raw_affiliation_strings":["Department of Computer Science, University of California, Irvine, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, California, United States of America","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102800694","display_name":"Yi Dai","orcid":null},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yi Dai","raw_affiliation_strings":["Department of Computer Science, University of California, Irvine, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, California, United States of America","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027169758","display_name":"Ahyeon Hwang","orcid":"https://orcid.org/0000-0002-4686-3077"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ahyeon Hwang","raw_affiliation_strings":["Department of Computer Science, University of California, Irvine, California, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-4686-3077","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, California, United States of America","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015163704","display_name":"Che-Yu Lee","orcid":"https://orcid.org/0000-0002-3039-4894"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Cheyu Lee","raw_affiliation_strings":["Department of Computer Science, University of California, Irvine, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, California, United States of America","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101243192","display_name":"Kaichi Xie","orcid":null},"institutions":[{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kaichi Xie","raw_affiliation_strings":["Department of Computer Science, University of California, Davis, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Davis, California, United States of America","institution_ids":["https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101889403","display_name":"Chutong Xiao","orcid":"https://orcid.org/0009-0009-3355-218X"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Chutong Xiao","raw_affiliation_strings":["Department of Computer Science, University of California, Irvine, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, California, United States of America","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000807861","display_name":"Min Xu","orcid":"https://orcid.org/0000-0002-0881-5891"},"institutions":[{"id":"https://openalex.org/I74973139","display_name":"Carnegie Mellon University","ror":"https://ror.org/05x2bcf33","country_code":"US","type":"education","lineage":["https://openalex.org/I74973139"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Min Xu","raw_affiliation_strings":["Department of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America","institution_ids":["https://openalex.org/I74973139"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005470509","display_name":"Matthew J. Girgenti","orcid":"https://orcid.org/0000-0003-1647-326X"},"institutions":[{"id":"https://openalex.org/I1322918889","display_name":"United States Department of Veterans Affairs","ror":"https://ror.org/05rsv9s98","country_code":"US","type":"government","lineage":["https://openalex.org/I1322918889"]},{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]},{"id":"https://openalex.org/I4210103836","display_name":"National Center for PTSD","ror":"https://ror.org/01dbbht76","country_code":"US","type":"other","lineage":["https://openalex.org/I1322918889","https://openalex.org/I4210103836"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Matthew J. Girgenti","raw_affiliation_strings":["Clinical Neurosciences Division, National Center for PTSD, U.S. Department of Veterans Affairs, West Haven, Connecticut, United States of America","Department of Psychiatry, School of Medicine, Yale University, New Haven, Connecticut, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Clinical Neurosciences Division, National Center for PTSD, U.S. Department of Veterans Affairs, West Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I1322918889","https://openalex.org/I4210103836"]},{"raw_affiliation_string":"Department of Psychiatry, School of Medicine, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100345410","display_name":"Jing Zhang","orcid":"https://orcid.org/0000-0002-5970-0509"},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jing Zhang","raw_affiliation_strings":["Department of Computer Science, University of California, Irvine, California, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-5970-0509","affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of California, Irvine, California, United States of America","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5000807861","https://openalex.org/A5005470509","https://openalex.org/A5015163704","https://openalex.org/A5027169758","https://openalex.org/A5052582390","https://openalex.org/A5100345410","https://openalex.org/A5101243192","https://openalex.org/A5101889403","https://openalex.org/A5102800694"],"corresponding_institution_ids":["https://openalex.org/I1322918889","https://openalex.org/I204250578","https://openalex.org/I32971472","https://openalex.org/I4210103836","https://openalex.org/I74973139","https://openalex.org/I84218800"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.0312,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.74638672,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"19","issue":"9","first_page":"e1011444","last_page":"e1011444"},"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9962999820709229,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9947999715805054,"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":0.6251873970031738},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5787067413330078},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5778520107269287},{"id":"https://openalex.org/keywords/graph-embedding","display_name":"Graph embedding","score":0.5406380295753479},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.5073665976524353},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4429943859577179},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4296224117279053},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4220011830329895},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4144488573074341},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.36160117387771606},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3308747708797455},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.23898649215698242},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15566304326057434}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6251873970031738},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5787067413330078},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5778520107269287},{"id":"https://openalex.org/C75564084","wikidata":"https://www.wikidata.org/wiki/Q5597085","display_name":"Graph embedding","level":3,"score":0.5406380295753479},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5073665976524353},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4429943859577179},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4296224117279053},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4220011830329895},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4144488573074341},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.36160117387771606},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3308747708797455},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.23898649215698242},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15566304326057434},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011340","descriptor_name":"Problem Solving","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011996","descriptor_name":"Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011996","descriptor_name":"Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011996","descriptor_name":"Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011996","descriptor_name":"Records","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1011444","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011444","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011444&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:37695793","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37695793","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:escholarship.org:ark:/13030/qt9cd5t02g","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/9cd5t02g","pdf_url":"https://escholarship.org/content/qt9cd5t02g/qt9cd5t02g.pdf","source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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":"PLoS Computational Biology, vol 19, iss 9","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10513318","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10513318","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10513318/pdf/pcbi.1011444.pdf","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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:ark:/13030/qt9cd5t02g","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1011444","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011444","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:f1fa8a0a4700406b85f458ebfaff7341","is_oa":true,"landing_page_url":"https://doaj.org/article/f1fa8a0a4700406b85f458ebfaff7341","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 19, Iss 9, p e1011444 (2023)","raw_type":"article"},{"id":"pmh:oai:figshare.com:article/29951540","is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/iHerd_an_integrative_hierarchical_graph_representation_learning_framework_to_quantify_network_changes_and_prioritize_risk_genes_in_disease/29951540","pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"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":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011444","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011444","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011444&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":[{"id":"https://metadata.un.org/sdg/17","score":0.4699999988079071,"display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G4423082541","display_name":null,"funder_award_id":"R01 NS128523","funder_id":"https://openalex.org/F4320337359","funder_display_name":"National Institute of Neurological Disorders and Stroke"},{"id":"https://openalex.org/G4902214262","display_name":null,"funder_award_id":"R01HG012572","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5050595528","display_name":null,"funder_award_id":"R01NS128523","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7046141272","display_name":null,"funder_award_id":"K01MH123896","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G747440273","display_name":null,"funder_award_id":"K01 MH123896","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G7571595803","display_name":null,"funder_award_id":"R01 HG012572","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"},{"id":"https://openalex.org/F4320337359","display_name":"National Institute of Neurological Disorders and Stroke","ror":"https://ror.org/01s5ya894"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4386615124.pdf","grobid_xml":"https://content.openalex.org/works/W4386615124.grobid-xml"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W1560916735","https://openalex.org/W1966327575","https://openalex.org/W1995193029","https://openalex.org/W2013326913","https://openalex.org/W2039032007","https://openalex.org/W2043191021","https://openalex.org/W2057069782","https://openalex.org/W2060705109","https://openalex.org/W2098598515","https://openalex.org/W2101296410","https://openalex.org/W2131681506","https://openalex.org/W2148253349","https://openalex.org/W2417483443","https://openalex.org/W2520902279","https://openalex.org/W2590269406","https://openalex.org/W2619332462","https://openalex.org/W2624431344","https://openalex.org/W2634894186","https://openalex.org/W2808087697","https://openalex.org/W2902709687","https://openalex.org/W2950177783","https://openalex.org/W2951659295","https://openalex.org/W2964912499","https://openalex.org/W3045759143","https://openalex.org/W3045979388","https://openalex.org/W3092003850","https://openalex.org/W3179318025","https://openalex.org/W3179788429","https://openalex.org/W3183416927","https://openalex.org/W3188894520","https://openalex.org/W3197477793","https://openalex.org/W3216781648","https://openalex.org/W4281778744","https://openalex.org/W4285728858","https://openalex.org/W4289835859","https://openalex.org/W4294558607","https://openalex.org/W4306391398","https://openalex.org/W6679686813","https://openalex.org/W6717041367"],"related_works":["https://openalex.org/W3036264823","https://openalex.org/W3206528106","https://openalex.org/W2912814903","https://openalex.org/W2123605750","https://openalex.org/W2088740331","https://openalex.org/W3038102983","https://openalex.org/W2950907416","https://openalex.org/W1559483280","https://openalex.org/W2082479932","https://openalex.org/W2932872266"],"abstract_inverted_index":{"Different":[0],"genes":[1,41,161,182,188,193],"form":[2],"complex":[3],"networks":[4],"within":[5,200,230],"cells":[6],"to":[7,34,117,177],"carry":[8],"out":[9],"critical":[10],"cellular":[11],"functions,":[12],"while":[13],"network":[14,36,75,180,196],"alterations":[15],"in":[16,70,112,162],"this":[17],"process":[18],"can":[19,154,211],"potentially":[20],"introduce":[21],"downstream":[22],"transcriptome":[23],"perturbations":[24],"and":[25,31,38,139,158,185,190,199,233],"phenotypic":[26],"variations.":[27],"Therefore,":[28],"developing":[29],"efficient":[30,98],"interpretable":[32],"methods":[33],"quantify":[35],"changes":[37,197],"pinpoint":[39,156],"driver":[40,123,181,208],"across":[42,198],"conditions":[43],"is":[44,220],"crucial.":[45],"We":[46,150],"propose":[47],"a":[48,57,65,71,119,134],"hierarchical":[49,95,173],"graph":[50,99,114,170],"representation":[51],"learning":[52,174],"method,":[53],"called":[54],"iHerd.":[55],"Given":[56],"set":[58],"of":[59,67,83,147],"networks,":[60],"iHerd":[61,102,132,153],"first":[62],"hierarchically":[63],"generates":[64],"series":[66],"coarsened":[68],"sub-graphs":[69],"data-driven":[72],"manner,":[73],"representing":[74],"modules":[76],"at":[77,93,223],"different":[78,163],"resolutions":[79],"(e.g.,":[80],"the":[81,108,148,231],"level":[82],"signaling":[84,201],"pathways).":[85],"Then,":[86],"it":[87],"sequentially":[88],"learns":[89],"low-dimensional":[90],"node":[91],"representations":[92],"all":[94],"levels":[96],"via":[97],"embedding.":[100],"Lastly,":[101],"projects":[103],"separate":[104],"gene":[105,124,209],"embeddings":[106],"onto":[107],"same":[109],"latent":[110],"space":[111],"its":[113,128],"alignment":[115],"module":[116],"calculate":[118],"rewiring":[120,137],"index":[121],"for":[122,172,207],"prioritization.":[125],"To":[126],"demonstrate":[127],"effectiveness,":[129],"we":[130],"applied":[131],"on":[133],"tumor-to-normal":[135],"GRN":[136],"analysis":[138,142],"cell-type-specific":[140],"GCN":[141],"using":[143],"single-cell":[144],"multiome":[145],"data":[146,228],"brain.":[149],"showed":[151],"that":[152],"effectively":[155],"novel":[157],"well-known":[159],"risk":[160],"diseases.":[164],"Distinct":[165],"from":[166],"existing":[167],"models,":[168],"iHerd's":[169],"coarsening":[171],"allows":[175],"us":[176,213],"successfully":[178],"classify":[179],"into":[183],"early":[184],"late":[186],"divergent":[187],"(EDGs":[189],"LDGs),":[191],"emphasizing":[192],"with":[194,214],"extensive":[195],"pathway":[202],"levels.":[203],"This":[204],"unique":[205],"approach":[206],"classification":[210],"provide":[212],"deeper":[215],"molecular":[216],"insights.":[217],"The":[218],"code":[219],"freely":[221],"available":[222],"https://github.com/aicb-ZhangLabs/iHerd.":[224],"All":[225],"other":[226],"relevant":[227],"are":[229],"manuscript":[232],"supporting":[234],"information":[235],"files.":[236]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":6}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
