{"id":"https://openalex.org/W4412795613","doi":"https://doi.org/10.1109/tcbbio.2025.3593917","title":"DGX: Uncovering General Behavior of Deep Graph Models With Model-Level Explanation","display_name":"DGX: Uncovering General Behavior of Deep Graph Models With Model-Level Explanation","publication_year":2025,"publication_date":"2025-07-31","ids":{"openalex":"https://openalex.org/W4412795613","doi":"https://doi.org/10.1109/tcbbio.2025.3593917","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811177"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3593917","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3593917","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042282783","display_name":"Jinlong Hu","orcid":"https://orcid.org/0000-0003-3602-7603"},"institutions":[{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jinlong Hu","raw_affiliation_strings":["Guangdong Provincial Key Laboratory of Multimodal Big Data Intelligent Analysis, School of Computer Science and Engineering, South China University of Technology, Guangzhou, China"],"raw_orcid":"https://orcid.org/0000-0003-3602-7603","affiliations":[{"raw_affiliation_string":"Guangdong Provincial Key Laboratory of Multimodal Big Data Intelligent Analysis, School of Computer Science and Engineering, South China University of Technology, Guangzhou, China","institution_ids":["https://openalex.org/I90610280"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100656307","display_name":"Jiacheng Liu","orcid":"https://orcid.org/0000-0003-0378-2311"},"institutions":[{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiacheng Liu","raw_affiliation_strings":["Guangdong Provincial Key Laboratory of Multimodal Big Data Intelligent Analysis, School of Computer Science and Engineering, South China University of Technology, Guangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Guangdong Provincial Key Laboratory of Multimodal Big Data Intelligent Analysis, School of Computer Science and Engineering, South China University of Technology, Guangzhou, China","institution_ids":["https://openalex.org/I90610280"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052760299","display_name":"Shoubin Dong","orcid":"https://orcid.org/0000-0003-0153-850X"},"institutions":[{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shoubin Dong","raw_affiliation_strings":["Guangdong Provincial Key Laboratory of Multimodal Big Data Intelligent Analysis, School of Computer Science and Engineering, South China University of Technology, Guangzhou, China"],"raw_orcid":"https://orcid.org/0000-0003-0153-850X","affiliations":[{"raw_affiliation_string":"Guangdong Provincial Key Laboratory of Multimodal Big Data Intelligent Analysis, School of Computer Science and Engineering, South China University of Technology, Guangzhou, China","institution_ids":["https://openalex.org/I90610280"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102928078","display_name":"Bin Liao","orcid":"https://orcid.org/0000-0003-3422-9092"},"institutions":[{"id":"https://openalex.org/I101479585","display_name":"South China Agricultural University","ror":"https://ror.org/05v9jqt67","country_code":"CN","type":"education","lineage":["https://openalex.org/I101479585"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bin Liao","raw_affiliation_strings":["College of Mathematics and Informatics, South China Agricultural University, Guangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Mathematics and Informatics, South China Agricultural University, Guangzhou, China","institution_ids":["https://openalex.org/I101479585"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101484374","display_name":"Junjie Liang","orcid":"https://orcid.org/0000-0001-6322-2231"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Junjie Liang","raw_affiliation_strings":["College of Information Sciences and Technology, Pennsylvania State University, University Park, PA, USA","College of Information Sciences and Technology, Pennsylvania State University, PA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Sciences and Technology, Pennsylvania State University, University Park, PA, USA","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"College of Information Sciences and Technology, Pennsylvania State University, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5004737962","display_name":"Vasant Honavar","orcid":"https://orcid.org/0000-0001-5399-3489"},"institutions":[{"id":"https://openalex.org/I130769515","display_name":"Pennsylvania State University","ror":"https://ror.org/04p491231","country_code":"US","type":"education","lineage":["https://openalex.org/I130769515"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vasant Honavar","raw_affiliation_strings":["College of Information Sciences and Technology, Pennsylvania State University, University Park, PA, USA","College of Information Sciences and Technology, Pennsylvania State University, PA, USA"],"raw_orcid":"https://orcid.org/0000-0001-5399-3489","affiliations":[{"raw_affiliation_string":"College of Information Sciences and Technology, Pennsylvania State University, University Park, PA, USA","institution_ids":["https://openalex.org/I130769515"]},{"raw_affiliation_string":"College of Information Sciences and Technology, Pennsylvania State University, PA, USA","institution_ids":["https://openalex.org/I130769515"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07106616,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"6","first_page":"2503","last_page":"2514"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11273","display_name":"Advanced Graph Neural Networks","score":0.9934999942779541,"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"}},"topics":[{"id":"https://openalex.org/T11273","display_name":"Advanced Graph Neural Networks","score":0.9934999942779541,"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/T12292","display_name":"Graph Theory and Algorithms","score":0.98580002784729,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"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/T11303","display_name":"Bayesian Modeling and Causal Inference","score":0.9657999873161316,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4878135025501251},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4739168584346771},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.25758540630340576}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4878135025501251},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4739168584346771},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.25758540630340576}],"mesh":[{"descriptor_ui":"D000067877","descriptor_name":"Autism Spectrum Disorder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000067877","descriptor_name":"Autism Spectrum Disorder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000067877","descriptor_name":"Autism Spectrum Disorder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000000981","qualifier_name":"diagnostic imaging","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D001921","descriptor_name":"Brain","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3593917","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3593917","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043","2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811177","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811177","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Climate action","id":"https://metadata.un.org/sdg/13","score":0.44999998807907104}],"awards":[{"id":"https://openalex.org/G499109307","display_name":null,"funder_award_id":"2025A1515011595","funder_id":"https://openalex.org/F4320321921","funder_display_name":"Natural Science Foundation of Guangdong Province"},{"id":"https://openalex.org/G7900852019","display_name":null,"funder_award_id":"2021A1515011942","funder_id":"https://openalex.org/F4320321921","funder_display_name":"Natural Science Foundation of Guangdong Province"}],"funders":[{"id":"https://openalex.org/F4320321921","display_name":"Natural Science Foundation of Guangdong Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":59,"referenced_works":["https://openalex.org/W1492230849","https://openalex.org/W1977340881","https://openalex.org/W2005821483","https://openalex.org/W2008857988","https://openalex.org/W2011350023","https://openalex.org/W2027264060","https://openalex.org/W2027945080","https://openalex.org/W2046938271","https://openalex.org/W2054203041","https://openalex.org/W2058046532","https://openalex.org/W2066532920","https://openalex.org/W2089572795","https://openalex.org/W2126811106","https://openalex.org/W2142732317","https://openalex.org/W2146406922","https://openalex.org/W2146584320","https://openalex.org/W2158200838","https://openalex.org/W2158804744","https://openalex.org/W2162232298","https://openalex.org/W2165246411","https://openalex.org/W2167868121","https://openalex.org/W2907492528","https://openalex.org/W2915130814","https://openalex.org/W2920200623","https://openalex.org/W2925177113","https://openalex.org/W2979481854","https://openalex.org/W2981731882","https://openalex.org/W2987509417","https://openalex.org/W3000120900","https://openalex.org/W3011667710","https://openalex.org/W3033892090","https://openalex.org/W3081295916","https://openalex.org/W3089930297","https://openalex.org/W3093687066","https://openalex.org/W3116239416","https://openalex.org/W3116637551","https://openalex.org/W3136405090","https://openalex.org/W3157427301","https://openalex.org/W3157999218","https://openalex.org/W3165031368","https://openalex.org/W3169752883","https://openalex.org/W3183761761","https://openalex.org/W3188579603","https://openalex.org/W4205692950","https://openalex.org/W4292982348","https://openalex.org/W4298363619","https://openalex.org/W4307717106","https://openalex.org/W4321350922","https://openalex.org/W4321485347","https://openalex.org/W4367043603","https://openalex.org/W4372330430","https://openalex.org/W4382318226","https://openalex.org/W4385287631","https://openalex.org/W4386147931","https://openalex.org/W4387934986","https://openalex.org/W4389991855","https://openalex.org/W4391582491","https://openalex.org/W4392405811","https://openalex.org/W4401494458"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Deep":[0],"graph":[1,35,40,56,68,87,95,190],"learning":[2],"models":[3,41,186],"have":[4],"recently":[5],"been":[6],"developed":[7],"to":[8,63,127,159,176],"learn":[9],"from":[10,164,188],"various":[11],"graphs":[12,62,77,109],"that":[13,37,59,78,155],"are":[14],"prevalent":[15],"in":[16,24,42,193],"describing":[17],"and":[18,93,110,141,173,181,198],"modeling":[19],"complex":[20],"systems,":[21],"including":[22],"those":[23],"bioinformatics.":[25,199],"However,":[26],"a":[27,53,105,129],"versatile":[28],"explanation":[29],"method":[30],"for":[31],"uncovering":[32],"the":[33,81,86,135,144,152,157,178,183],"general":[34],"patterns":[36,154],"guide":[38],"deep":[39,55,67],"making":[43],"predictions":[44],"remains":[45],"elusive.":[46],"In":[47],"this":[48],"paper,":[49],"we":[50,142],"propose":[51],"DGX,":[52],"novel":[54],"model":[57,132,145,158],"explainer":[58],"generates":[60],"explanatory":[61],"explain":[64,128,143],"trained,":[65],"opaque-box":[66],"models.":[69],"Its":[70],"effectiveness":[71],"is":[72],"demonstrated":[73],"by":[74,85,103,122,133,150],"producing":[75],"multiple":[76],"collectively":[79],"encode":[80],"structural":[82,153],"knowledge":[83,118],"captured":[84],"neural":[88],"network":[89],"on":[90,116,146],"both":[91],"synthetic":[92],"real":[94,189],"data.":[96],"Importantly,":[97],"DGX":[98,126],"can":[99,111],"produce":[100],"diverse":[101],"explanations":[102,114],"generating":[104],"set":[106],"of":[107,138,185],"distinguishable":[108],"provide":[112],"customized":[113,174],"based":[115],"prior":[117],"or":[119],"constraints":[120],"specified":[121],"users.":[123],"We":[124],"apply":[125],"mutagenicity":[130],"prediction":[131],"exploring":[134],"underlying":[136,179],"groups":[137],"mutagenic":[139],"compounds,":[140],"brain":[147],"functional":[148],"networks":[149],"revealing":[151],"enable":[156],"differentiate":[160],"autism":[161],"spectrum":[162],"disorder":[163],"healthy":[165],"controls.":[166],"These":[167],"findings":[168],"offer":[169],"an":[170],"effective,":[171],"diverse,":[172],"approach":[175],"explaining":[177],"mechanisms":[180],"enhancing":[182],"understanding":[184],"learned":[187],"data,":[191],"particularly":[192],"fields":[194],"such":[195],"as":[196],"biomedicine":[197]},"counts_by_year":[],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
