{"id":"https://openalex.org/W4408323919","doi":"https://doi.org/10.1109/jbhi.2025.3550353","title":"ExplainMIX: Explaining Drug Response Prediction in Directed Graph Neural Networks With Multi-Omics Fusion","display_name":"ExplainMIX: Explaining Drug Response Prediction in Directed Graph Neural Networks With Multi-Omics Fusion","publication_year":2025,"publication_date":"2025-03-11","ids":{"openalex":"https://openalex.org/W4408323919","doi":"https://doi.org/10.1109/jbhi.2025.3550353","pmid":"https://pubmed.ncbi.nlm.nih.gov/40067713"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2025.3550353","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3550353","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"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 Journal of Biomedical and Health Informatics","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/A5001963009","display_name":"Ying Xiang","orcid":"https://orcid.org/0009-0004-8560-271X"},"institutions":[{"id":"https://openalex.org/I140221134","display_name":"Anhui Agricultural University","ror":"https://ror.org/0327f3359","country_code":"CN","type":"education","lineage":["https://openalex.org/I140221134"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying Xiang","raw_affiliation_strings":["School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, China","School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, China"],"raw_orcid":"https://orcid.org/0009-0004-8560-271X","affiliations":[{"raw_affiliation_string":"School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, China","institution_ids":["https://openalex.org/I140221134"]},{"raw_affiliation_string":"School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, China","institution_ids":["https://openalex.org/I140221134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100755097","display_name":"Xiaodi Li","orcid":"https://orcid.org/0000-0001-5124-7159"},"institutions":[{"id":"https://openalex.org/I140221134","display_name":"Anhui Agricultural University","ror":"https://ror.org/0327f3359","country_code":"CN","type":"education","lineage":["https://openalex.org/I140221134"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaodi Li","raw_affiliation_strings":["School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, China","School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, China","institution_ids":["https://openalex.org/I140221134"]},{"raw_affiliation_string":"School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, China","institution_ids":["https://openalex.org/I140221134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053984606","display_name":"Qian Gao","orcid":"https://orcid.org/0000-0003-1784-8991"},"institutions":[{"id":"https://openalex.org/I140221134","display_name":"Anhui Agricultural University","ror":"https://ror.org/0327f3359","country_code":"CN","type":"education","lineage":["https://openalex.org/I140221134"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qian Gao","raw_affiliation_strings":["School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, China","School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, China","institution_ids":["https://openalex.org/I140221134"]},{"raw_affiliation_string":"School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, China","institution_ids":["https://openalex.org/I140221134"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065943710","display_name":"Junfeng Xia","orcid":"https://orcid.org/0000-0003-3024-1705"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]},{"id":"https://openalex.org/I2802624667","display_name":"Hefei Institutes of Physical Science","ror":"https://ror.org/046n57345","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I2802624667"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junfeng Xia","raw_affiliation_strings":["Institutes of Physical Science and Information Technology, Anhui University, Hefei, China","Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China"],"raw_orcid":"https://orcid.org/0000-0003-3024-1705","affiliations":[{"raw_affiliation_string":"Institutes of Physical Science and Information Technology, Anhui University, Hefei, China","institution_ids":["https://openalex.org/I143868143","https://openalex.org/I2802624667"]},{"raw_affiliation_string":"Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044447237","display_name":"Zhenyu Yue","orcid":"https://orcid.org/0000-0002-9370-2540"},"institutions":[{"id":"https://openalex.org/I140221134","display_name":"Anhui Agricultural University","ror":"https://ror.org/0327f3359","country_code":"CN","type":"education","lineage":["https://openalex.org/I140221134"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenyu Yue","raw_affiliation_strings":["School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, China","School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, China"],"raw_orcid":"https://orcid.org/0000-0002-9370-2540","affiliations":[{"raw_affiliation_string":"School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, China","institution_ids":["https://openalex.org/I140221134"]},{"raw_affiliation_string":"School of Information and Artificial Intelligence, Anhui Agricultural University, Hefei, Anhui, China","institution_ids":["https://openalex.org/I140221134"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":6.2173,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.9662836,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"29","issue":"7","first_page":"5339","last_page":"5349"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9984999895095825,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9929999709129333,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9902999997138977,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials 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":0.6601462960243225},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.5233603715896606},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5054008960723877},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4515867829322815},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4123288691043854},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3403937816619873},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.1521053910255432}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6601462960243225},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.5233603715896606},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5054008960723877},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4515867829322815},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4123288691043854},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3403937816619873},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.1521053910255432}],"mesh":[{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","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":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":true},{"descriptor_ui":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":true},{"descriptor_ui":"D000970","descriptor_name":"Antineoplastic Agents","qualifier_ui":"Q000627","qualifier_name":"therapeutic use","is_major_topic":true},{"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000188","qualifier_name":"drug therapy","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055432","descriptor_name":"Metabolomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D057285","descriptor_name":"Precision Medicine","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2025.3550353","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3550353","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"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 Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:40067713","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40067713","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 journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2543759693","display_name":null,"funder_award_id":"62472005","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6253636927","display_name":null,"funder_award_id":"62102004","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1987219048","https://openalex.org/W2058867629","https://openalex.org/W2075010670","https://openalex.org/W2108933868","https://openalex.org/W2116341502","https://openalex.org/W2152883907","https://openalex.org/W2159887157","https://openalex.org/W2432718434","https://openalex.org/W2461427403","https://openalex.org/W2507626327","https://openalex.org/W2536263232","https://openalex.org/W2604314403","https://openalex.org/W2742007096","https://openalex.org/W2770428174","https://openalex.org/W2770664828","https://openalex.org/W2777794149","https://openalex.org/W2807021761","https://openalex.org/W2911286998","https://openalex.org/W2944727022","https://openalex.org/W2950063908","https://openalex.org/W2955502047","https://openalex.org/W2970726176","https://openalex.org/W3000469142","https://openalex.org/W3014569644","https://openalex.org/W3044334750","https://openalex.org/W3080922200","https://openalex.org/W3124474911","https://openalex.org/W3130891725","https://openalex.org/W3192677404","https://openalex.org/W3194668998","https://openalex.org/W3198971962","https://openalex.org/W4205156191","https://openalex.org/W4292723103","https://openalex.org/W4296480486","https://openalex.org/W4297387432","https://openalex.org/W4300862723","https://openalex.org/W4312214400","https://openalex.org/W4317493085","https://openalex.org/W4319731255","https://openalex.org/W4383340501","https://openalex.org/W4386046819","https://openalex.org/W6679434410","https://openalex.org/W6762415773","https://openalex.org/W6767229288","https://openalex.org/W6767288045","https://openalex.org/W6786048916","https://openalex.org/W6810583929","https://openalex.org/W6843289217"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W3046775127","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474"],"abstract_inverted_index":{"The":[0],"intricacies":[1],"of":[2,58,136,144,179],"cancer":[3],"present":[4],"formidable":[5],"challenges":[6,169],"in":[7,14,133,146,170],"achieving":[8,21],"effective":[9],"treatments.":[10],"Despite":[11],"extensive":[12],"research":[13,166],"computational":[15],"methods":[16],"for":[17],"drug":[18,78,127,173],"response":[19,174],"prediction,":[20],"personalized":[22,172],"treatment":[23],"insights":[24,123],"remains":[25],"challenging.":[26],"Emerging":[27],"solutions":[28],"combine":[29],"multiple":[30],"omics":[31],"data,":[32],"leveraging":[33,93],"graph":[34,73,117],"neural":[35,74],"networks":[36,75],"to":[37,76,161,163],"integrate":[38],"molecular":[39],"interactions":[40],"into":[41,124],"the":[42,56,134,142,177],"reasoning":[43],"process.":[44],"However,":[45],"effectively":[46],"modeling":[47],"and":[48,87,101,110,116,131,148],"harnessing":[49],"this":[50],"information,":[51,119],"as":[52,54,98],"well":[53],"gaining":[55],"trust":[57],"clinical":[59],"professionals":[60],"remain":[61],"complex.":[62],"This":[63,158],"paper":[64],"introduces":[65],"ExplainMIX,":[66],"a":[67,153],"pioneering":[68],"approach":[69,159],"that":[70],"utilizes":[71],"directed":[72,90],"predict":[77],"responses":[79],"with":[80],"interpretability.":[81],"ExplainMIX":[82,103,145],"adeptly":[83],"captures":[84],"intricate":[85],"structures":[86],"features":[88],"within":[89,176],"heterogeneous":[91],"graphs,":[92],"diverse":[94],"data":[95],"modalities":[96],"such":[97],"genomics,":[99],"proteomics,":[100],"metabolomics.":[102],"goes":[104],"beyond":[105],"prediction":[106,147,175],"by":[107,151,167],"generating":[108],"transparent":[109],"interpretable":[111,171],"explanations.":[112],"Incorporating":[113],"edge-level,":[114],"meta-path,":[115],"structure":[118],"it":[120],"provides":[121],"meaningful":[122],"factors":[125],"influencing":[126],"response,":[128],"supporting":[129],"clinicians":[130],"researchers":[132],"development":[135],"targeted":[137],"therapies.":[138],"Empirical":[139],"results":[140],"validate":[141],"efficacy":[143],"interpretation":[149],"tasks":[150],"constructing":[152],"quantitative":[154],"evaluation":[155],"ground":[156],"truth.":[157],"aims":[160],"contribute":[162],"precision":[164],"medicine":[165],"addressing":[168],"landscape":[178],"cancer.":[180]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
