{"id":"https://openalex.org/W7125374531","doi":"https://doi.org/10.1109/jbhi.2026.3656496","title":"An Explainable Molecular Token Estimation Method for Knowledge-Aware Drug-Drug Interaction Prediction","display_name":"An Explainable Molecular Token Estimation Method for Knowledge-Aware Drug-Drug Interaction Prediction","publication_year":2026,"publication_date":"2026-01-21","ids":{"openalex":"https://openalex.org/W7125374531","doi":"https://doi.org/10.1109/jbhi.2026.3656496","pmid":"https://pubmed.ncbi.nlm.nih.gov/41564067"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2026.3656496","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2026.3656496","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/A5123600413","display_name":"Hui Yu","orcid":null},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hui Yu","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi’an, China"],"raw_orcid":"https://orcid.org/0000-0002-5314-8127","affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi’an, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123543719","display_name":"Chao Song","orcid":null},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chao Song","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi’an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi’an, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102975434","display_name":"Jiahao Yuan","orcid":"https://orcid.org/0009-0007-7808-2068"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiahao Yuan","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi’an, China"],"raw_orcid":"https://orcid.org/0009-0009-4820-9210","affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi’an, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028985861","display_name":"Xinkun Li","orcid":null},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinkun Li","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi’an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi’an, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123611132","display_name":"Xiao Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiao Zhang","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi’an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi’an, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123626186","display_name":"Yang Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210107780","display_name":"Xi'an Medical University","ror":"https://ror.org/01fmc2233","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210107780"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Yang","raw_affiliation_strings":["School of Pharmacy, Xi’an Medical University, Xi’an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pharmacy, Xi’an Medical University, Xi’an, China","institution_ids":["https://openalex.org/I4210107780"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063672612","display_name":"Zhe Yu","orcid":"https://orcid.org/0009-0009-1370-6954"},"institutions":[{"id":"https://openalex.org/I4210154136","display_name":"Tang Du Hospital","ror":"https://ror.org/04yvdan45","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210154136"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhe Yu","raw_affiliation_strings":["Department of Orthopedic Surgery, Orthopedics Oncology Institute of Chinese PLA, Tangdu Hospital, Air Force Military Medical University, Xi’an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Orthopedic Surgery, Orthopedics Oncology Institute of Chinese PLA, Tangdu Hospital, Air Force Military Medical University, Xi’an, China","institution_ids":["https://openalex.org/I4210154136"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000609872","display_name":"Jian\u2010Yu Shi","orcid":"https://orcid.org/0000-0002-2303-273X"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian-Yu Shi","raw_affiliation_strings":["School of Life Sciences, Northwestern Polytechnical University, Xi’an, China"],"raw_orcid":"https://orcid.org/0000-0002-2303-273X","affiliations":[{"raw_affiliation_string":"School of Life Sciences, Northwestern Polytechnical University, Xi’an, China","institution_ids":["https://openalex.org/I17145004"]}]}],"institutions":[],"countries_distinct_count":1,"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":0.116889,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"30","issue":"6","first_page":"4907","last_page":"4919"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.8723999857902527,"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":0.8723999857902527,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.0820000022649765,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.016899999231100082,"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/security-token","display_name":"Security token","score":0.7253000140190125},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6211000084877014},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.5773000121116638},{"id":"https://openalex.org/keywords/expressive-power","display_name":"Expressive power","score":0.4700999855995178},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.46160000562667847},{"id":"https://openalex.org/keywords/upper-and-lower-bounds","display_name":"Upper and lower bounds","score":0.44609999656677246},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4187999963760376},{"id":"https://openalex.org/keywords/axiom","display_name":"Axiom","score":0.38769999146461487},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.3799999952316284}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8108999729156494},{"id":"https://openalex.org/C48145219","wikidata":"https://www.wikidata.org/wiki/Q1335365","display_name":"Security token","level":2,"score":0.7253000140190125},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.6241000294685364},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6211000084877014},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.5773000121116638},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.48159998655319214},{"id":"https://openalex.org/C195818886","wikidata":"https://www.wikidata.org/wiki/Q5421724","display_name":"Expressive power","level":2,"score":0.4700999855995178},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.46160000562667847},{"id":"https://openalex.org/C77553402","wikidata":"https://www.wikidata.org/wiki/Q13222579","display_name":"Upper and lower bounds","level":2,"score":0.44609999656677246},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4187999963760376},{"id":"https://openalex.org/C167729594","wikidata":"https://www.wikidata.org/wiki/Q17736","display_name":"Axiom","level":2,"score":0.38769999146461487},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.3799999952316284},{"id":"https://openalex.org/C2780586882","wikidata":"https://www.wikidata.org/wiki/Q7520643","display_name":"Simple (philosophy)","level":2,"score":0.35659998655319214},{"id":"https://openalex.org/C75564084","wikidata":"https://www.wikidata.org/wiki/Q5597085","display_name":"Graph embedding","level":3,"score":0.33160001039505005},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.3237000107765198},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3188000023365021},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3140999972820282},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.31349998712539673},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.29910001158714294},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.29750001430511475},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.2935999929904938},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.2930999994277954},{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.2892000079154968},{"id":"https://openalex.org/C100776233","wikidata":"https://www.wikidata.org/wiki/Q2532492","display_name":"Bridge (graph theory)","level":2,"score":0.2786000072956085},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.27140000462532043},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.2597000002861023},{"id":"https://openalex.org/C2777462759","wikidata":"https://www.wikidata.org/wiki/Q18395344","display_name":"Word embedding","level":3,"score":0.25029999017715454}],"mesh":[{"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":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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/jbhi.2026.3656496","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2026.3656496","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:41564067","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41564067","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":[{"score":0.43696320056915283,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G4276050119","display_name":null,"funder_award_id":"62372375","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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"In":[0],"molecular":[1,37,62],"representation":[2],"learning(MRL),":[3],"tokens":[4,25,44,95],"(e.g.,":[5],"atoms,":[6],"motifs,":[7],"and":[8,96,130,151,173],"fingerprints)":[9],"are":[10],"the":[11,28,53,56,59,69,85,92,153,165,175],"basic":[12],"elements":[13],"to":[14,26,91,136,147,164],"represent":[15],"molecules.":[16],"It":[17],"is":[18,88,144],"a":[19,79,98,113,125,132],"common":[20],"practice":[21],"by":[22],"using":[23],"various":[24,191],"enhance":[27],"expressive":[29],"power":[30],"of":[31,55,61,76,94,102,127,155,178],"Graph":[32],"Neural":[33],"Networks":[34],"(GNNs)":[35],"on":[36,58,107,190],"graphs.":[38],"Although":[39],"prior":[40],"GNNs-based":[41],"methods":[42],"employing":[43],"achieve":[45],"promising":[46],"performances":[47],"in":[48,168],"drug-drug":[49],"interaction":[50],"(DDI)":[51],"prediction,":[52],"influence":[54],"token":[57],"expressiveness":[60],"embedding":[63],"models":[64],"remains":[65],"underexplored.":[66],"To":[67],"bridge":[68],"gap,":[70],"we":[71,110,159],"provide":[72],"an":[73],"axiomatic":[74],"definition":[75],"MRL":[77],"from":[78],"frequency":[80],"domain":[81],"perspective,":[82],"revealing":[83],"that":[84,161],"model's":[86],"performance":[87,189],"closely":[89],"related":[90],"number":[93],"deriving":[97],"theoretical":[99,170],"upper":[100,171],"bound":[101,172],"likelihood-based":[103],"model":[104],"convergency.":[105],"Building":[106],"these":[108],"insights,":[109],"propose":[111],"SimMotifPro,":[112],"simple":[114],"yet":[115],"efficient":[116],"motif-based":[117],"method,":[118],"for":[119,193],"DDI":[120,194],"prediction.":[121,195],"Specifically,":[122],"SimMotifPro":[123,162],"uses":[124],"variant":[126],"DeeperGCN":[128],"encoder":[129],"builds":[131],"motif-motif":[133],"knowledge":[134],"graph":[135],"capture":[137],"motif":[138],"interconnections.":[139],"A":[140],"Motif":[141],"Ranker":[142],"module":[143],"also":[145],"introduced":[146],"decouple":[148],"learned":[149],"representations":[150],"differentiate":[152],"contributions":[154],"selected":[156],"motifs.":[157],"Empirically,":[158],"demonstrate":[160],"adheres":[163],"properties":[166],"demonstrated":[167],"our":[169,179,185],"validate":[174],"general":[176],"applicability":[177],"theory":[180],"across":[181],"different":[182],"methods.":[183],"Furthermore,":[184],"approach":[186],"achieves":[187],"state-of-the-art":[188],"benchmarks":[192]},"counts_by_year":[],"updated_date":"2026-06-06T06:22:57.294733","created_date":"2026-01-23T00:00:00"}