{"id":"https://openalex.org/W4411010383","doi":"https://doi.org/10.1186/s12859-025-06157-6","title":"HLN-DDI: hierarchical molecular representation learning with co-attention mechanism for drug-drug interaction prediction","display_name":"HLN-DDI: hierarchical molecular representation learning with co-attention mechanism for drug-drug interaction prediction","publication_year":2025,"publication_date":"2025-06-04","ids":{"openalex":"https://openalex.org/W4411010383","doi":"https://doi.org/10.1186/s12859-025-06157-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/40468206"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06157-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06157-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06157-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06157-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103658110","display_name":"Luo Yue","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yue Luo","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085608332","display_name":"Lei Deng","orcid":"https://orcid.org/0000-0003-2869-1619"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Lei Deng","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, China. leideng@csu.edu.cn"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, China. leideng@csu.edu.cn","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051404499","display_name":"Zhijian Huang","orcid":"https://orcid.org/0000-0002-8241-0761"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhijian Huang","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University, Changsha, China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5103658110"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.3746,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.82857361,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"26","issue":"1","first_page":"152","last_page":"152"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"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":1.0,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9890999794006348,"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":0.9876000285148621,"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/drug","display_name":"Drug","score":0.7872999310493469},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.7094264030456543},{"id":"https://openalex.org/keywords/drug-drug-interaction","display_name":"Drug-drug interaction","score":0.6718129515647888},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.567561686038971},{"id":"https://openalex.org/keywords/drug-target","display_name":"Drug target","score":0.5645901560783386},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5593979358673096},{"id":"https://openalex.org/keywords/drug-interaction","display_name":"Drug interaction","score":0.45843157172203064},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.45704442262649536},{"id":"https://openalex.org/keywords/drug-repositioning","display_name":"Drug repositioning","score":0.4195113778114319},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4167254865169525},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3429816961288452},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.28060251474380493},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2542228102684021},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16960620880126953},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09039583802223206},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.06363481283187866}],"concepts":[{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.7872999310493469},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.7094264030456543},{"id":"https://openalex.org/C2910466267","wikidata":"https://www.wikidata.org/wiki/Q718753","display_name":"Drug-drug interaction","level":3,"score":0.6718129515647888},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.567561686038971},{"id":"https://openalex.org/C2989108626","wikidata":"https://www.wikidata.org/wiki/Q904407","display_name":"Drug target","level":2,"score":0.5645901560783386},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5593979358673096},{"id":"https://openalex.org/C97320921","wikidata":"https://www.wikidata.org/wiki/Q718753","display_name":"Drug interaction","level":3,"score":0.45843157172203064},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.45704442262649536},{"id":"https://openalex.org/C103637391","wikidata":"https://www.wikidata.org/wiki/Q5308921","display_name":"Drug repositioning","level":3,"score":0.4195113778114319},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4167254865169525},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3429816961288452},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.28060251474380493},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2542228102684021},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16960620880126953},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09039583802223206},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.06363481283187866},{"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},{"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/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"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":"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":"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":"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},{"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":4,"locations":[{"id":"doi:10.1186/s12859-025-06157-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06157-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06157-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40468206","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40468206","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:71020640ab1e4fe2a261a0f4efa4250e","is_oa":true,"landing_page_url":"https://doaj.org/article/71020640ab1e4fe2a261a0f4efa4250e","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-17 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:10948748","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12135231","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06157-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06157-6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06157-6","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1231421488","display_name":null,"funder_award_id":"under","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2008773563","display_name":null,"funder_award_id":"62272490","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G508633068","display_name":null,"funder_award_id":"U23A2032","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5299854802","display_name":null,"funder_award_id":"U23A20321","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6676365692","display_name":null,"funder_award_id":"U23A203","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7610172040","display_name":null,"funder_award_id":"No. 62272490","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8863666567","display_name":null,"funder_award_id":"and No.","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"},{"id":"https://openalex.org/F4320321514","display_name":"Central South University","ror":"https://ror.org/00f1zfq44"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4411010383.pdf","grobid_xml":"https://content.openalex.org/works/W4411010383.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1924938698","https://openalex.org/W1975147762","https://openalex.org/W1981276685","https://openalex.org/W1992475241","https://openalex.org/W2022476850","https://openalex.org/W2031932867","https://openalex.org/W2036291018","https://openalex.org/W2061075125","https://openalex.org/W2116877707","https://openalex.org/W2119002393","https://openalex.org/W2151357092","https://openalex.org/W2165863045","https://openalex.org/W2283196293","https://openalex.org/W2561981131","https://openalex.org/W2767891136","https://openalex.org/W2786016794","https://openalex.org/W2907492528","https://openalex.org/W2945591540","https://openalex.org/W3044296243","https://openalex.org/W3096561213","https://openalex.org/W3102794373","https://openalex.org/W3104426963","https://openalex.org/W3121015296","https://openalex.org/W3152893301","https://openalex.org/W3157889929","https://openalex.org/W3208102118","https://openalex.org/W4285165731","https://openalex.org/W4285794944","https://openalex.org/W4295105988","https://openalex.org/W4306317062","https://openalex.org/W4313405519","https://openalex.org/W4318150241","https://openalex.org/W4318952048","https://openalex.org/W4321227311","https://openalex.org/W6640416549","https://openalex.org/W6736685754","https://openalex.org/W6745537798"],"related_works":["https://openalex.org/W4319455836","https://openalex.org/W2558461040","https://openalex.org/W4393906247","https://openalex.org/W4402504391","https://openalex.org/W2144815258","https://openalex.org/W3082755771","https://openalex.org/W2782683161","https://openalex.org/W4240902522","https://openalex.org/W1480660337","https://openalex.org/W2912785940"],"abstract_inverted_index":{"By":[0],"leveraging":[1],"hierarchical":[2],"molecular":[3],"structures":[4],"and":[5,18],"employing":[6],"a":[7],"co-attention":[8],"mechanism":[9],"to":[10,23],"effectively":[11],"integrate":[12],"multi-level":[13],"representations,":[14,21],"HLN-DDI":[15],"generates":[16],"comprehensive":[17],"precise":[19],"drug":[20],"leading":[22],"substantially":[24],"improved":[25],"predictions":[26],"of":[27],"potential":[28],"drug-drug":[29],"interactions.":[30]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}
