{"id":"https://openalex.org/W7126046341","doi":"https://doi.org/10.1109/bibm66473.2025.11356758","title":"DPAT: Dual-Path Alignment Transformer for Enhanced miRNA-mRNA Target Prediction via Cross-Modal Fusion","display_name":"DPAT: Dual-Path Alignment Transformer for Enhanced miRNA-mRNA Target Prediction via Cross-Modal Fusion","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126046341","doi":"https://doi.org/10.1109/bibm66473.2025.11356758"},"language":"en","primary_location":{"id":"doi:10.1109/bibm66473.2025.11356758","doi":"https://doi.org/10.1109/bibm66473.2025.11356758","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356758","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"volume":null,"type":"conference-paper","indexed_in":["crossref"],"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/A5113318183","display_name":"Shanruo Xu","orcid":"https://orcid.org/0009-0007-6416-8231","observed_orcids":["https://orcid.org/0009-0007-6416-8231"]},"institutions":[{"id":"https://openalex.org/I4210159968","display_name":"Duke Kunshan University","ror":"https://ror.org/04sr5ys16","country_code":"CN","type":"education","lineage":["https://openalex.org/I170897317","https://openalex.org/I37461747","https://openalex.org/I4210159968"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shanruo Xu","raw_affiliation_strings":["Applied Mathematics and Computational Sciences/Computer Science Duke Kunshan University,Kunshan,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Applied Mathematics and Computational Sciences/Computer Science Duke Kunshan University,Kunshan,China","institution_ids":["https://openalex.org/I4210159968"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5157049106","display_name":"Runkun Guo","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Runkun Guo","raw_affiliation_strings":["Boston University,Department of Mathematics and Statistics,Boston,MA,USA,02215"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Boston University,Department of Mathematics and Statistics,Boston,MA,USA,02215","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072005545","display_name":"Julio E. Castrill\u00f3n-Cand\u00e1s","orcid":"https://orcid.org/0000-0002-7913-8840","observed_orcids":["https://orcid.org/0000-0002-7913-8840"]},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Julio Castrillon","raw_affiliation_strings":["Boston University,Department of Mathematics and Statistics,Boston,MA,USA,02215"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Boston University,Department of Mathematics and Statistics,Boston,MA,USA,02215","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038318511","display_name":"Han Li","orcid":"https://orcid.org/0000-0003-2298-332X","observed_orcids":["https://orcid.org/0000-0003-2298-332X"]},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Han Li","raw_affiliation_strings":["Boston University,Department of Computer Science,Boston,MA,USA,02215"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Boston University,Department of Computer Science,Boston,MA,USA,02215","institution_ids":["https://openalex.org/I111088046"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070448763","display_name":"Mark Kon","orcid":"https://orcid.org/0000-0001-5902-9412","observed_orcids":["https://orcid.org/0000-0001-5902-9412"]},"institutions":[{"id":"https://openalex.org/I111088046","display_name":"Boston University","ror":"https://ror.org/05qwgg493","country_code":"US","type":"education","lineage":["https://openalex.org/I111088046"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark Kon","raw_affiliation_strings":["Boston University,Department of Mathematics and Statistics,Boston,MA,USA,02215"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Boston University,Department of Mathematics and Statistics,Boston,MA,USA,02215","institution_ids":["https://openalex.org/I111088046"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"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":0.72708758,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1897","last_page":"1902"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.47119998931884766,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10062","display_name":"MicroRNA in disease regulation","score":0.47119998931884766,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.08659999817609787,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10604","display_name":"RNA Research and Splicing","score":0.05770000070333481,"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/microrna-binding-sites","display_name":"microRNA binding sites","score":0.671999990940094},{"id":"https://openalex.org/keywords/cross-modal-attention-fusion","display_name":"cross-modal attention fusion","score":0.8050000071525574},{"id":"https://openalex.org/keywords/adaptive-gating","display_name":"adaptive gating","score":0.7839999794960022},{"id":"https://openalex.org/keywords/rna-secondary-structure","display_name":"RNA secondary structure","score":0.3889999985694885}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7164000272750854},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.6065999865531921},{"id":"https://openalex.org/C158525013","wikidata":"https://www.wikidata.org/wiki/Q2593739","display_name":"Fusion","level":2,"score":0.597599983215332},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.524399995803833},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.4381999969482422},{"id":"https://openalex.org/C33954974","wikidata":"https://www.wikidata.org/wiki/Q486494","display_name":"Sensor fusion","level":2,"score":0.4205000102519989},{"id":"https://openalex.org/C2780980858","wikidata":"https://www.wikidata.org/wiki/Q110022","display_name":"Dual (grammatical number)","level":2,"score":0.4020000100135803},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.3772999942302704},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3684999942779541},{"id":"https://openalex.org/C131584629","wikidata":"https://www.wikidata.org/wiki/Q4308705","display_name":"Coupling (piping)","level":2,"score":0.35850000381469727},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3562999963760376},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.32690000534057617},{"id":"https://openalex.org/C60115397","wikidata":"https://www.wikidata.org/wiki/Q5188732","display_name":"Crossmodal","level":4,"score":0.30869999527931213},{"id":"https://openalex.org/C2777735758","wikidata":"https://www.wikidata.org/wiki/Q817765","display_name":"Path (computing)","level":2,"score":0.30809998512268066},{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.28029999136924744},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.27950000762939453},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.27630001306533813},{"id":"https://openalex.org/C26760741","wikidata":"https://www.wikidata.org/wiki/Q160402","display_name":"Perception","level":2,"score":0.2718000113964081},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.27090001106262207}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356758","doi":"https://doi.org/10.1109/bibm66473.2025.11356758","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356758","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"sustainable_development_goals_aurora":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W612353151","https://openalex.org/W2018908310","https://openalex.org/W2074231493","https://openalex.org/W2097117768","https://openalex.org/W2123250471","https://openalex.org/W2134629862","https://openalex.org/W2194775991","https://openalex.org/W2333207005","https://openalex.org/W2470357604","https://openalex.org/W2752782242","https://openalex.org/W2806518291","https://openalex.org/W2884170967","https://openalex.org/W2951559372","https://openalex.org/W3206717311","https://openalex.org/W4391255983","https://openalex.org/W4402543874","https://openalex.org/W4412823215"],"related_works":["https://openalex.org/W4394988916","https://openalex.org/W2884170967","https://openalex.org/W2967290176","https://openalex.org/W4416723026","https://openalex.org/W3126804378","https://openalex.org/W4412823215","https://openalex.org/W3012361895","https://openalex.org/W2949901326","https://openalex.org/W4396994669","https://openalex.org/W4404328723"],"abstract_inverted_index":{"Accurate":[0],"microRNA-mRNA":[1],"target":[2],"prediction":[3],"is":[4],"limited":[5],"by":[6],"rigid":[7],"seed-matching":[8],"rules":[9],"and":[10,15,58,95,108],"weak":[11],"coupling":[12],"between":[13],"structural":[14],"semantic":[16,32],"information.":[17],"We":[18],"present":[19],"DPAT,":[20],"a":[21],"novel":[22],"framework":[23],"that":[24],"integrates":[25],"biologically":[26],"informed":[27],"alignment":[28],"encoding":[29],"with":[30,55,79],"transformer-based":[31],"modeling":[33],"through":[34,67,102],"cross-modal":[35],"attention":[36,56],"fusion.":[37],"DPAT":[38,87],"employs":[39],"dual":[40],"pathways:":[41],"(i)":[42],"Multi-Attention":[43],"Biological":[44],"Sequence":[45],"Encoder":[46],"(MABSE)":[47],"processes":[48],"10-channel":[49],"nucleotide-pairing":[50],"matrices":[51],"via":[52,74],"multi-scale":[53],"convolutions":[54],"mechanisms,":[57],"(ii)":[59],"the":[60,84],"Semantic":[61],"Path":[62],"Module":[63],"leverages":[64],"RNA-BERT":[65],"embeddings":[66],"ConvBiLSTM":[68],"processing.":[69],"These":[70],"representations":[71],"are":[72],"fused":[73],"CrossModal":[75],"Attention":[76],"Fusion":[77],"(CMAF)":[78],"adaptive":[80],"gating.":[81],"Evaluated":[82],"on":[83],"miRAW":[85],"dataset,":[86],"achieves":[88],"77.90":[89],"%":[90,93,97],"F1-score,":[91],"82.06":[92],"accuracy,":[94],"83.55":[96],"precision,":[98],"advancing":[99],"state-of-the-art":[100],"methods":[101],"interpretable":[103],"predictions":[104],"identifying":[105],"both":[106],"canonical":[107],"non-canonical":[109],"miRNA":[110],"binding":[111],"sites.":[112],"Code:":[113],"https://github.com/DPATcodebase/DPAT.":[114]},"counts_by_year":[],"updated_date":"2026-10-28T10:33:24.094632","created_date":"2026-01-30T00:00:00"}