{"id":"https://openalex.org/W4390992199","doi":"https://doi.org/10.1109/bibm58861.2023.10385972","title":"DeepDualEPI: Predicting Promoter-Enhancer Interactions Based on DNA Sequence and Genomic Signals","display_name":"DeepDualEPI: Predicting Promoter-Enhancer Interactions Based on DNA Sequence and Genomic Signals","publication_year":2023,"publication_date":"2023-12-05","ids":{"openalex":"https://openalex.org/W4390992199","doi":"https://doi.org/10.1109/bibm58861.2023.10385972"},"language":"en","primary_location":{"id":"doi:10.1109/bibm58861.2023.10385972","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10385972","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","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/A5006420025","display_name":"Tao Song","orcid":"https://orcid.org/0000-0002-0130-3340"},"institutions":[{"id":"https://openalex.org/I143413998","display_name":"Qingdao University of Science and Technology","ror":"https://ror.org/041j8js14","country_code":"CN","type":"education","lineage":["https://openalex.org/I143413998"]},{"id":"https://openalex.org/I4210128818","display_name":"Institute of Software","ror":"https://ror.org/033dfsn42","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210128818"]},{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tao Song","raw_affiliation_strings":["China University of Petroleum,College of Computer Science and Technology, Qingdao Institute of Software,Qingdao,China","College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, China"],"affiliations":[{"raw_affiliation_string":"China University of Petroleum,College of Computer Science and Technology, Qingdao Institute of Software,Qingdao,China","institution_ids":["https://openalex.org/I143413998","https://openalex.org/I4210162190"]},{"raw_affiliation_string":"College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, China","institution_ids":["https://openalex.org/I4210128818","https://openalex.org/I4210162190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112863401","display_name":"Haonan Song","orcid":"https://orcid.org/0009-0003-2183-2586"},"institutions":[{"id":"https://openalex.org/I143413998","display_name":"Qingdao University of Science and Technology","ror":"https://ror.org/041j8js14","country_code":"CN","type":"education","lineage":["https://openalex.org/I143413998"]},{"id":"https://openalex.org/I4210128818","display_name":"Institute of Software","ror":"https://ror.org/033dfsn42","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210128818"]},{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haonan Song","raw_affiliation_strings":["China University of Petroleum,College of Computer Science and Technology, Qingdao Institute of Software,Qingdao,China","College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, China"],"affiliations":[{"raw_affiliation_string":"China University of Petroleum,College of Computer Science and Technology, Qingdao Institute of Software,Qingdao,China","institution_ids":["https://openalex.org/I143413998","https://openalex.org/I4210162190"]},{"raw_affiliation_string":"College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, China","institution_ids":["https://openalex.org/I4210128818","https://openalex.org/I4210162190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023015161","display_name":"Zhiyi Pan","orcid":"https://orcid.org/0000-0002-0635-0349"},"institutions":[{"id":"https://openalex.org/I143413998","display_name":"Qingdao University of Science and Technology","ror":"https://ror.org/041j8js14","country_code":"CN","type":"education","lineage":["https://openalex.org/I143413998"]},{"id":"https://openalex.org/I4210128818","display_name":"Institute of Software","ror":"https://ror.org/033dfsn42","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210128818"]},{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhiyi Pan","raw_affiliation_strings":["China University of Petroleum,College of Computer Science and Technology, Qingdao Institute of Software,Qingdao,China","College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, China"],"affiliations":[{"raw_affiliation_string":"China University of Petroleum,College of Computer Science and Technology, Qingdao Institute of Software,Qingdao,China","institution_ids":["https://openalex.org/I143413998","https://openalex.org/I4210162190"]},{"raw_affiliation_string":"College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, China","institution_ids":["https://openalex.org/I4210128818","https://openalex.org/I4210162190"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101916532","display_name":"Yuan Gao","orcid":"https://orcid.org/0009-0007-2080-3088"},"institutions":[{"id":"https://openalex.org/I143413998","display_name":"Qingdao University of Science and Technology","ror":"https://ror.org/041j8js14","country_code":"CN","type":"education","lineage":["https://openalex.org/I143413998"]},{"id":"https://openalex.org/I4210128818","display_name":"Institute of Software","ror":"https://ror.org/033dfsn42","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210128818"]},{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuan Gao","raw_affiliation_strings":["China University of Petroleum,College of Computer Science and Technology, Qingdao Institute of Software,Qingdao,China","College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, China"],"affiliations":[{"raw_affiliation_string":"China University of Petroleum,College of Computer Science and Technology, Qingdao Institute of Software,Qingdao,China","institution_ids":["https://openalex.org/I143413998","https://openalex.org/I4210162190"]},{"raw_affiliation_string":"College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, China","institution_ids":["https://openalex.org/I4210128818","https://openalex.org/I4210162190"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Qing Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I143413998","display_name":"Qingdao University of Science and Technology","ror":"https://ror.org/041j8js14","country_code":"CN","type":"education","lineage":["https://openalex.org/I143413998"]},{"id":"https://openalex.org/I4210128818","display_name":"Institute of Software","ror":"https://ror.org/033dfsn42","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210128818"]},{"id":"https://openalex.org/I4210162190","display_name":"China University of Petroleum, East China","ror":"https://ror.org/05gbn2817","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210162190"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qing Yang","raw_affiliation_strings":["China University of Petroleum,College of Computer Science and Technology, Qingdao Institute of Software,Qingdao,China","College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, China"],"affiliations":[{"raw_affiliation_string":"China University of Petroleum,College of Computer Science and Technology, Qingdao Institute of Software,Qingdao,China","institution_ids":["https://openalex.org/I143413998","https://openalex.org/I4210162190"]},{"raw_affiliation_string":"College of Computer Science and Technology, Qingdao Institute of Software, China University of Petroleum, Qingdao, China","institution_ids":["https://openalex.org/I4210128818","https://openalex.org/I4210162190"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075937111","display_name":"Xingguang Wang","orcid":"https://orcid.org/0000-0002-0520-4980"},"institutions":[{"id":"https://openalex.org/I154099455","display_name":"Shandong University","ror":"https://ror.org/0207yh398","country_code":"CN","type":"education","lineage":["https://openalex.org/I154099455"]},{"id":"https://openalex.org/I4210116517","display_name":"Shandong Provincial Hospital","ror":"https://ror.org/02ar2nf05","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210116517"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xingguang Wang","raw_affiliation_strings":["Shandong University,Shandong Provincial Hospital,Department of Respiratory and Critical Care Medicine,Jinan,China","Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong University, Jinan, China"],"affiliations":[{"raw_affiliation_string":"Shandong University,Shandong Provincial Hospital,Department of Respiratory and Critical Care Medicine,Jinan,China","institution_ids":["https://openalex.org/I4210116517"]},{"raw_affiliation_string":"Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital, Shandong University, Jinan, China","institution_ids":["https://openalex.org/I4210116517","https://openalex.org/I154099455"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5006420025"],"corresponding_institution_ids":["https://openalex.org/I143413998","https://openalex.org/I4210128818","https://openalex.org/I4210162190"],"apc_list":null,"apc_paid":null,"fwci":0.4539,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.68401839,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"2889","last_page":"2895"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9991000294685364,"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"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9991000294685364,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9979000091552734,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9900000095367432,"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/computer-science","display_name":"Computer science","score":0.6229004859924316},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.6173943281173706},{"id":"https://openalex.org/keywords/enhancer","display_name":"Enhancer","score":0.5516765713691711},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.55158931016922},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48701149225234985},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.41764092445373535},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3445875346660614},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2739788293838501},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.24492940306663513},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.20577898621559143},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.12301477789878845}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6229004859924316},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.6173943281173706},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.5516765713691711},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.55158931016922},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48701149225234985},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.41764092445373535},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3445875346660614},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2739788293838501},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.24492940306663513},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.20577898621559143},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.12301477789878845}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm58861.2023.10385972","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm58861.2023.10385972","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null},{"id":"https://openalex.org/F4320337495","display_name":"Technology Development","ror":null},{"id":"https://openalex.org/F4320337504","display_name":"Research and Development","ror":"https://ror.org/027s68j25"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":36,"referenced_works":["https://openalex.org/W1986586739","https://openalex.org/W2031057223","https://openalex.org/W2131186458","https://openalex.org/W2168191908","https://openalex.org/W2333286569","https://openalex.org/W2582377823","https://openalex.org/W2597655663","https://openalex.org/W2735099323","https://openalex.org/W2768844315","https://openalex.org/W2896457183","https://openalex.org/W2898598946","https://openalex.org/W2911079020","https://openalex.org/W2951218167","https://openalex.org/W2971769670","https://openalex.org/W2989837622","https://openalex.org/W3002247544","https://openalex.org/W3015468748","https://openalex.org/W3093812284","https://openalex.org/W3177318507","https://openalex.org/W4205731547","https://openalex.org/W4220837717","https://openalex.org/W4220942069","https://openalex.org/W4221067645","https://openalex.org/W4223533630","https://openalex.org/W4224326349","https://openalex.org/W4225259708","https://openalex.org/W4282926403","https://openalex.org/W4285794944","https://openalex.org/W4296025979","https://openalex.org/W4304588242","https://openalex.org/W4313210659","https://openalex.org/W4313816476","https://openalex.org/W4324144341","https://openalex.org/W4385194941","https://openalex.org/W4385245566","https://openalex.org/W6746002186"],"related_works":["https://openalex.org/W2113330652","https://openalex.org/W2061914098","https://openalex.org/W4393004084","https://openalex.org/W4309683845","https://openalex.org/W2118646732","https://openalex.org/W2152841149","https://openalex.org/W2586783543","https://openalex.org/W4387598842","https://openalex.org/W4380075502","https://openalex.org/W2973036402"],"abstract_inverted_index":{"Enhancer-promoter":[0],"interactions":[1,19,57],"are":[2,165],"one":[3],"of":[4,11,17,101,121,136,193,201,228],"the":[5,9,98,104,113,119,133,137,146,191,199,202,205,225],"essential":[6],"mechanisms":[7],"in":[8,152,219],"regulation":[10],"gene":[12],"expression,":[13],"and":[14,51,68,74,86,91,155,159,215],"Accurate":[15],"identification":[16],"enhancer-promoter":[18,56],"(EPIs)":[20],"is":[21],"challenging.":[22],"In":[23,36],"recent":[24],"years,":[25],"many":[26],"deep":[27,44,209],"learning":[28,45,210],"methods":[29],"have":[30],"been":[31],"used":[32,60],"for":[33,54,103],"EPI":[34,93,143,178,229],"prediction.":[35,230],"this":[37,184,220],"study,":[38],"we":[39,106,123],"propose":[40],"DeepDualEPI,":[41,122],"a":[42],"dual-channel":[43],"model":[46,114,148,174],"based":[47],"on":[48,126,167],"genomic":[49,72,213],"signals":[50,214],"DNA":[52,83,194,216],"sequences,":[53],"predicting":[55],"(EPI).":[58],"We":[59],"network":[61,75],"architectures":[62,76],"such":[63,77],"as":[64,78],"Dilated":[65],"CNN,":[66],"BiLSTM,":[67],"Transformer":[69],"to":[70,81,111,117,131,223],"process":[71],"signals,":[73],"multiscale":[79],"CNN":[80],"extract":[82],"sequence":[84,195],"features,":[85],"finally":[87],"obtained":[88],"hybrid":[89,207],"features":[90],"output":[92],"prediction":[94,144,179],"probabilities.":[95],"To":[96],"obtain":[97],"best":[99],"combination":[100],"parameters":[102],"model,":[105],"conducted":[107,124],"several":[108],"ablation":[109,188],"experiments":[110,125,189],"optimize":[112],"parameters.":[115],"And":[116,183],"validate":[118],"performance":[120,200],"four":[127],"independent":[128],"test":[129],"sets":[130],"verify":[132],"generalization":[134],"ability":[135],"model.":[138,203],"Compared":[139],"with":[140],"other":[141],"state-of-the-art":[142],"models,":[145],"DeepDualEPI":[147],"shows":[149],"significant":[150],"improvement":[151],"both":[153],"AUC":[154],"AUPR":[156],"evaluation":[157],"metrics":[158],"experimentally":[160],"demonstrates":[161,186],"that":[162,172,190],"better":[163],"results":[164],"achieved":[166],"every":[168],"chromosome,":[169],"which":[170],"proves":[171],"our":[173],"can":[175,197],"stably":[176],"perform":[177],"across":[180],"cell":[181],"lines.":[182],"paper":[185,221],"through":[187],"inclusion":[192],"information":[196],"improve":[198,224],"Therefore,":[204],"two-channel":[206],"feature":[208],"approach":[211],"via":[212],"sequences":[217],"proposed":[218],"helps":[222],"overall":[226],"accuracy":[227]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}
