{"id":"https://openalex.org/W4410226715","doi":"https://doi.org/10.1109/jbhi.2025.3568145","title":"A Finetuning Deep Learning Framework for Pan-Species Promoters Identification With Pseudo Time Series Analysis on Time and Frequency Space","display_name":"A Finetuning Deep Learning Framework for Pan-Species Promoters Identification With Pseudo Time Series Analysis on Time and Frequency Space","publication_year":2025,"publication_date":"2025-05-09","ids":{"openalex":"https://openalex.org/W4410226715","doi":"https://doi.org/10.1109/jbhi.2025.3568145","pmid":"https://pubmed.ncbi.nlm.nih.gov/40343817"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2025.3568145","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3568145","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/A5109685363","display_name":"Ruimeng Li","orcid":null},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ruimeng Li","raw_affiliation_strings":["School of Future Technology, Xi'an Jiaotong University, Shaanxi, China","School of Future Technology, Xi&#x0027;an Jiaotong university, Shaanxi, China"],"affiliations":[{"raw_affiliation_string":"School of Future Technology, Xi'an Jiaotong University, Shaanxi, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Future Technology, Xi&#x0027;an Jiaotong university, Shaanxi, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074144985","display_name":"Qinke Peng","orcid":"https://orcid.org/0000-0002-5448-8529"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qinke Peng","raw_affiliation_strings":["School of Future Technology, Xi'an Jiaotong University, Shaanxi, China","School of Future Technology, Xi&#x0027;an Jiaotong university, Shaanxi, China"],"affiliations":[{"raw_affiliation_string":"School of Future Technology, Xi'an Jiaotong University, Shaanxi, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"School of Future Technology, Xi&#x0027;an Jiaotong university, Shaanxi, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057848410","display_name":"Haozhou Li","orcid":"https://orcid.org/0009-0001-0955-470X"},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haozhou Li","raw_affiliation_strings":["Systems Engineering Institute, Xi'an Jiaotong University, Shaanxi, China","Systems Engineering Institute, Xi&#x0027; an Jiaotong University, China"],"affiliations":[{"raw_affiliation_string":"Systems Engineering Institute, Xi'an Jiaotong University, Shaanxi, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Systems Engineering Institute, Xi&#x0027; an Jiaotong University, China","institution_ids":["https://openalex.org/I87445476"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110314110","display_name":"Wentong Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I87445476","display_name":"Xi'an Jiaotong University","ror":"https://ror.org/017zhmm22","country_code":"CN","type":"education","lineage":["https://openalex.org/I87445476"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wentong Sun","raw_affiliation_strings":["Systems Engineering Institute, Xi'an Jiaotong University, Shaanxi, China","Systems Engineering Institute, Xi&#x0027; an Jiaotong University, China"],"affiliations":[{"raw_affiliation_string":"Systems Engineering Institute, Xi'an Jiaotong University, Shaanxi, China","institution_ids":["https://openalex.org/I87445476"]},{"raw_affiliation_string":"Systems Engineering Institute, Xi&#x0027; an Jiaotong University, China","institution_ids":["https://openalex.org/I87445476"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5109685363"],"corresponding_institution_ids":["https://openalex.org/I87445476"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.04461696,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"29","issue":"9","first_page":"6940","last_page":"6952"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10320","display_name":"Neural Networks and Applications","score":0.33469998836517334,"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"}},"topics":[{"id":"https://openalex.org/T10320","display_name":"Neural Networks and Applications","score":0.33469998836517334,"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/T11878","display_name":"Solid-state spectroscopy and crystallography","score":0.32739999890327454,"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":0.639363169670105},{"id":"https://openalex.org/keywords/time-series","display_name":"Time series","score":0.6152201294898987},{"id":"https://openalex.org/keywords/series","display_name":"Series (stratigraphy)","score":0.5574159622192383},{"id":"https://openalex.org/keywords/time\u2013frequency-analysis","display_name":"Time\u2013frequency analysis","score":0.50211501121521},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.48786211013793945},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3532482385635376},{"id":"https://openalex.org/keywords/telecommunications","display_name":"Telecommunications","score":0.13622817397117615},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08301937580108643}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.639363169670105},{"id":"https://openalex.org/C151406439","wikidata":"https://www.wikidata.org/wiki/Q186588","display_name":"Time series","level":2,"score":0.6152201294898987},{"id":"https://openalex.org/C143724316","wikidata":"https://www.wikidata.org/wiki/Q312468","display_name":"Series (stratigraphy)","level":2,"score":0.5574159622192383},{"id":"https://openalex.org/C142433447","wikidata":"https://www.wikidata.org/wiki/Q7806653","display_name":"Time\u2013frequency analysis","level":3,"score":0.50211501121521},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.48786211013793945},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3532482385635376},{"id":"https://openalex.org/C76155785","wikidata":"https://www.wikidata.org/wiki/Q418","display_name":"Telecommunications","level":1,"score":0.13622817397117615},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08301937580108643},{"id":"https://openalex.org/C554190296","wikidata":"https://www.wikidata.org/wiki/Q47528","display_name":"Radar","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"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":"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":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","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},{"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":"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}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2025.3568145","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3568145","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:40343817","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40343817","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":[{"display_name":"Life in Land","score":0.4099999964237213,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1973310562","https://openalex.org/W1978643997","https://openalex.org/W2003463914","https://openalex.org/W2033655940","https://openalex.org/W2079701597","https://openalex.org/W2095903180","https://openalex.org/W2117357746","https://openalex.org/W2134977238","https://openalex.org/W2140948028","https://openalex.org/W2263206910","https://openalex.org/W2520774990","https://openalex.org/W2578051997","https://openalex.org/W2788577764","https://openalex.org/W2809624722","https://openalex.org/W2908351833","https://openalex.org/W2911489562","https://openalex.org/W2932524182","https://openalex.org/W2963739921","https://openalex.org/W2979343233","https://openalex.org/W3039032764","https://openalex.org/W3081166989","https://openalex.org/W3089220885","https://openalex.org/W3117695338","https://openalex.org/W3127238141","https://openalex.org/W3160412534","https://openalex.org/W3166898278","https://openalex.org/W4200013827","https://openalex.org/W4221109414","https://openalex.org/W4221128536","https://openalex.org/W4221138063","https://openalex.org/W4226040666","https://openalex.org/W4280583453","https://openalex.org/W4282925451","https://openalex.org/W4283369191","https://openalex.org/W4285405240","https://openalex.org/W4297257598","https://openalex.org/W4303859523","https://openalex.org/W4320489764","https://openalex.org/W4379984736","https://openalex.org/W4389331567","https://openalex.org/W4390874837","https://openalex.org/W4391575908","https://openalex.org/W4392510964","https://openalex.org/W4393159595","https://openalex.org/W4400413801"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"Promoters":[0],"are":[1,21],"genomic":[2],"sequences":[3],"harbouring":[4],"specific":[5],"motifs,":[6],"such":[7],"as":[8,23,77],"the":[9,15,40,85,115,158,167,175],"TATA-":[10],"box":[11,17],"for":[12,18,34,67],"eukaryotes":[13],"and":[14,64,109,120,126,153,170],"Pribnow":[16],"prokaryotes,":[19],"which":[20],"known":[22],"regulatory":[24,30],"elements.":[25,90],"Accurate":[26],"identification":[27,99],"of":[28,42,88,151,166],"these":[29],"elements":[31,108],"is":[32,92],"essential":[33],"deciphering":[35],"transcriptional":[36],"regulation":[37],"mechanisms.":[38],"However,":[39],"heterogeneity":[41,87],"promoters":[43,76],"across":[44,101,123,143],"different":[45,102],"species":[46,110,122],"poses":[47],"a":[48,93,154,171],"significant":[49],"challenge":[50],"in":[51,106,157,174],"this":[52,81],"task.":[53],"In":[54],"our":[55],"study,":[56],"we":[57,136],"introduce":[58],"two":[59],"deep":[60],"learning":[61],"methods,":[62],"ProTriCNN":[63,74,139],"TransPro,":[65],"designed":[66],"promoter":[68,72,89],"identification.":[69],"Based":[70],"on":[71],"representation,":[73],"treats":[75],"pseudo-time":[78],"series,":[79],"utilizing":[80],"approach":[82],"to":[83,97,113,179],"capture":[84],"intricate":[86],"TransPro":[91,104,161],"ProTriCNN-based":[94],"Fine-tuning":[95],"framework":[96],"improve":[98],"performance":[100],"species.":[103],"lies":[105],"utilizes":[107],"evolutionary":[111],"trees":[112],"represent":[114],"locality":[116],"difference":[117],"between":[118],"source":[119],"target":[121],"various":[124],"levels":[125],"time-frequency":[127],"space,":[128],"respectively.":[129],"With":[130],"systematic":[131],"experiments":[132],"using":[133],"real":[134],"datasets,":[135],"demonstrate":[137],"that":[138],"outperfroms":[140],"state-of-the-art":[141],"methods":[142],"all":[144],"species,":[145],"achieving":[146],"an":[147],"average":[148],"accuracy":[149,164],"improvement":[150,165],"2.1%":[152],"20%":[155],"enhancement":[156,173],"Matthews":[159,176],"coefficient.":[160],"further":[162],"attains":[163],"highest":[168],"8%":[169],"25%":[172],"coefficient":[177],"compared":[178],"ProTriCNN.":[180]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-05-10T00:00:00"}
