{"id":"https://openalex.org/W7125585700","doi":"https://doi.org/10.1186/s12859-026-06367-6","title":"EDEN: multiscale expected density of nucleotide encoding for enhanced DNA sequence classification with hybrid deep learning","display_name":"EDEN: multiscale expected density of nucleotide encoding for enhanced DNA sequence classification with hybrid deep learning","publication_year":2026,"publication_date":"2026-01-24","ids":{"openalex":"https://openalex.org/W7125585700","doi":"https://doi.org/10.1186/s12859-026-06367-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/41580658"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-026-06367-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06367-6","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","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://doi.org/10.1186/s12859-026-06367-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003254513","display_name":"Samad Zabihi","orcid":"https://orcid.org/0000-0001-7544-0199"},"institutions":[{"id":"https://openalex.org/I166459259","display_name":"Shiraz University","ror":"https://ror.org/028qtbk54","country_code":"IR","type":"education","lineage":["https://openalex.org/I166459259"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Saman Zabihi","raw_affiliation_strings":["Department of Computer Science, Engineering, and IT, Shiraz University, Shiraz, Iran. s.zabihi@shirazu.ac.ir"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Engineering, and IT, Shiraz University, Shiraz, Iran. s.zabihi@shirazu.ac.ir","institution_ids":["https://openalex.org/I166459259"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022739916","display_name":"Sattar Hashemi","orcid":"https://orcid.org/0000-0001-6981-8810"},"institutions":[{"id":"https://openalex.org/I166459259","display_name":"Shiraz University","ror":"https://ror.org/028qtbk54","country_code":"IR","type":"education","lineage":["https://openalex.org/I166459259"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Sattar Hashemi","raw_affiliation_strings":["Department of Computer Science, Engineering, and IT, Shiraz University, Shiraz, Iran"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Engineering, and IT, Shiraz University, Shiraz, Iran","institution_ids":["https://openalex.org/I166459259"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069995453","display_name":"Eghbal G. Mansoori","orcid":"https://orcid.org/0000-0002-8207-5916"},"institutions":[{"id":"https://openalex.org/I166459259","display_name":"Shiraz University","ror":"https://ror.org/028qtbk54","country_code":"IR","type":"education","lineage":["https://openalex.org/I166459259"]}],"countries":["IR"],"is_corresponding":false,"raw_author_name":"Eghbal Mansoori","raw_affiliation_strings":["Department of Computer Science, Engineering, and IT, Shiraz University, Shiraz, Iran"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Engineering, and IT, Shiraz University, Shiraz, Iran","institution_ids":["https://openalex.org/I166459259"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5003254513"],"corresponding_institution_ids":["https://openalex.org/I166459259"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":12.6498,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.96043516,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"27","issue":"1","first_page":"40","last_page":"40"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9179999828338623,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9179999828338623,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.06319999694824219,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.0026000000070780516,"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/deep-learning","display_name":"Deep learning","score":0.7264999747276306},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.5936999917030334},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5928000211715698},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5781999826431274},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.5709999799728394},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5396999716758728},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4819999933242798},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.46860000491142273}],"concepts":[{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.7264999747276306},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7250000238418579},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.5936999917030334},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5928000211715698},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.590499997138977},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5781999826431274},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5728999972343445},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.5709999799728394},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5396999716758728},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4819999933242798},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.46860000491142273},{"id":"https://openalex.org/C84148353","wikidata":"https://www.wikidata.org/wiki/Q863908","display_name":"Nucleic acid sequence","level":3,"score":0.41920000314712524},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.38089999556541443},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.36320000886917114},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.35030001401901245},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.3416999876499176},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.3296999931335449},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.3215000033378601},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3172000050544739},{"id":"https://openalex.org/C40506919","wikidata":"https://www.wikidata.org/wiki/Q7452469","display_name":"Sequence learning","level":2,"score":0.3109000027179718},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.30709999799728394},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.28110000491142273},{"id":"https://openalex.org/C17757408","wikidata":"https://www.wikidata.org/wiki/Q4135516","display_name":"genomic DNA","level":3,"score":0.27799999713897705},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2728999853134155},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2711000144481659},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.25110000371932983}],"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":"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":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","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":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-026-06367-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06367-6","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41580658","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41580658","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:857e73a33d43427fa9c39e52ebc0fba1","is_oa":true,"landing_page_url":"https://doaj.org/article/857e73a33d43427fa9c39e52ebc0fba1","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 27, Iss 1, Pp 1-24 (2026)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11687047","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12879454","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12879454","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12879454/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-026-06367-6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-026-06367-6","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":31,"referenced_works":["https://openalex.org/W1973898086","https://openalex.org/W1991330646","https://openalex.org/W2046157432","https://openalex.org/W2100495367","https://openalex.org/W2129103781","https://openalex.org/W2136946483","https://openalex.org/W2166162901","https://openalex.org/W2963341956","https://openalex.org/W2997574889","https://openalex.org/W3127238141","https://openalex.org/W3130819465","https://openalex.org/W3133006703","https://openalex.org/W3164264961","https://openalex.org/W3170986249","https://openalex.org/W4220872625","https://openalex.org/W4226301219","https://openalex.org/W4316339774","https://openalex.org/W4321254242","https://openalex.org/W4376866944","https://openalex.org/W4378086593","https://openalex.org/W4387966606","https://openalex.org/W4391650128","https://openalex.org/W4397049907","https://openalex.org/W4401103147","https://openalex.org/W4404357048","https://openalex.org/W4407024726","https://openalex.org/W4408537402","https://openalex.org/W4410869848","https://openalex.org/W4410961217","https://openalex.org/W4411583590","https://openalex.org/W4412888838"],"related_works":[],"abstract_inverted_index":{"BACKGROUND:":[0],"DNA":[1],"sequences":[2],"are":[3,111],"fundamental":[4],"carriers":[5],"of":[6,43,96],"genetic":[7],"information,":[8],"and":[9,21,33,59,63,82,109,124,136],"their":[10],"accurate":[11],"classification":[12],"is":[13],"essential":[14],"for":[15,128,144],"understanding":[16],"gene":[17],"regulation,":[18],"disease":[19],"mechanisms,":[20],"translational":[22],"genomics.":[23],"Existing":[24],"encoding":[25,49],"methods":[26],"often":[27],"fail":[28],"to":[29],"capture":[30],"both":[31],"local":[32],"long-range":[34],"dependencies":[35],"simultaneously.":[36],"RESULTS:":[37],"We":[38],"introduce":[39],"EDEN":[40,56,87,118],"(Expected":[41],"Density":[42],"Nucleotide":[44],"Encoding),":[45],"a":[46,67],"unified":[47],"multiscale":[48,126],"framework":[50],"based":[51],"on":[52],"kernel":[53],"density":[54],"estimation.":[55],"captures":[57],"position-specific":[58],"context-dependent":[60],"nucleotide":[61],"patterns":[62],"integrates":[64],"them":[65],"into":[66],"hybrid":[68],"deep":[69],"learning":[70],"architecture.":[71],"Across":[72],"sixteen":[73],"benchmark":[74],"datasets":[75,110],"covering":[76],"promoter":[77,80],"detection,":[78,81],"core":[79],"transcription":[83],"factor":[84],"binding":[85],"prediction,":[86],"achieves":[88],"the":[89],"best":[90],"average":[91],"performance":[92],"while":[93],"using":[94],"orders":[95],"magnitude":[97],"fewer":[98],"parameters":[99],"compared":[100],"with":[101],"state-of-the-art":[102],"models.":[103],"All":[104],"source":[105],"code,":[106],"pretrained":[107],"models,":[108],"publicly":[112],"available":[113],"at:":[114],"https://github.com/zabihis/EDEN":[115],".":[116],"CONCLUSIONS:":[117],"provides":[119],"an":[120],"efficient,":[121],"biologically":[122],"informed,":[123],"interpretable":[125],"representation":[127],"genomic":[129,146],"sequence":[130],"classification.":[131],"Its":[132],"favorable":[133],"parameter-performance":[134],"ratio":[135],"robust":[137],"consistency":[138],"across":[139],"tasks":[140],"underscore":[141],"its":[142],"practicality":[143],"large-scale":[145],"applications.":[147]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2026-01-25T00:00:00"}