{"id":"https://openalex.org/W4416255879","doi":"https://doi.org/10.1093/bib/bbaf608","title":"CREATE: a novel attention-based framework for efficient classification of transposable elements","display_name":"CREATE: a novel attention-based framework for efficient classification of transposable elements","publication_year":2025,"publication_date":"2025-11-01","ids":{"openalex":"https://openalex.org/W4416255879","doi":"https://doi.org/10.1093/bib/bbaf608","pmid":"https://pubmed.ncbi.nlm.nih.gov/41241820"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf608","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf608","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in 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/10.1093/bib/bbaf608","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071113955","display_name":"Yang Qi","orcid":"https://orcid.org/0000-0002-5742-9532"},"institutions":[{"id":"https://openalex.org/I99418890","display_name":"Northwestern Polytechnic University","ror":"https://ror.org/05wn69s11","country_code":"US","type":"education","lineage":["https://openalex.org/I99418890"]},{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Yang Qi","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Road, Xi\u2019an 710129 ,"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Road, Xi\u2019an 710129 ,","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I99418890"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065346494","display_name":"Yiqi Chen","orcid":"https://orcid.org/0009-0008-3163-3018"},"institutions":[{"id":"https://openalex.org/I99418890","display_name":"Northwestern Polytechnic University","ror":"https://ror.org/05wn69s11","country_code":"US","type":"education","lineage":["https://openalex.org/I99418890"]},{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Yiqi Chen","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Road, Xi\u2019an 710129 ,"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Road, Xi\u2019an 710129 ,","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I99418890"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102776209","display_name":"Yingfu Wu","orcid":null},"institutions":[{"id":"https://openalex.org/I99418890","display_name":"Northwestern Polytechnic University","ror":"https://ror.org/05wn69s11","country_code":"US","type":"education","lineage":["https://openalex.org/I99418890"]},{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Yingfu Wu","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Road, Xi\u2019an 710129 ,"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Road, Xi\u2019an 710129 ,","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I99418890"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062279899","display_name":"Yang Guo","orcid":"https://orcid.org/0000-0002-3972-9945"},"institutions":[{"id":"https://openalex.org/I76214153","display_name":"Lanzhou University","ror":"https://ror.org/01mkqqe32","country_code":"CN","type":"education","lineage":["https://openalex.org/I76214153"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Guo","raw_affiliation_strings":["School of Information Science and Engineering, Lanzhou University , 222 South Tianshui Road, Lanzhou 730000 ,"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Engineering, Lanzhou University , 222 South Tianshui Road, Lanzhou 730000 ,","institution_ids":["https://openalex.org/I76214153"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041895155","display_name":"Meihong Gao","orcid":"https://orcid.org/0000-0002-9935-7979"},"institutions":[{"id":"https://openalex.org/I4210100953","display_name":"Xi'an University of Finance and Economics","ror":"https://ror.org/01b9y2p27","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210100953"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Meihong Gao","raw_affiliation_strings":["School of Information, Xi\u2019an University of Finance and Economics , 360 Changning Road, Xi\u2019an 710100 ,"],"affiliations":[{"raw_affiliation_string":"School of Information, Xi\u2019an University of Finance and Economics , 360 Changning Road, Xi\u2019an 710100 ,","institution_ids":["https://openalex.org/I4210100953"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031936014","display_name":"Fuhao Zhang","orcid":"https://orcid.org/0009-0001-4336-431X"},"institutions":[{"id":"https://openalex.org/I4210088176","display_name":"North West Agriculture and Forestry University","ror":null,"country_code":"CN","type":null,"lineage":["https://openalex.org/I4210088176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fuhao Zhang","raw_affiliation_strings":["College of Information Engineering, Northwest A&F University , 3 Taicheng Road, Yangling 712100 ,"],"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Northwest A&F University , 3 Taicheng Road, Yangling 712100 ,","institution_ids":["https://openalex.org/I4210088176"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088826157","display_name":"Xingyu Liao","orcid":"https://orcid.org/0000-0002-0061-1317"},"institutions":[{"id":"https://openalex.org/I99418890","display_name":"Northwestern Polytechnic University","ror":"https://ror.org/05wn69s11","country_code":"US","type":"education","lineage":["https://openalex.org/I99418890"]},{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Xingyu Liao","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Road, Xi\u2019an 710129 ,"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Road, Xi\u2019an 710129 ,","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I99418890"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009944817","display_name":"Xuequn Shang","orcid":"https://orcid.org/0000-0002-7249-8210"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]},{"id":"https://openalex.org/I99418890","display_name":"Northwestern Polytechnic University","ror":"https://ror.org/05wn69s11","country_code":"US","type":"education","lineage":["https://openalex.org/I99418890"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Xuequn Shang","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Road, Xi\u2019an 710129 ,"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University , 1 Dongxiang Road, Xi\u2019an 710129 ,","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I99418890"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5071113955"],"corresponding_institution_ids":["https://openalex.org/I17145004","https://openalex.org/I99418890"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":3.6453,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.93502048,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"26","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.7689999938011169,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10434","display_name":"Chromosomal and Genetic Variations","score":0.7689999938011169,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.05559999868273735,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.042500000447034836,"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/transposable-element","display_name":"Transposable element","score":0.6539000272750854},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.565500020980835},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.49140000343322754},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.4767000079154968},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.46810001134872437},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.451200008392334},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4228000044822693},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.420199990272522}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7950999736785889},{"id":"https://openalex.org/C4918238","wikidata":"https://www.wikidata.org/wiki/Q121438","display_name":"Transposable element","level":4,"score":0.6539000272750854},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.565500020980835},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5647000074386597},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.49140000343322754},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4767000079154968},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.46810001134872437},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.451200008392334},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4228000044822693},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.420199990272522},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.40209999680519104},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3982999920845032},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.36899998784065247},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34779998660087585},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.31929999589920044},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.31610000133514404},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.29670000076293945},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.2718000113964081},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.260699987411499},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.2605000138282776},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2572999894618988}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004251","descriptor_name":"DNA Transposable Elements","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":"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":"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf608","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf608","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41241820","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41241820","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:11427966","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12619909","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12619909/pdf/bbaf608.pdf","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"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf608","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf608","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","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/G3825787491","display_name":null,"funder_award_id":"62433016","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"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":63,"referenced_works":["https://openalex.org/W1482190741","https://openalex.org/W1924770834","https://openalex.org/W1969465720","https://openalex.org/W1980340421","https://openalex.org/W1999078569","https://openalex.org/W2021344630","https://openalex.org/W2042086471","https://openalex.org/W2059864757","https://openalex.org/W2064155145","https://openalex.org/W2066320476","https://openalex.org/W2079308685","https://openalex.org/W2082330286","https://openalex.org/W2083697678","https://openalex.org/W2092026879","https://openalex.org/W2129581281","https://openalex.org/W2130212962","https://openalex.org/W2132141594","https://openalex.org/W2134783286","https://openalex.org/W2134965616","https://openalex.org/W2150766729","https://openalex.org/W2154949160","https://openalex.org/W2157668348","https://openalex.org/W2157701113","https://openalex.org/W2165226158","https://openalex.org/W2168909179","https://openalex.org/W2222590335","https://openalex.org/W2353701210","https://openalex.org/W2623168030","https://openalex.org/W2772231999","https://openalex.org/W2774657098","https://openalex.org/W2839902083","https://openalex.org/W2892332606","https://openalex.org/W2900520464","https://openalex.org/W2901901698","https://openalex.org/W2914329983","https://openalex.org/W2914356973","https://openalex.org/W2920529045","https://openalex.org/W2947464213","https://openalex.org/W2950589160","https://openalex.org/W2962949934","https://openalex.org/W2964199361","https://openalex.org/W2994632914","https://openalex.org/W3017049640","https://openalex.org/W3025472913","https://openalex.org/W3083835261","https://openalex.org/W3133711058","https://openalex.org/W3146366485","https://openalex.org/W3189749656","https://openalex.org/W3195386820","https://openalex.org/W3205442753","https://openalex.org/W3211590855","https://openalex.org/W4212957584","https://openalex.org/W4213026783","https://openalex.org/W4283276269","https://openalex.org/W4285592949","https://openalex.org/W4309825753","https://openalex.org/W4311049139","https://openalex.org/W4312094581","https://openalex.org/W4386846548","https://openalex.org/W4387666675","https://openalex.org/W4393991132","https://openalex.org/W4399366736","https://openalex.org/W4401441624"],"related_works":[],"abstract_inverted_index":{"Transposable":[0],"elements":[1,36],"(TEs)":[2],"are":[3,71,214],"DNA":[4],"sequences":[5],"that":[6,180],"can":[7],"move":[8],"within":[9,156],"a":[10,14,105,163,170],"genome.":[11,46],"They":[12],"constitute":[13],"substantial":[15],"portion":[16],"of":[17,33,87,96,122,145,174,205],"the":[18,45,48,93,113,118,142,157,203],"eukaryotic":[19],"genome":[20,29],"and":[21,28,70,117,128,187,211],"play":[22],"essential":[23],"roles":[24],"in":[25,99,191],"gene":[26],"regulation":[27],"evolution.":[30],"Accurate":[31],"classification":[32,166,173,193],"these":[34,63,83,88],"repetitive":[35],"is":[37],"crucial":[38],"for":[39,136,201],"investigating":[40],"their":[41],"potential":[42,200],"impact":[43],"on":[44,67],"Over":[47],"past":[49],"few":[50],"decades,":[51],"several":[52],"alignment-based":[53],"tools":[54],"have":[55,78],"been":[56,79],"developed":[57],"to":[58,81,91,141,153,168],"annotate":[59],"TE":[60,138,146,206],"types.":[61],"While":[62],"methods":[64,186],"rely":[65],"heavily":[66],"prior":[68],"knowledge":[69],"often":[72],"computationally":[73],"expensive,":[74],"machine":[75],"learning-based":[76],"approaches":[77,89],"proposed":[80],"overcome":[82],"limitations.":[84],"However,":[85],"most":[86],"fail":[90],"capture":[92],"multiscale":[94],"features":[95],"TEs,":[97],"resulting":[98],"suboptimal":[100],"performance.":[101],"Here,":[102],"we":[103,148],"propose":[104],"novel":[106],"framework":[107],"called":[108],"CREATE,":[109],"which":[110],"simultaneously":[111],"integrates":[112],"global":[114],"pattern":[115],"distribution":[116],"local":[119],"sequence":[120],"profile":[121],"TEs":[123],"using":[124],"Convolutional":[125],"neural":[126,130],"networks":[127],"Recurrent":[129],"nEtworks":[131],"with":[132],"an":[133],"Attention":[134],"mechanism":[135],"efficient":[137],"classification.":[139],"Due":[140],"hierarchical":[143,165,192],"structure":[144],"groups,":[147],"trained":[149],"nine":[150],"classifiers":[151],"corresponding":[152],"parent":[154],"nodes":[155],"class":[158],"hierarchy.":[159],"We":[160],"further":[161],"applied":[162],"top-down":[164],"strategy":[167],"achieve":[169],"more":[171],"complete":[172],"unknown":[175],"TEs.":[176],"Comprehensive":[177],"experiments":[178],"demonstrate":[179],"CREATE":[181,197],"outperforms":[182],"existing":[183],"TE-type":[184],"annotation":[185],"achieves":[188],"superior":[189],"performance":[190],"tasks.":[194],"In":[195],"conclusion,":[196],"exhibits":[198],"great":[199],"improving":[202],"accuracy":[204],"annotation.":[207],"The":[208],"source":[209],"code":[210],"demo":[212],"data":[213],"available":[215],"at":[216],"https://github.com/yangqi-cs/CREATE.":[217]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-22T08:09:32.410652","created_date":"2025-11-16T00:00:00"}
