{"id":"https://openalex.org/W4410230586","doi":"https://doi.org/10.1186/s12859-025-06136-x","title":"PCVR: a pre-trained contextualized visual representation for DNA sequence classification","display_name":"PCVR: a pre-trained contextualized visual representation for DNA sequence classification","publication_year":2025,"publication_date":"2025-05-09","ids":{"openalex":"https://openalex.org/W4410230586","doi":"https://doi.org/10.1186/s12859-025-06136-x","pmid":"https://pubmed.ncbi.nlm.nih.gov/40346458"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-025-06136-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06136-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06136-x","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06136-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102003322","display_name":"Jiarui Zhou","orcid":"https://orcid.org/0009-0009-5396-6988"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiarui Zhou","raw_affiliation_strings":["School of Artificial Intelligence and Data Science, University of Science and Technology of China, Hefei, 230026, Anhui Province, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Artificial Intelligence and Data Science, University of Science and Technology of China, Hefei, 230026, Anhui Province, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003916965","display_name":"Hui Wu","orcid":"https://orcid.org/0009-0005-3392-4829"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hui Wu","raw_affiliation_strings":["Department of Electronic Engineering and Information Science, University of Science and Technology of China, Hefei, 230026, Anhui Province, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electronic Engineering and Information Science, University of Science and Technology of China, Hefei, 230026, Anhui Province, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101838831","display_name":"Kang Du","orcid":"https://orcid.org/0000-0001-9947-2320"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kang Du","raw_affiliation_strings":["Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, Anhui Province, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, Anhui Province, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046805800","display_name":"Wengang Zhou","orcid":"https://orcid.org/0000-0003-1690-9836"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wengang Zhou","raw_affiliation_strings":["Department of Electronic Engineering and Information Science, University of Science and Technology of China, Hefei, 230026, Anhui Province, China. zhwg@ustc.edu.cn"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electronic Engineering and Information Science, University of Science and Technology of China, Hefei, 230026, Anhui Province, China. zhwg@ustc.edu.cn","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019668551","display_name":"Cong\u2010Zhao Zhou","orcid":"https://orcid.org/0000-0002-6881-7151"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cong-Zhao Zhou","raw_affiliation_strings":["Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, Anhui Province, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, Anhui Province, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5078141810","display_name":"Houqiang Li","orcid":"https://orcid.org/0000-0003-2188-3028"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Houqiang Li","raw_affiliation_strings":["Department of Electronic Engineering and Information Science, University of Science and Technology of China, Hefei, 230026, Anhui Province, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electronic Engineering and Information Science, University of Science and Technology of China, Hefei, 230026, Anhui Province, China","institution_ids":["https://openalex.org/I126520041"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.576,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.65771762,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"26","issue":"1","first_page":"125","last_page":"125"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5867000222206116,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.5867000222206116,"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":0.35010001063346863,"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":0.005100000184029341,"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/dna-microarray","display_name":"DNA microarray","score":0.6353532075881958},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5471158027648926},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.5120237469673157},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5119324922561646},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5081186294555664},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5022726058959961},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4511425495147705},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.4005778431892395},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.3909476101398468},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3843543827533722},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.36667943000793457},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26710355281829834},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2667885422706604},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.09182009100914001},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.07137632369995117}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.6353532075881958},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5471158027648926},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.5120237469673157},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5119324922561646},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5081186294555664},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5022726058959961},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4511425495147705},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.4005778431892395},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.3909476101398468},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3843543827533722},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.36667943000793457},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26710355281829834},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2667885422706604},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.09182009100914001},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.07137632369995117},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"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":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"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":4,"locations":[{"id":"doi:10.1186/s12859-025-06136-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06136-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06136-x","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40346458","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40346458","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:81655f0c99874dc3b0871da87ca54c68","is_oa":true,"landing_page_url":"https://doaj.org/article/81655f0c99874dc3b0871da87ca54c68","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 26, Iss 1, Pp 1-24 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12065381","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12065381","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-025-06136-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-025-06136-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-025-06136-x","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410230586.pdf","grobid_xml":"https://content.openalex.org/works/W4410230586.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W2013405042","https://openalex.org/W2055043387","https://openalex.org/W2064675550","https://openalex.org/W2098475202","https://openalex.org/W2108598243","https://openalex.org/W2141202455","https://openalex.org/W2194775991","https://openalex.org/W2250539671","https://openalex.org/W2555479509","https://openalex.org/W2601362634","https://openalex.org/W2789843538","https://openalex.org/W2896457183","https://openalex.org/W2911079020","https://openalex.org/W2914393402","https://openalex.org/W2938868597","https://openalex.org/W2950785362","https://openalex.org/W2950954328","https://openalex.org/W2962739339","https://openalex.org/W2968450569","https://openalex.org/W2968770021","https://openalex.org/W2970971581","https://openalex.org/W3008594856","https://openalex.org/W3046109898","https://openalex.org/W3079675143","https://openalex.org/W3120828528","https://openalex.org/W3137047737","https://openalex.org/W3145257564","https://openalex.org/W3185619636","https://openalex.org/W3213133098","https://openalex.org/W3216181783","https://openalex.org/W4226107243","https://openalex.org/W4293150093","https://openalex.org/W4293868461","https://openalex.org/W4294052446","https://openalex.org/W4298126241","https://openalex.org/W4312919733","https://openalex.org/W4313156423","https://openalex.org/W4380881660","https://openalex.org/W4384523012","https://openalex.org/W4386835737","https://openalex.org/W4391853703","https://openalex.org/W4401567681"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2062195135","https://openalex.org/W2415545834","https://openalex.org/W2069695727","https://openalex.org/W2795079307","https://openalex.org/W2150084125","https://openalex.org/W2118505788","https://openalex.org/W2793058541","https://openalex.org/W1802639773","https://openalex.org/W1983629434"],"abstract_inverted_index":{"BACKGROUND:":[0],"The":[1],"classification":[2,204],"of":[3,64,75,136,139,186,219],"DNA":[4,62,113,202],"sequences":[5,49,63],"is":[6],"pivotal":[7],"in":[8],"bioinformatics,":[9],"essentially":[10],"for":[11,112,210,225],"genetic":[12],"information":[13,82,99,221],"analysis.":[14],"Traditional":[15],"alignment-based":[16],"tools":[17],"tend":[18],"to":[19,46,195,215],"have":[20],"slow":[21],"speed":[22],"and":[23,41,53,96,142,176,191,206,222],"low":[24],"recall.":[25],"Machine":[26],"learning":[27],"methods":[28,173],"learn":[29,143],"implicit":[30],"patterns":[31],"from":[32,72],"data":[33,134],"with":[34,119,151,164],"encoding":[35],"techniques":[36],"such":[37],"as":[38],"k-mer":[39],"counting":[40],"ordinal":[42],"encoding,":[43],"which":[44],"fail":[45],"handle":[47],"long":[48],"or":[50],"sacrifice":[51],"structural":[52],"sequential":[54,81],"information.":[55,129],"Frequency":[56],"chaos":[57],"game":[58],"representation":[59],"(FCGR)":[60],"converts":[61],"arbitrary":[65],"lengths":[66],"into":[67,123],"fixed-size":[68],"images,":[69],"breaking":[70],"free":[71],"the":[73,132,137,149,184,187],"constraints":[74],"sequence":[76,114,203],"length":[77],"while":[78],"preserving":[79],"more":[80,127,144],"than":[83],"other":[84],"representations.":[85],"However,":[86],"existing":[87,172],"works":[88],"merely":[89],"consider":[90],"local":[91],"information,":[92],"ignoring":[93],"long-range":[94],"dependencies":[95],"global":[97,128,220],"contextual":[98],"within":[100],"FCGR":[101,118],"image.":[102],"RESULTS:":[103],"We":[104],"propose":[105],"PCVR,":[106],"a":[107,120,152],"Pre-trained":[108,155],"Contextualized":[109],"Visual":[110],"Representation":[111],"classification.":[115],"PCVR":[116,156,170,199,226],"encodes":[117],"vision":[121,140,188],"transformer":[122,141,189],"contextualized":[124],"features":[125],"containing":[126],"To":[130],"meet":[131],"substantial":[133],"requirements":[135],"training":[138],"robust":[145],"features,":[146],"we":[147],"pre-train":[148],"encoder":[150,190],"masked":[153,192],"autoencoder.":[154],"exhibits":[157],"impressive":[158],"performance":[159,196],"on":[160,174],"three":[161],"datasets":[162],"even":[163],"only":[165],"unsupervised":[166],"learning.":[167],"After":[168],"fine-tuning,":[169],"outperforms":[171],"superkingdom":[175],"phylum":[177],"levels.":[178],"Additionally,":[179],"our":[180],"ablation":[181],"studies":[182],"confirm":[183],"contribution":[185],"autoencoder":[193],"pre-training":[194],"improvement.":[197],"CONCLUSIONS:":[198],"significantly":[200],"improves":[201],"accuracy":[205],"shows":[207],"strong":[208],"potential":[209],"new":[211],"species":[212],"discovery":[213],"due":[214],"its":[216],"effective":[217],"capture":[218],"robustness.":[223],"Codes":[224],"are":[227],"available":[228],"at":[229],"https://github.com/jiaruizhou/PCVR":[230],".":[231]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}