{"id":"https://openalex.org/W7118483724","doi":"https://doi.org/10.1093/bioinformatics/btaf657","title":"NanoSSL: attention mechanism-based self-supervised learning method for protein identification using nanopores","display_name":"NanoSSL: attention mechanism-based self-supervised learning method for protein identification using nanopores","publication_year":2025,"publication_date":"2025-12-05","ids":{"openalex":"https://openalex.org/W7118483724","doi":"https://doi.org/10.1093/bioinformatics/btaf657","pmid":"https://pubmed.ncbi.nlm.nih.gov/41499226"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf657","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf657","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/btaf657","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5122274389","display_name":"Yong Xie","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yong Xie","raw_affiliation_strings":["Department of Biomedical Engineering, Xiangya School of Basic Medical Sciences, Central South University , Changsha, Hunan 410013,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Xiangya School of Basic Medical Sciences, Central South University , Changsha, Hunan 410013,","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101684788","display_name":"Jindong Li","orcid":"https://orcid.org/0000-0001-9050-2896"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jindong Li","raw_affiliation_strings":["Department of Biomedical Engineering, Xiangya School of Basic Medical Sciences, Central South University , Changsha, Hunan 410013,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Xiangya School of Basic Medical Sciences, Central South University , Changsha, Hunan 410013,","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019781796","display_name":"Ziyan Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ziyan Zhang","raw_affiliation_strings":["Department of Biomedical Engineering, Xiangya School of Basic Medical Sciences, Central South University , Changsha, Hunan 410013,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Xiangya School of Basic Medical Sciences, Central South University , Changsha, Hunan 410013,","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066273890","display_name":"Bin Meng","orcid":"https://orcid.org/0000-0003-4214-7011"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bin Meng","raw_affiliation_strings":["Department of Biomedical Engineering, Xiangya School of Basic Medical Sciences, Central South University , Changsha, Hunan 410013,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Xiangya School of Basic Medical Sciences, Central South University , Changsha, Hunan 410013,","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081784268","display_name":"Shuaijian Dai","orcid":"https://orcid.org/0000-0003-4747-9090"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shuaijian Dai","raw_affiliation_strings":["Department of Biomedical Engineering, Xiangya School of Basic Medical Sciences, Central South University , Changsha, Hunan 410013,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Xiangya School of Basic Medical Sciences, Central South University , Changsha, Hunan 410013,","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yuchen Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuchen Zhou","raw_affiliation_strings":["Xiangya School of Medicine, Central South University , Changsha, Hunan 410013,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xiangya School of Medicine, Central South University , Changsha, Hunan 410013,","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051195038","display_name":"Eamonn Kennedy","orcid":"https://orcid.org/0000-0002-9211-1271"},"institutions":[{"id":"https://openalex.org/I223532165","display_name":"University of Utah","ror":"https://ror.org/03r0ha626","country_code":"US","type":"education","lineage":["https://openalex.org/I223532165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eamonn Kennedy","raw_affiliation_strings":["Division of Epidemiology, Internal Medicine, University of Utah , Salt Lake City, UT 84112,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Epidemiology, Internal Medicine, University of Utah , Salt Lake City, UT 84112,","institution_ids":["https://openalex.org/I223532165"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Niandong Jiao","orcid":null},"institutions":[{"id":"https://openalex.org/I142078773","display_name":"Shenyang Institute of Automation","ror":"https://ror.org/00ft6nj33","country_code":"CN","type":"facility","lineage":["https://openalex.org/I142078773","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Niandong Jiao","raw_affiliation_strings":["State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences , Shenyang, Liaoning 110169,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Robotics, Shenyang Institute of Automation, Chinese Academy of Sciences , Shenyang, Liaoning 110169,","institution_ids":["https://openalex.org/I142078773"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079943141","display_name":"H. Isaac Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]},{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]},{"id":"https://openalex.org/I198357462","display_name":"Changsha University","ror":"https://ror.org/011d8sm39","country_code":"CN","type":"education","lineage":["https://openalex.org/I198357462"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haobin Chen","raw_affiliation_strings":["Department of Biomedical Engineering, Xiangya School of Basic Medical Sciences, Central South University , Changsha, Hunan 410013,","Furong Laboratory , Changsha, Hunan 410000,","National Engineering Research Center of Personalized Diagnostic and Therapeutic , Changsha, Hunan 410000,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Xiangya School of Basic Medical Sciences, Central South University , Changsha, Hunan 410013,","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"Furong Laboratory , Changsha, Hunan 410000,","institution_ids":["https://openalex.org/I198357462"]},{"raw_affiliation_string":"National Engineering Research Center of Personalized Diagnostic and Therapeutic , Changsha, Hunan 410000,","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000654757","display_name":"Zhuxin Dong","orcid":"https://orcid.org/0000-0001-9059-2430"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]},{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]},{"id":"https://openalex.org/I198357462","display_name":"Changsha University","ror":"https://ror.org/011d8sm39","country_code":"CN","type":"education","lineage":["https://openalex.org/I198357462"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhuxin Dong","raw_affiliation_strings":["Department of Biomedical Engineering, Xiangya School of Basic Medical Sciences, Central South University , Changsha, Hunan 410013,","Furong Laboratory , Changsha, Hunan 410000,","National Engineering Research Center of Personalized Diagnostic and Therapeutic , Changsha, Hunan 410000,"],"raw_orcid":"https://orcid.org/0000-0001-9059-2430","affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Xiangya School of Basic Medical Sciences, Central South University , Changsha, Hunan 410013,","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"Furong Laboratory , Changsha, Hunan 410000,","institution_ids":["https://openalex.org/I198357462"]},{"raw_affiliation_string":"National Engineering Research Center of Personalized Diagnostic and Therapeutic , Changsha, Hunan 410000,","institution_ids":["https://openalex.org/I170215575"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5122274389"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.53149748,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.9919999837875366,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11582","display_name":"Nanopore and Nanochannel Transport Studies","score":0.9919999837875366,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10062","display_name":"MicroRNA in disease regulation","score":0.0005000000237487257,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T12166","display_name":"Ion-surface interactions and analysis","score":0.00039999998989515007,"subfield":{"id":"https://openalex.org/subfields/2206","display_name":"Computational Mechanics"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6718999743461609},{"id":"https://openalex.org/keywords/nanopore","display_name":"Nanopore","score":0.579800009727478},{"id":"https://openalex.org/keywords/statistical-learning","display_name":"Statistical learning","score":0.3921999931335449},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.3831000030040741},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3666999936103821},{"id":"https://openalex.org/keywords/protein-detection","display_name":"Protein detection","score":0.3093999922275543}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7013999819755554},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6718999743461609},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6126000285148621},{"id":"https://openalex.org/C141795571","wikidata":"https://www.wikidata.org/wiki/Q580942","display_name":"Nanopore","level":2,"score":0.579800009727478},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3935000002384186},{"id":"https://openalex.org/C2982736386","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Statistical learning","level":2,"score":0.3921999931335449},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.3831000030040741},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3666999936103821},{"id":"https://openalex.org/C3019566124","wikidata":"https://www.wikidata.org/wiki/Q85794778","display_name":"Protein detection","level":2,"score":0.3093999922275543},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.27129998803138733},{"id":"https://openalex.org/C40506919","wikidata":"https://www.wikidata.org/wiki/Q7452469","display_name":"Sequence learning","level":2,"score":0.2556000053882599},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.251800000667572}],"mesh":[{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069553","descriptor_name":"Supervised Machine 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":"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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016229","descriptor_name":"Amyloid beta-Peptides","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058608","descriptor_name":"Nanopores","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaf657","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf657","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41499226","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41499226","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12777981","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12777981/","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf657","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf657","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5344348062","display_name":null,"funder_award_id":"2023005","funder_id":"https://openalex.org/F4320326907","funder_display_name":"State Key Laboratory of Robotics"},{"id":"https://openalex.org/G6702659087","display_name":null,"funder_award_id":"2023YFF1205900","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G8922029147","display_name":null,"funder_award_id":"32271520","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"},{"id":"https://openalex.org/F4320326907","display_name":"State Key Laboratory of Robotics","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W1973247626","https://openalex.org/W1993527536","https://openalex.org/W2151164439","https://openalex.org/W2329887558","https://openalex.org/W2502056833","https://openalex.org/W2620091427","https://openalex.org/W2735310269","https://openalex.org/W2794284562","https://openalex.org/W2794569677","https://openalex.org/W2884001105","https://openalex.org/W2905810301","https://openalex.org/W2947918850","https://openalex.org/W3002408315","https://openalex.org/W3019166713","https://openalex.org/W3126419250","https://openalex.org/W3140102771","https://openalex.org/W3172882582","https://openalex.org/W3207924272","https://openalex.org/W4206042814","https://openalex.org/W4206240086","https://openalex.org/W4210629385","https://openalex.org/W4220690319","https://openalex.org/W4226095014","https://openalex.org/W4284964191","https://openalex.org/W4285728626","https://openalex.org/W4286579687","https://openalex.org/W4297243252","https://openalex.org/W4297965505","https://openalex.org/W4309646997","https://openalex.org/W4311718393","https://openalex.org/W4389947730","https://openalex.org/W4391463585","https://openalex.org/W4391876502","https://openalex.org/W4392519792","https://openalex.org/W4396896738","https://openalex.org/W4399012928","https://openalex.org/W4401415707","https://openalex.org/W4402454718"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Nanopores":[1],"are":[2,21,43,159],"cutting-edge":[3],"interdisciplinary":[4],"tools":[5],"that":[6,71],"can":[7],"analyze":[8],"biomolecules":[9],"at":[10,256],"the":[11,29,51,100,133,169,173,243],"single-molecule":[12,41],"level":[13],"for":[14,35,58,99,195],"many":[15],"applications,":[16],"e.g.":[17],"DNA":[18],"sequencing.":[19],"Efforts":[20],"underway":[22],"to":[23,26,48,126],"extend":[24],"nanopores":[25],"proteomics,":[27],"including":[28],"development":[30,52],"of":[31,55,102,112,135,153,157,172,245],"machine":[32,56],"learning":[33,57,66,93,236],"algorithms":[34],"protein":[36,103,139,192],"sequencing":[37,140],"and":[38,46,53,81,115,162,198,223,232,237],"identification.":[39],"However,":[40],"data":[42,63,125],"intrinsically":[44],"noisy":[45],"hard":[47],"process.":[49],"Moreover,":[50],"performance":[54,216,246],"nanopore":[59,76,175,190],"is":[60,67,147,254],"jeopardized":[61],"by":[62,132],"scarcity.":[64],"Self-supervised":[65],"an":[68,214],"emerging":[69],"method":[70],"may":[72],"yield":[73],"advantages":[74],"in":[75,137,180],"scenarios.":[77],"RESULTS:":[78],"We":[79],"propose":[80],"experimentally":[82],"validate":[83],"Nanopore":[84],"analysis":[85],"using":[86,164,205],"Self-Supervised":[87],"Learning":[88,168],"(NanoSSL),":[89],"a":[90,108,165,187],"generative":[91],"self-supervised":[92,113,235],"framework":[94],"based":[95],"on":[96],"attention":[97,238],"mechanisms":[98],"identification":[101,179],"signals":[104],"from":[105,123],"nanopores.":[106,208],"Leveraging":[107],"two-step":[109],"approach":[110],"consisting":[111],"pre-training":[114],"supervised":[116],"fine-tuning,":[117],"NanoSSL":[118,212],"learns":[119],"useful":[120],"feature":[121,170],"representations":[122,171],"empirical":[124],"facilitate":[127],"downstream":[128],"classification":[129],"tasks.":[130],"Inspired":[131],"concept":[134],"fragmentation":[136],"conventional":[138],"technologies,":[141],"during":[142],"pretraining":[143],"each":[144],"translocation":[145],"event":[146],"split":[148],"into":[149],"multiple":[150],"non-overlapping":[151],"fragments":[152],"equal":[154],"size,":[155],"some":[156],"which":[158],"randomly":[160],"masked":[161,166],"reconstructed":[163,174],"autoencoder.":[167],"events":[176],"facilitates":[177],"molecular":[178],"fine-tuning.":[181],"In":[182],"this":[183],"study,":[184],"we":[185],"retested":[186],"publicly":[188],"available":[189,255],"multiplexed":[191],"sensing":[193],"dataset":[194],"model":[196],"iteration,":[197],"subsequently":[199],"measured":[200],"Alzheimer's":[201],"disease":[202],"biomarker":[203],"A\u03b21-42":[204],"homemade":[206],"solid-state":[207],"Empirical":[209],"results":[210],"indicated":[211],"achieved":[213],"unprecedented":[215],"across":[217],"four":[218],"metrics:":[219],"accuracy,":[220],"precision,":[221],"recall,":[222],"F1":[224],"score,":[225],"when":[226],"classifying":[227],"two":[228],"mutated":[229],"A\u03b21-42,":[230],"E22G":[231],"G37R.":[233],"The":[234,251],"mechanism":[239],"were":[240],"verified":[241],"as":[242],"source":[244],"gains.":[247],"AVAILABILITY":[248],"AND":[249],"IMPLEMENTATION:":[250],"main":[252],"program":[253],"https://doi.org/10.5281/zenodo.17172822.":[257]},"counts_by_year":[],"updated_date":"2026-06-03T09:05:47.796612","created_date":"2026-01-08T00:00:00"}