{"id":"https://openalex.org/W4413118600","doi":"https://doi.org/10.1109/access.2025.3596851","title":"SUPERMAGOv2: Protein Function Prediction via Transformer Embeddings and Bitscore-Weighted Features","display_name":"SUPERMAGOv2: Protein Function Prediction via Transformer Embeddings and Bitscore-Weighted Features","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4413118600","doi":"https://doi.org/10.1109/access.2025.3596851"},"language":"en","primary_location":{"id":"doi:10.1109/access.2025.3596851","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3596851","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1109/access.2025.3596851","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065375346","display_name":"Gabriel Bianchin de Oliveira","orcid":"https://orcid.org/0000-0002-1238-4860"},"institutions":[{"id":"https://openalex.org/I181391015","display_name":"Universidade Estadual de Campinas (UNICAMP)","ror":"https://ror.org/04wffgt70","country_code":"BR","type":"education","lineage":["https://openalex.org/I181391015"]}],"countries":["BR"],"is_corresponding":true,"raw_author_name":"Gabriel Bianchin de Oliveira","raw_affiliation_strings":["Institute of Computing, University of Campinas, Campinas, Brazil"],"affiliations":[{"raw_affiliation_string":"Institute of Computing, University of Campinas, Campinas, Brazil","institution_ids":["https://openalex.org/I181391015"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065725754","display_name":"H\u00e9lio Pedrini","orcid":"https://orcid.org/0000-0003-0125-630X"},"institutions":[{"id":"https://openalex.org/I181391015","display_name":"Universidade Estadual de Campinas (UNICAMP)","ror":"https://ror.org/04wffgt70","country_code":"BR","type":"education","lineage":["https://openalex.org/I181391015"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Helio Pedrini","raw_affiliation_strings":["Institute of Computing, University of Campinas, Campinas, Brazil"],"affiliations":[{"raw_affiliation_string":"Institute of Computing, University of Campinas, Campinas, Brazil","institution_ids":["https://openalex.org/I181391015"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042140271","display_name":"Zanoni Dias","orcid":"https://orcid.org/0000-0003-3333-6822"},"institutions":[{"id":"https://openalex.org/I181391015","display_name":"Universidade Estadual de Campinas (UNICAMP)","ror":"https://ror.org/04wffgt70","country_code":"BR","type":"education","lineage":["https://openalex.org/I181391015"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Zanoni Dias","raw_affiliation_strings":["Institute of Computing, University of Campinas, Campinas, Brazil"],"affiliations":[{"raw_affiliation_string":"Institute of Computing, University of Campinas, Campinas, Brazil","institution_ids":["https://openalex.org/I181391015"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5065375346"],"corresponding_institution_ids":["https://openalex.org/I181391015"],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.18273035,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"13","issue":null,"first_page":"139743","last_page":"139757"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9958000183105469,"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":0.9958000183105469,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9890999794006348,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.979200005531311,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/computer-science","display_name":"Computer science","score":0.6088050603866577},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.47050970792770386},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4145793914794922},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4016302824020386},{"id":"https://openalex.org/keywords/voltage","display_name":"Voltage","score":0.08530697226524353},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.07503816485404968},{"id":"https://openalex.org/keywords/electrical-engineering","display_name":"Electrical engineering","score":0.07427072525024414}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6088050603866577},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.47050970792770386},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4145793914794922},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4016302824020386},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.08530697226524353},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.07503816485404968},{"id":"https://openalex.org/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.07427072525024414}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/access.2025.3596851","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3596851","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:b7f9cd21bc7e40f18c5403b51d5707b7","is_oa":true,"landing_page_url":"https://doaj.org/article/b7f9cd21bc7e40f18c5403b51d5707b7","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":"IEEE Access, Vol 13, Pp 139743-139757 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2025.3596851","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2025.3596851","pdf_url":null,"source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4825757795","display_name":null,"funder_award_id":"161015/2021-2","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G5531426115","display_name":null,"funder_award_id":"304836/2022-2","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G6155042635","display_name":null,"funder_award_id":"302530/2022-3","funder_id":"https://openalex.org/F4320322025","funder_display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico"},{"id":"https://openalex.org/G8838853693","display_name":null,"funder_award_id":"2017/12646-3","funder_id":"https://openalex.org/F4320320671","funder_display_name":"National Research Foundation"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"},{"id":"https://openalex.org/F4320322025","display_name":"Conselho Nacional de Desenvolvimento Cient\u00edfico e Tecnol\u00f3gico","ror":"https://ror.org/03swz6y49"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1982088273","https://openalex.org/W2000950277","https://openalex.org/W2098432760","https://openalex.org/W2103017472","https://openalex.org/W2108984616","https://openalex.org/W2158714788","https://openalex.org/W2166985665","https://openalex.org/W2170747616","https://openalex.org/W2194775991","https://openalex.org/W2549139847","https://openalex.org/W2615066396","https://openalex.org/W2618530766","https://openalex.org/W2793433991","https://openalex.org/W2951731136","https://openalex.org/W2989608901","https://openalex.org/W2997546679","https://openalex.org/W3126817587","https://openalex.org/W3128878755","https://openalex.org/W3137270128","https://openalex.org/W3143063265","https://openalex.org/W3146944767","https://openalex.org/W3177500196","https://openalex.org/W3177828909","https://openalex.org/W4205443055","https://openalex.org/W4210547400","https://openalex.org/W4220934922","https://openalex.org/W4233120011","https://openalex.org/W4236358448","https://openalex.org/W4312097792","https://openalex.org/W4312881242","https://openalex.org/W4313056876","https://openalex.org/W4327550249","https://openalex.org/W4379882058","https://openalex.org/W4382632527","https://openalex.org/W4383058125","https://openalex.org/W4385245566","https://openalex.org/W4386076522","https://openalex.org/W4391021820","https://openalex.org/W4396627752","https://openalex.org/W4399408236","https://openalex.org/W4400140828","https://openalex.org/W4400878682","https://openalex.org/W4402816271","https://openalex.org/W4403834725","https://openalex.org/W4404092049","https://openalex.org/W4404387678","https://openalex.org/W4405488670","https://openalex.org/W4405694388","https://openalex.org/W4406739182"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2033914206","https://openalex.org/W2042327336"],"abstract_inverted_index":{"Sequencing":[0],"technologies":[1],"have":[2,60],"advanced":[3],"considerably":[4],"in":[5],"recent":[6],"years,":[7],"leading":[8,176],"to":[9,63,99],"the":[10,22,131],"sequencing":[11,33],"of":[12,16,25,85,161],"a":[13,36,115,156],"vast":[14],"number":[15],"proteins":[17,27,41],"through":[18],"laboratory":[19],"methods.":[20],"However,":[21],"functional":[23,65],"annotation":[24],"these":[26],"has":[28],"not":[29],"kept":[30],"pace":[31],"with":[32,44,88,147],"efforts,":[34],"creating":[35],"significant":[37],"gap":[38],"between":[39],"sequenced":[40],"and":[42,80,123],"those":[43],"known":[45],"functions.":[46],"To":[47],"address":[48],"this":[49,68],"challenge,":[50],"computational":[51],"approaches":[52,169],"based":[53,76,182],"solely":[54],"on":[55,77,183],"amino":[56,184],"acid":[57,185],"sequence":[58],"features":[59,101],"been":[61],"developed":[62],"improve":[64],"predictions.":[66,150],"In":[67,151],"study,":[69],"we":[70,138,153],"introduce":[71,154],"two":[72],"novel":[73,116],"approaches,":[74],"one":[75],"machine":[78,86,92],"learning":[79,87],"another":[81],"using":[82],"an":[83,125,141],"ensemble":[84,142],"local":[89],"alignment.":[90],"Our":[91],"learning-based":[93],"model":[94,128,143],"(SUPERMAGOv2)":[95],"utilizes":[96],"transformer-based":[97],"backbones":[98],"extract":[100],"from":[102,120],"multiple":[103],"layers,":[104],"which":[105],"are":[106],"then":[107],"processed":[108],"by":[109,124],"six":[110],"multilayer":[111],"perceptrons":[112],"that":[113,129,144],"incorporate":[114],"bitscore-weighted":[117],"input":[118],"derived":[119],"DIAMOND":[121],"alignments,":[122],"image":[126],"classification":[127,181],"converts":[130],"extracted":[132],"feature":[133],"vectors":[134],"into":[135],"images.":[136],"Furthermore,":[137],"present":[139],"SUPERMAGOv2+,":[140],"combines":[145],"SUPERMAGOv2":[146],"enhanced":[148],"DIAMOND-based":[149],"addition,":[152],"SUPERMAGOv2+Web,":[155],"lightweight":[157],"web":[158],"server":[159],"version":[160],"SUPERMAGOv2+.":[162],"Both":[163],"proposed":[164],"methods":[165],"consistently":[166],"outperform":[167],"state-of-the-art":[168],"across":[170],"various":[171],"analyses,":[172],"establishing":[173],"themselves":[174],"as":[175],"methodologies":[177],"for":[178],"protein":[179],"function":[180],"sequences.":[186]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
