{"id":"https://openalex.org/W4391075279","doi":"https://doi.org/10.1093/bioinformatics/btae031","title":"Insights into the inner workings of transformer models for protein function prediction","display_name":"Insights into the inner workings of transformer models for protein function prediction","publication_year":2024,"publication_date":"2024-01-19","ids":{"openalex":"https://openalex.org/W4391075279","doi":"https://doi.org/10.1093/bioinformatics/btae031","pmid":"https://pubmed.ncbi.nlm.nih.gov/38244570"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae031","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae031","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae031/56284972/btae031.pdf","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://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae031/56284972/btae031.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040381687","display_name":"Markus Wenzel","orcid":"https://orcid.org/0000-0002-6540-1476"},"institutions":[{"id":"https://openalex.org/I2800274787","display_name":"Fraunhofer Institute for Telecommunications, Heinrich Hertz Institute","ror":"https://ror.org/02tbr6331","country_code":"DE","type":"facility","lineage":["https://openalex.org/I2800274787","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Markus Wenzel","raw_affiliation_strings":["Department of Artificial Intelligence, Fraunhofer Institute for Telecommunications, Heinrich-Hertz-Institut, HHI , Einsteinufer 37 , 10587 Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Artificial Intelligence, Fraunhofer Institute for Telecommunications, Heinrich-Hertz-Institut, HHI , Einsteinufer 37 , 10587 Berlin, Germany","institution_ids":["https://openalex.org/I2800274787"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016953274","display_name":"Erik Gr\u00fcner","orcid":null},"institutions":[{"id":"https://openalex.org/I2800274787","display_name":"Fraunhofer Institute for Telecommunications, Heinrich Hertz Institute","ror":"https://ror.org/02tbr6331","country_code":"DE","type":"facility","lineage":["https://openalex.org/I2800274787","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Erik Gr\u00fcner","raw_affiliation_strings":["Department of Artificial Intelligence, Fraunhofer Institute for Telecommunications, Heinrich-Hertz-Institut, HHI , Einsteinufer 37 , 10587 Berlin, Germany"],"affiliations":[{"raw_affiliation_string":"Department of Artificial Intelligence, Fraunhofer Institute for Telecommunications, Heinrich-Hertz-Institut, HHI , Einsteinufer 37 , 10587 Berlin, Germany","institution_ids":["https://openalex.org/I2800274787"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034797797","display_name":"Nils Strodthoff","orcid":"https://orcid.org/0000-0003-4447-0162"},"institutions":[{"id":"https://openalex.org/I129877168","display_name":"Carl von Ossietzky Universit\u00e4t Oldenburg","ror":"https://ror.org/033n9gh91","country_code":"DE","type":"education","lineage":["https://openalex.org/I129877168"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Nils Strodthoff","raw_affiliation_strings":["School VI - Medicine and Health Services, Carl von Ossietzky University of Oldenburg , Ammerl\u00e4nder Heerstr. 114-118 , 26129 Oldenburg, Germany"],"affiliations":[{"raw_affiliation_string":"School VI - Medicine and Health Services, Carl von Ossietzky University of Oldenburg , Ammerl\u00e4nder Heerstr. 114-118 , 26129 Oldenburg, Germany","institution_ids":["https://openalex.org/I129877168"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5040381687"],"corresponding_institution_ids":["https://openalex.org/I2800274787"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.4346,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.92822671,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"40","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9987000226974487,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9987000226974487,"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":0.9973000288009644,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.996999979019165,"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/computer-science","display_name":"Computer science","score":0.7262813448905945},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.6897314786911011},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5644497275352478},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5504459142684937},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.49993896484375},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4356442987918854},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.32463109493255615},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13556507229804993}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7262813448905945},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.6897314786911011},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5644497275352478},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5504459142684937},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.49993896484375},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4356442987918854},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.32463109493255615},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13556507229804993},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072417","descriptor_name":"Protein Domains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","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":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btae031","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae031","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae031/56284972/btae031.pdf","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:38244570","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38244570","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:10950482","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10950482","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10950482/pdf/btae031.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"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"},{"id":"pmh:oai:publica.fraunhofer.de:publica/475298","is_oa":true,"landing_page_url":"https://publica.fraunhofer.de/handle/publica/475298","pdf_url":null,"source":{"id":"https://openalex.org/S4306400318","display_name":"Fraunhofer-Publica (Fraunhofer-Gesellschaft)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4923324","host_organization_name":"Fraunhofer-Gesellschaft","host_organization_lineage":["https://openalex.org/I4923324"],"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":null,"raw_type":"journal article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae031","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae031","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae031/56284972/btae031.pdf","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/G3031800739","display_name":null,"funder_award_id":"BIFOLD","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G4533892997","display_name":null,"funder_award_id":"01IS18037","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G5269777170","display_name":null,"funder_award_id":"01IS18037A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G7225624288","display_name":null,"funder_award_id":"This work was","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"},{"id":"https://openalex.org/G7624340995","display_name":null,"funder_award_id":"01IS18025A","funder_id":"https://openalex.org/F4320321114","funder_display_name":"Bundesministerium f\u00fcr Bildung und Forschung"}],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4391075279.pdf"},"referenced_works_count":98,"referenced_works":["https://openalex.org/W1144107824","https://openalex.org/W1554885991","https://openalex.org/W1787224781","https://openalex.org/W2042655455","https://openalex.org/W2045204781","https://openalex.org/W2098432760","https://openalex.org/W2102461176","https://openalex.org/W2103017472","https://openalex.org/W2107158607","https://openalex.org/W2110065044","https://openalex.org/W2110679449","https://openalex.org/W2117486996","https://openalex.org/W2121926265","https://openalex.org/W2166637863","https://openalex.org/W2173591891","https://openalex.org/W2187089797","https://openalex.org/W2227395312","https://openalex.org/W2436075400","https://openalex.org/W2511680692","https://openalex.org/W2569156823","https://openalex.org/W2615066396","https://openalex.org/W2657631929","https://openalex.org/W2737546073","https://openalex.org/W2762638728","https://openalex.org/W2766352633","https://openalex.org/W2807567459","https://openalex.org/W2887029338","https://openalex.org/W2892210937","https://openalex.org/W2901045238","https://openalex.org/W2908663744","https://openalex.org/W2921802966","https://openalex.org/W2945726413","https://openalex.org/W2949342052","https://openalex.org/W2951731136","https://openalex.org/W2953008890","https://openalex.org/W2953073956","https://openalex.org/W2956569764","https://openalex.org/W2958089299","https://openalex.org/W2966590054","https://openalex.org/W2971227267","https://openalex.org/W2980789587","https://openalex.org/W2981731882","https://openalex.org/W2989608901","https://openalex.org/W2999481648","https://openalex.org/W3000982932","https://openalex.org/W3003257820","https://openalex.org/W3031914912","https://openalex.org/W3037888463","https://openalex.org/W3040052015","https://openalex.org/W3100711616","https://openalex.org/W3103145119","https://openalex.org/W3107600318","https://openalex.org/W3112376646","https://openalex.org/W3112600195","https://openalex.org/W3118936575","https://openalex.org/W3127238141","https://openalex.org/W3132191748","https://openalex.org/W3133523710","https://openalex.org/W3134751001","https://openalex.org/W3146366485","https://openalex.org/W3146944767","https://openalex.org/W3162614523","https://openalex.org/W3163595068","https://openalex.org/W3166142427","https://openalex.org/W3177500196","https://openalex.org/W3177828909","https://openalex.org/W3179436811","https://openalex.org/W3198923619","https://openalex.org/W3199799076","https://openalex.org/W3201757323","https://openalex.org/W3202070718","https://openalex.org/W3211795435","https://openalex.org/W4205773061","https://openalex.org/W4206386249","https://openalex.org/W4220991280","https://openalex.org/W4225687252","https://openalex.org/W4236358448","https://openalex.org/W4281291878","https://openalex.org/W4283588627","https://openalex.org/W4288066876","https://openalex.org/W4288089799","https://openalex.org/W4290546426","https://openalex.org/W4310498446","https://openalex.org/W4317369987","https://openalex.org/W4317868880","https://openalex.org/W4318071656","https://openalex.org/W4327550249","https://openalex.org/W4362471278","https://openalex.org/W4362664122","https://openalex.org/W4367052125","https://openalex.org/W6676731462","https://openalex.org/W6741895047","https://openalex.org/W6754669440","https://openalex.org/W6761236773","https://openalex.org/W6769627184","https://openalex.org/W6780110802","https://openalex.org/W6786498300","https://openalex.org/W6850026054"],"related_works":["https://openalex.org/W2081900870","https://openalex.org/W2345479200","https://openalex.org/W2183306018","https://openalex.org/W2849310602","https://openalex.org/W3006008237","https://openalex.org/W2419146053","https://openalex.org/W4388890789","https://openalex.org/W2088247287","https://openalex.org/W2049082574","https://openalex.org/W3081644756"],"abstract_inverted_index":{"Source":[0],"code":[1],"can":[2],"be":[3],"accessed":[4],"at":[5],"https://github.com/markuswenzel/xai-proteins.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":3}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
