{"id":"https://openalex.org/W4400493769","doi":"https://doi.org/10.1093/bioinformatics/btae445","title":"Fine-tuning protein embeddings for functional similarity evaluation","display_name":"Fine-tuning protein embeddings for functional similarity evaluation","publication_year":2024,"publication_date":"2024-07-10","ids":{"openalex":"https://openalex.org/W4400493769","doi":"https://doi.org/10.1093/bioinformatics/btae445","pmid":"https://pubmed.ncbi.nlm.nih.gov/38985218"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae445","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae445","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/8/btae445/58736621/btae445.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/article-pdf/40/8/btae445/58736621/btae445.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5075086152","display_name":"Andrew Dickson","orcid":"https://orcid.org/0000-0002-1146-6346"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Andrew Dickson","raw_affiliation_strings":["Departments of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California , Berkeley, CA 94720, United States"],"affiliations":[{"raw_affiliation_string":"Departments of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California , Berkeley, CA 94720, United States","institution_ids":["https://openalex.org/I95457486"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5062246663","display_name":"Mohammad R. K. Mofrad","orcid":"https://orcid.org/0000-0001-7004-4859"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mohammad R K Mofrad","raw_affiliation_strings":["Departments of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California , Berkeley, CA 94720, United States"],"affiliations":[{"raw_affiliation_string":"Departments of Bioengineering and Mechanical Engineering, Molecular Cell Biomechanics Laboratory, University of California , Berkeley, CA 94720, United States","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5075086152"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.7846,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.90865922,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"40","issue":"8","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":0.9997000098228455,"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":0.9997000098228455,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9929999709129333,"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/interpretability","display_name":"Interpretability","score":0.8507537841796875},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6952309608459473},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.6617329120635986},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6434058547019958},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5723523497581482},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5660517811775208},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.5403793454170227},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.508063793182373},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.5030786395072937},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4588954448699951},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4165412187576294},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.36436623334884644},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3515380024909973},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.18921101093292236},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1877700686454773},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11856922507286072},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10973584651947021}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.8507537841796875},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6952309608459473},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.6617329120635986},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6434058547019958},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5723523497581482},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5660517811775208},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.5403793454170227},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.508063793182373},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.5030786395072937},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4588954448699951},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4165412187576294},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.36436623334884644},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3515380024909973},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.18921101093292236},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1877700686454773},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11856922507286072},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10973584651947021},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0}],"mesh":[{"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":"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":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae445","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae445","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/8/btae445/58736621/btae445.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:38985218","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38985218","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:11299545","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11299545","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11299545/pdf/btae445.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"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae445","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae445","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/40/8/btae445/58736621/btae445.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":[{"id":"https://metadata.un.org/sdg/4","score":0.6700000166893005,"display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4400493769.pdf"},"referenced_works_count":39,"referenced_works":["https://openalex.org/W2068916031","https://openalex.org/W2098432760","https://openalex.org/W2101234009","https://openalex.org/W2103017472","https://openalex.org/W2103148772","https://openalex.org/W2107785922","https://openalex.org/W2108984616","https://openalex.org/W2110857277","https://openalex.org/W2117486996","https://openalex.org/W2158714788","https://openalex.org/W2164154943","https://openalex.org/W2187089797","https://openalex.org/W2618735189","https://openalex.org/W2899867782","https://openalex.org/W2953008890","https://openalex.org/W2953367535","https://openalex.org/W2966590054","https://openalex.org/W2989608901","https://openalex.org/W2998702515","https://openalex.org/W3096655658","https://openalex.org/W3112376646","https://openalex.org/W3118936575","https://openalex.org/W3143063265","https://openalex.org/W3177500196","https://openalex.org/W3207928532","https://openalex.org/W4205773061","https://openalex.org/W4236358448","https://openalex.org/W4309609816","https://openalex.org/W4317388119","https://openalex.org/W4318071656","https://openalex.org/W4320710091","https://openalex.org/W4327550249","https://openalex.org/W4367602258","https://openalex.org/W4378838672","https://openalex.org/W4387541035","https://openalex.org/W4389946938","https://openalex.org/W4392168151","https://openalex.org/W6675354045","https://openalex.org/W6852327111"],"related_works":["https://openalex.org/W2905433371","https://openalex.org/W2888392564","https://openalex.org/W4310278675","https://openalex.org/W4388422664","https://openalex.org/W4390569940","https://openalex.org/W4361193272","https://openalex.org/W2963326959","https://openalex.org/W4388685194","https://openalex.org/W4312407344","https://openalex.org/W2894289927"],"abstract_inverted_index":{"github.com/mofradlab/go_metric.":[0]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-02T15:55:50.835912","created_date":"2025-10-10T00:00:00"}
