{"id":"https://openalex.org/W4416034470","doi":"https://doi.org/10.18653/v1/2025.findings-emnlp.1255","title":"Protein Large Language Models: A Comprehensive Survey","display_name":"Protein Large Language Models: A Comprehensive Survey","publication_year":2025,"publication_date":"2025-01-01","ids":{"openalex":"https://openalex.org/W4416034470","doi":"https://doi.org/10.18653/v1/2025.findings-emnlp.1255"},"language":null,"primary_location":{"id":"doi:10.18653/v1/2025.findings-emnlp.1255","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2025.findings-emnlp.1255","pdf_url":"https://aclanthology.org/2025.findings-emnlp.1255.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Findings of the Association for Computational Linguistics: EMNLP 2025","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://aclanthology.org/2025.findings-emnlp.1255.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Yijia Xiao","orcid":null},"institutions":[{"id":"https://openalex.org/I2799637951","display_name":"Abraham Baldwin Agricultural College","ror":"https://ror.org/04089t965","country_code":"US","type":"education","lineage":["https://openalex.org/I2799637951"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yijia Xiao","raw_affiliation_strings":["UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M","institution_ids":["https://openalex.org/I2799637951"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112946948","display_name":"Wanjia Zhao","orcid":null},"institutions":[{"id":"https://openalex.org/I2799637951","display_name":"Abraham Baldwin Agricultural College","ror":"https://ror.org/04089t965","country_code":"US","type":"education","lineage":["https://openalex.org/I2799637951"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wanjia Zhao","raw_affiliation_strings":["UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M","institution_ids":["https://openalex.org/I2799637951"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026460845","display_name":"Junkai Zhang","orcid":"https://orcid.org/0000-0002-6407-6173"},"institutions":[{"id":"https://openalex.org/I2799637951","display_name":"Abraham Baldwin Agricultural College","ror":"https://ror.org/04089t965","country_code":"US","type":"education","lineage":["https://openalex.org/I2799637951"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Junkai Zhang","raw_affiliation_strings":["UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M","institution_ids":["https://openalex.org/I2799637951"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yiqiao Jin","orcid":null},"institutions":[{"id":"https://openalex.org/I2799637951","display_name":"Abraham Baldwin Agricultural College","ror":"https://ror.org/04089t965","country_code":"US","type":"education","lineage":["https://openalex.org/I2799637951"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yiqiao Jin","raw_affiliation_strings":["UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M","institution_ids":["https://openalex.org/I2799637951"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100399276","display_name":"Han Zhang","orcid":"https://orcid.org/0000-0002-0166-1973"},"institutions":[{"id":"https://openalex.org/I2799637951","display_name":"Abraham Baldwin Agricultural College","ror":"https://ror.org/04089t965","country_code":"US","type":"education","lineage":["https://openalex.org/I2799637951"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Han Zhang","raw_affiliation_strings":["UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M","institution_ids":["https://openalex.org/I2799637951"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zhicheng Ren","orcid":null},"institutions":[{"id":"https://openalex.org/I2799637951","display_name":"Abraham Baldwin Agricultural College","ror":"https://ror.org/04089t965","country_code":"US","type":"education","lineage":["https://openalex.org/I2799637951"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhicheng Ren","raw_affiliation_strings":["UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M","institution_ids":["https://openalex.org/I2799637951"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111089828","display_name":"Renliang Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I2799637951","display_name":"Abraham Baldwin Agricultural College","ror":"https://ror.org/04089t965","country_code":"US","type":"education","lineage":["https://openalex.org/I2799637951"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Renliang Sun","raw_affiliation_strings":["UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M","institution_ids":["https://openalex.org/I2799637951"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5118899416","display_name":"Haocheng Wang","orcid":"https://orcid.org/0009-0004-4757-2740"},"institutions":[{"id":"https://openalex.org/I2799637951","display_name":"Abraham Baldwin Agricultural College","ror":"https://ror.org/04089t965","country_code":"US","type":"education","lineage":["https://openalex.org/I2799637951"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haixin Wang","raw_affiliation_strings":["UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M","institution_ids":["https://openalex.org/I2799637951"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034248530","display_name":"Guangquan Wan","orcid":"https://orcid.org/0000-0003-3922-4231"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Guancheng Wan","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101593399","display_name":"Lu Pan","orcid":"https://orcid.org/0000-0001-6564-0939"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pan Lu","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079262206","display_name":"Xiao Luo","orcid":"https://orcid.org/0000-0002-8708-5881"},"institutions":[{"id":"https://openalex.org/I2799637951","display_name":"Abraham Baldwin Agricultural College","ror":"https://ror.org/04089t965","country_code":"US","type":"education","lineage":["https://openalex.org/I2799637951"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiao Luo","raw_affiliation_strings":["UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M","institution_ids":["https://openalex.org/I2799637951"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100329827","display_name":"Yanwen Zhang","orcid":"https://orcid.org/0000-0003-1833-3885"},"institutions":[{"id":"https://openalex.org/I2799637951","display_name":"Abraham Baldwin Agricultural College","ror":"https://ror.org/04089t965","country_code":"US","type":"education","lineage":["https://openalex.org/I2799637951"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu Zhang","raw_affiliation_strings":["UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M","institution_ids":["https://openalex.org/I2799637951"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005779176","display_name":"James Zou","orcid":"https://orcid.org/0000-0001-8880-4764"},"institutions":[{"id":"https://openalex.org/I2799637951","display_name":"Abraham Baldwin Agricultural College","ror":"https://ror.org/04089t965","country_code":"US","type":"education","lineage":["https://openalex.org/I2799637951"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James Zou","raw_affiliation_strings":["UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M","institution_ids":["https://openalex.org/I2799637951"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025213473","display_name":"Yizhou Sun","orcid":"https://orcid.org/0000-0003-1812-6843"},"institutions":[{"id":"https://openalex.org/I2799637951","display_name":"Abraham Baldwin Agricultural College","ror":"https://ror.org/04089t965","country_code":"US","type":"education","lineage":["https://openalex.org/I2799637951"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yizhou Sun","raw_affiliation_strings":["UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M","institution_ids":["https://openalex.org/I2799637951"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100445442","display_name":"Dawei Wang","orcid":"https://orcid.org/0000-0002-6651-4261"},"institutions":[{"id":"https://openalex.org/I2799637951","display_name":"Abraham Baldwin Agricultural College","ror":"https://ror.org/04089t965","country_code":"US","type":"education","lineage":["https://openalex.org/I2799637951"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Wang","raw_affiliation_strings":["UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"UCLA  Stanford Georgia Tech  UW-Madison  Texas A&M","institution_ids":["https://openalex.org/I2799637951"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":15,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":3.8619,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.94040017,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"23080","last_page":"23103"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.3587000072002411,"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":0.3587000072002411,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.08079999685287476,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.06629999727010727,"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/association","display_name":"Association (psychology)","score":0.3285999894142151},{"id":"https://openalex.org/keywords/data-collection","display_name":"Data collection","score":0.3061999976634979},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.28189998865127563},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.2565000057220459},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.2540000081062317}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5077000260353088},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37130001187324524},{"id":"https://openalex.org/C142853389","wikidata":"https://www.wikidata.org/wiki/Q744778","display_name":"Association (psychology)","level":2,"score":0.3285999894142151},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3075000047683716},{"id":"https://openalex.org/C133462117","wikidata":"https://www.wikidata.org/wiki/Q4929239","display_name":"Data collection","level":2,"score":0.3061999976634979},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.28189998865127563},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.2676999866962433},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.26100000739097595},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.2565000057220459},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.2540000081062317},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.25360000133514404}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.18653/v1/2025.findings-emnlp.1255","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2025.findings-emnlp.1255","pdf_url":"https://aclanthology.org/2025.findings-emnlp.1255.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Findings of the Association for Computational Linguistics: EMNLP 2025","raw_type":"proceedings-article"}],"best_oa_location":{"id":"doi:10.18653/v1/2025.findings-emnlp.1255","is_oa":true,"landing_page_url":"https://doi.org/10.18653/v1/2025.findings-emnlp.1255","pdf_url":"https://aclanthology.org/2025.findings-emnlp.1255.pdf","source":null,"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Findings of the Association for Computational Linguistics: EMNLP 2025","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2176371381","display_name":null,"funder_award_id":"U54HG012517","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2901143931","display_name":"III: Medium: Collaborative Research: Collaborative Machine-Learning-Centric Data Analytics at Scale","funder_award_id":"2106859","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8481604737","display_name":"Collaborative Research: III: Medium: VirtualLab: Integrating Deep Graph Learning and Causal Inference for Multi-Agent Dynamical Systems","funder_award_id":"2312501","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4416034470.pdf","grobid_xml":"https://content.openalex.org/works/W4416034470.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Yijia":[0],"Xiao,":[1],"Wanjia":[2],"Zhao,":[3],"Junkai":[4],"Zhang,":[5,9,23],"Yiqiao":[6],"Jin,":[7],"Han":[8],"Zhicheng":[10],"Ren,":[11],"Renliang":[12],"Sun,":[13,27],"Haixin":[14],"Wang,":[15],"Guancheng":[16],"Wan,":[17],"Pan":[18],"Lu,":[19],"Xiao":[20],"Luo,":[21],"Yu":[22],"James":[24],"Zou,":[25],"Yizhou":[26],"Wei":[28],"Wang.":[29],"Findings":[30],"of":[31],"the":[32],"Association":[33],"for":[34],"Computational":[35],"Linguistics:":[36],"EMNLP":[37],"2025.":[38,39]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":2}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-11-08T00:00:00"}
