{"id":"https://openalex.org/W4414585655","doi":"https://doi.org/10.1007/978-3-032-06118-8_22","title":"Do Protein Transformers Have Biological Intelligence?","display_name":"Do Protein Transformers Have Biological Intelligence?","publication_year":2025,"publication_date":"2025-09-28","ids":{"openalex":"https://openalex.org/W4414585655","doi":"https://doi.org/10.1007/978-3-032-06118-8_22"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-032-06118-8_22","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-032-06118-8_22","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047243024","display_name":"Fudong Lin","orcid":"https://orcid.org/0000-0003-0457-2527"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fudong Lin","raw_affiliation_strings":["University of Delaware, Newark, DE, 19716, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Delaware, Newark, DE, 19716, USA","institution_ids":["https://openalex.org/I86501945"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017177739","display_name":"Wenzhang Du","orcid":"https://orcid.org/0009-0004-4834-7895"},"institutions":[{"id":"https://openalex.org/I139759216","display_name":"Beijing University of Posts and Telecommunications","ror":"https://ror.org/04w9fbh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I139759216"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wanrou Du","raw_affiliation_strings":["Beijing University of Posts and Telecommunications, Haidian, Beijing, 100876, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing University of Posts and Telecommunications, Haidian, Beijing, 100876, China","institution_ids":["https://openalex.org/I139759216"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007536769","display_name":"Jinchan Liu","orcid":"https://orcid.org/0009-0001-1470-328X"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jinchan Liu","raw_affiliation_strings":["Yale University, New Haven, CT, 06520, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Yale University, New Haven, CT, 06520, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5099024190","display_name":"Tarikul I. Milon","orcid":null},"institutions":[{"id":"https://openalex.org/I79516672","display_name":"University of Louisiana at Lafayette","ror":"https://ror.org/01x8rc503","country_code":"US","type":"education","lineage":["https://openalex.org/I2799628689","https://openalex.org/I79516672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tarikul Milon","raw_affiliation_strings":["University of Louisiana at Lafayette, Lafayette, LA, 70504, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Louisiana at Lafayette, Lafayette, LA, 70504, USA","institution_ids":["https://openalex.org/I79516672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115816065","display_name":"Shelby Meche","orcid":null},"institutions":[{"id":"https://openalex.org/I79516672","display_name":"University of Louisiana at Lafayette","ror":"https://ror.org/01x8rc503","country_code":"US","type":"education","lineage":["https://openalex.org/I2799628689","https://openalex.org/I79516672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shelby Meche","raw_affiliation_strings":["University of Louisiana at Lafayette, Lafayette, LA, 70504, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Louisiana at Lafayette, Lafayette, LA, 70504, USA","institution_ids":["https://openalex.org/I79516672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053790111","display_name":"Xu Wu","orcid":"https://orcid.org/0000-0002-1176-8440"},"institutions":[{"id":"https://openalex.org/I79516672","display_name":"University of Louisiana at Lafayette","ror":"https://ror.org/01x8rc503","country_code":"US","type":"education","lineage":["https://openalex.org/I2799628689","https://openalex.org/I79516672"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wu Xu","raw_affiliation_strings":["University of Louisiana at Lafayette, Lafayette, LA, 70504, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Louisiana at Lafayette, Lafayette, LA, 70504, USA","institution_ids":["https://openalex.org/I79516672"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091040593","display_name":"Xiaoqi Qin","orcid":"https://orcid.org/0000-0002-5788-0657"},"institutions":[{"id":"https://openalex.org/I139759216","display_name":"Beijing University of Posts and Telecommunications","ror":"https://ror.org/04w9fbh59","country_code":"CN","type":"education","lineage":["https://openalex.org/I139759216"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoqi Qin","raw_affiliation_strings":["Beijing University of Posts and Telecommunications, Haidian, Beijing, 100876, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Beijing University of Posts and Telecommunications, Haidian, Beijing, 100876, China","institution_ids":["https://openalex.org/I139759216"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061718239","display_name":"Xu Yuan","orcid":"https://orcid.org/0000-0003-3775-3033"},"institutions":[{"id":"https://openalex.org/I86501945","display_name":"University of Delaware","ror":"https://ror.org/01sbq1a82","country_code":"US","type":"education","lineage":["https://openalex.org/I86501945"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xu Yuan","raw_affiliation_strings":["University of Delaware, Newark, DE, 19716, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Delaware, Newark, DE, 19716, USA","institution_ids":["https://openalex.org/I86501945"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5061718239"],"corresponding_institution_ids":["https://openalex.org/I86501945"],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.43387969,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"373","last_page":"390"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","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"}},"topics":[{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","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"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9894000291824341,"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"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9854999780654907,"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/transformer","display_name":"Transformer","score":0.6460999846458435},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.5562000274658203},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.477400004863739},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.4180000126361847},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.3840000033378601},{"id":"https://openalex.org/keywords/protein-structure-prediction","display_name":"Protein structure prediction","score":0.36000001430511475},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.3490999937057495},{"id":"https://openalex.org/keywords/protein-domain","display_name":"Protein domain","score":0.34209999442100525}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7976999878883362},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.6460999846458435},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5837000012397766},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.5562000274658203},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.477400004863739},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4228000044822693},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.4180000126361847},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.3840000033378601},{"id":"https://openalex.org/C18051474","wikidata":"https://www.wikidata.org/wiki/Q899656","display_name":"Protein structure prediction","level":3,"score":0.36000001430511475},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3490999937057495},{"id":"https://openalex.org/C144292202","wikidata":"https://www.wikidata.org/wiki/Q898273","display_name":"Protein domain","level":3,"score":0.34209999442100525},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.33070001006126404},{"id":"https://openalex.org/C171897839","wikidata":"https://www.wikidata.org/wiki/Q417841","display_name":"Protein family","level":3,"score":0.33059999346733093},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.30959999561309814},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.28839999437332153},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.28780001401901245},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.2849999964237213},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.2727999985218048},{"id":"https://openalex.org/C207685749","wikidata":"https://www.wikidata.org/wiki/Q2088941","display_name":"Domain knowledge","level":2,"score":0.2694000005722046},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.2685000002384186},{"id":"https://openalex.org/C2992918937","wikidata":"https://www.wikidata.org/wiki/Q7239","display_name":"Biological organism","level":3,"score":0.26759999990463257},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.25600001215934753}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/978-3-032-06118-8_22","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-032-06118-8_22","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1849277567","https://openalex.org/W2099837668","https://openalex.org/W2183341477","https://openalex.org/W2190008860","https://openalex.org/W2194775991","https://openalex.org/W2295107390","https://openalex.org/W2331143823","https://openalex.org/W2606462007","https://openalex.org/W2765793020","https://openalex.org/W2780572554","https://openalex.org/W2946794439","https://openalex.org/W2949999016","https://openalex.org/W2951433247","https://openalex.org/W2962858109","https://openalex.org/W2988157455","https://openalex.org/W3010219363","https://openalex.org/W3035253074","https://openalex.org/W3035422918","https://openalex.org/W3047237378","https://openalex.org/W3101609372","https://openalex.org/W3111174583","https://openalex.org/W3119058950","https://openalex.org/W3131500599","https://openalex.org/W3138516171","https://openalex.org/W3146944767","https://openalex.org/W3159481202","https://openalex.org/W3176196997","https://openalex.org/W3176482836","https://openalex.org/W3177079919","https://openalex.org/W3177500196","https://openalex.org/W3177828909","https://openalex.org/W3179485843","https://openalex.org/W3202105508","https://openalex.org/W3210684683","https://openalex.org/W3211728297","https://openalex.org/W4214612132","https://openalex.org/W4214614183","https://openalex.org/W4223581484","https://openalex.org/W4230405732","https://openalex.org/W4234609530","https://openalex.org/W4285010209","https://openalex.org/W4312453724","https://openalex.org/W4312694537","https://openalex.org/W4312933868","https://openalex.org/W4313156423","https://openalex.org/W4384891029","https://openalex.org/W4385768130","https://openalex.org/W4386806329","https://openalex.org/W4390874672","https://openalex.org/W4399554035","https://openalex.org/W4402857029"],"related_works":[],"abstract_inverted_index":null,"counts_by_year":[],"updated_date":"2026-06-13T06:13:01.061226","created_date":"2025-10-10T00:00:00"}