{"id":"https://openalex.org/W4412718912","doi":"https://doi.org/10.1109/tai.2025.3592637","title":"Towards General Protein Structure Representation Learning With a Protein Size Prompt","display_name":"Towards General Protein Structure Representation Learning With a Protein Size Prompt","publication_year":2025,"publication_date":"2025-07-25","ids":{"openalex":"https://openalex.org/W4412718912","doi":"https://doi.org/10.1109/tai.2025.3592637"},"language":"en","primary_location":{"id":"doi:10.1109/tai.2025.3592637","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tai.2025.3592637","pdf_url":null,"source":{"id":"https://openalex.org/S4210169448","display_name":"IEEE Transactions on Artificial Intelligence","issn_l":"2691-4581","issn":["2691-4581"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Artificial Intelligence","raw_type":"journal-article"},"type":"article","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":null,"display_name":"Ao Shen","orcid":"https://orcid.org/0009-0001-1937-6855"},"institutions":[{"id":"https://openalex.org/I133868755","display_name":"Shanghai Medical College of Fudan University","ror":"https://ror.org/01zntxs11","country_code":"CN","type":"education","lineage":["https://openalex.org/I133868755","https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ao Shen","raw_affiliation_strings":["Digital Medical Research Center, School of Basic Medical Science, Fudan University, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Digital Medical Research Center, School of Basic Medical Science, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I133868755"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011879942","display_name":"Mingzhi Yuan","orcid":"https://orcid.org/0000-0003-1322-7530"},"institutions":[{"id":"https://openalex.org/I133868755","display_name":"Shanghai Medical College of Fudan University","ror":"https://ror.org/01zntxs11","country_code":"CN","type":"education","lineage":["https://openalex.org/I133868755","https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingzhi Yuan","raw_affiliation_strings":["Digital Medical Research Center, School of Basic Medical Science, Fudan University, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Digital Medical Research Center, School of Basic Medical Science, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I133868755"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103062942","display_name":"Yingfan Ma","orcid":"https://orcid.org/0009-0004-7335-785X"},"institutions":[{"id":"https://openalex.org/I133868755","display_name":"Shanghai Medical College of Fudan University","ror":"https://ror.org/01zntxs11","country_code":"CN","type":"education","lineage":["https://openalex.org/I133868755","https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yingfan Ma","raw_affiliation_strings":["Digital Medical Research Center, School of Basic Medical Science, Fudan University, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Digital Medical Research Center, School of Basic Medical Science, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I133868755"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Qiao Huang","orcid":"https://orcid.org/0000-0002-3579-538X"},"institutions":[{"id":"https://openalex.org/I133868755","display_name":"Shanghai Medical College of Fudan University","ror":"https://ror.org/01zntxs11","country_code":"CN","type":"education","lineage":["https://openalex.org/I133868755","https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiao Huang","raw_affiliation_strings":["Digital Medical Research Center, School of Basic Medical Science, Fudan University, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Digital Medical Research Center, School of Basic Medical Science, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I133868755"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100594305","display_name":"Jie Du","orcid":null},"institutions":[{"id":"https://openalex.org/I133868755","display_name":"Shanghai Medical College of Fudan University","ror":"https://ror.org/01zntxs11","country_code":"CN","type":"education","lineage":["https://openalex.org/I133868755","https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jie Du","raw_affiliation_strings":["Digital Medical Research Center, School of Basic Medical Science, Fudan University, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Digital Medical Research Center, School of Basic Medical Science, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I133868755"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zhijuan Cao","orcid":"https://orcid.org/0000-0002-0926-733X"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhijuan Cao","raw_affiliation_strings":["School of Pharmacy, Fudan University, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"School of Pharmacy, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039752906","display_name":"Manning Wang","orcid":null},"institutions":[{"id":"https://openalex.org/I133868755","display_name":"Shanghai Medical College of Fudan University","ror":"https://ror.org/01zntxs11","country_code":"CN","type":"education","lineage":["https://openalex.org/I133868755","https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Manning Wang","raw_affiliation_strings":["Digital Medical Research Center, School of Basic Medical Science, Fudan University, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Digital Medical Research Center, School of Basic Medical Science, Fudan University, Shanghai, China","institution_ids":["https://openalex.org/I133868755"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I133868755"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.1620928,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"7","issue":"2","first_page":"1158","last_page":"1167"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9940000176429749,"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":0.9940000176429749,"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":0.9926999807357788,"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":0.9891999959945679,"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/representation","display_name":"Representation (politics)","score":0.5726361870765686},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4040069878101349},{"id":"https://openalex.org/keywords/political-science","display_name":"Political science","score":0.07160115242004395}],"concepts":[{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5726361870765686},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4040069878101349},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.07160115242004395},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/tai.2025.3592637","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tai.2025.3592637","pdf_url":null,"source":{"id":"https://openalex.org/S4210169448","display_name":"IEEE Transactions on Artificial Intelligence","issn_l":"2691-4581","issn":["2691-4581"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Artificial Intelligence","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8385852964","display_name":null,"funder_award_id":"24J22800800","funder_id":"https://openalex.org/F4320336652","funder_display_name":"Science and Technology Innovation Plan Of Shanghai Science and Technology Commission"}],"funders":[{"id":"https://openalex.org/F4320336652","display_name":"Science and Technology Innovation Plan Of Shanghai Science and Technology Commission","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1490161904","https://openalex.org/W1901129140","https://openalex.org/W1993046136","https://openalex.org/W2064030835","https://openalex.org/W2069032538","https://openalex.org/W2102245393","https://openalex.org/W2111973517","https://openalex.org/W2148853951","https://openalex.org/W2170747616","https://openalex.org/W2776525063","https://openalex.org/W2953169496","https://openalex.org/W2955138922","https://openalex.org/W2968494487","https://openalex.org/W3100159300","https://openalex.org/W3163965514","https://openalex.org/W3177828909","https://openalex.org/W4210400672","https://openalex.org/W4256395558","https://openalex.org/W4283032119","https://openalex.org/W4309506674","https://openalex.org/W4312056999","https://openalex.org/W4312222866","https://openalex.org/W4321769975","https://openalex.org/W4323065907","https://openalex.org/W4323438792","https://openalex.org/W4365444089","https://openalex.org/W4375858802","https://openalex.org/W4381332577","https://openalex.org/W4384927547","https://openalex.org/W4385152156","https://openalex.org/W4387772748","https://openalex.org/W4388665407","https://openalex.org/W4389126617","https://openalex.org/W4389225229","https://openalex.org/W4390871487","https://openalex.org/W4391449530","https://openalex.org/W4394711270","https://openalex.org/W4396789292","https://openalex.org/W4399041810","https://openalex.org/W4399391276","https://openalex.org/W4400275265","https://openalex.org/W4402589989","https://openalex.org/W4406033692","https://openalex.org/W4406408768"],"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/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"Deep":[0],"learning-based":[1],"protein":[2,87,93,115],"function":[3],"analysis":[4],"is":[5,17,32],"rapidly":[6],"advancing,":[7],"but":[8],"most":[9],"methods":[10,55],"rely":[11],"heavily":[12],"on":[13,43,48,74],"labeled":[14],"data,":[15],"which":[16,67],"typically":[18],"scarce":[19],"due":[20],"to":[21,102,110,146],"the":[22,40,57,75,99,138,147],"need":[23],"for":[24],"expensive":[25],"wet":[26],"lab":[27],"experiments.":[28],"Self-supervised":[29],"learning":[30,89],"(SSL)":[31],"a":[33,71,85,92],"viable":[34],"solution":[35],"because":[36],"it":[37],"can":[38],"improve":[39],"model":[41,101],"performance":[42,139],"downstream":[44,65,111,124],"tasks":[45,112],"by":[46],"pre-training":[47,63,107],"large-scale":[49],"unlabeled":[50],"data.":[51],"However,":[52],"existing":[53],"SSL":[54],"overlook":[56],"disparities":[58],"in":[59,140],"data":[60,127,131],"distributions":[61],"between":[62],"and":[64,108,129],"tasks,":[66,125],"we":[68,83],"show":[69,133],"has":[70],"large":[72],"influence":[73],"effectiveness":[76],"of":[77,119],"SSL.":[78],"To":[79],"tackle":[80],"this":[81],"problem,":[82],"propose":[84],"new":[86],"representation":[88],"framework":[90],"with":[91,113,143],"size":[94,116],"prompt":[95],"(ProSP).":[96],"ProSP":[97,135],"allows":[98],"pre-trained":[100],"learn":[103],"size-related":[104],"information":[105],"during":[106],"adapt":[109],"different":[114],"distributions.":[117],"Results":[118],"48":[120],"experiments":[121,142],"across":[122],"eight":[123],"three":[126],"splits,":[128],"two":[130],"representations":[132],"that":[134],"successfully":[136],"improves":[137],"all":[141],"minimal":[144],"modifications":[145],"original":[148],"model.":[149]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
