{"id":"https://openalex.org/W4406259988","doi":"https://doi.org/10.1109/bibm62325.2024.10822035","title":"Protein Representation Learning with Sequence Information Embedding: Does it Always Lead to a Better Performance?","display_name":"Protein Representation Learning with Sequence Information Embedding: Does it Always Lead to a Better Performance?","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406259988","doi":"https://doi.org/10.1109/bibm62325.2024.10822035"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822035","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822035","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-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":"https://openalex.org/A5108971669","display_name":"Yang Tan","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Tan","raw_affiliation_strings":["Shanghai Jiao Tong University,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065268874","display_name":"Lirong Zheng","orcid":"https://orcid.org/0000-0001-6803-5048"},"institutions":[{"id":"https://openalex.org/I27837315","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291","country_code":"US","type":"education","lineage":["https://openalex.org/I27837315"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lirong Zheng","raw_affiliation_strings":["University of Michigan,MI,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Michigan,MI,USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090728932","display_name":"Bozitao Zhong","orcid":"https://orcid.org/0000-0001-9363-6099"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bozitao Zhong","raw_affiliation_strings":["Shanghai Jiao Tong University,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009852060","display_name":"Liang Hong","orcid":"https://orcid.org/0000-0003-1101-7046"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liang Hong","raw_affiliation_strings":["Shanghai Jiao Tong University,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027695625","display_name":"Bingxin Zhou","orcid":"https://orcid.org/0000-0002-3897-9766"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bingxin Zhou","raw_affiliation_strings":["Shanghai Jiao Tong University,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.2041,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.5874804,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"233","last_page":"239"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","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/T12254","display_name":"Machine Learning in Bioinformatics","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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9944999814033508,"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":0.9939000010490417,"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":0.6423915028572083},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.6404028534889221},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5876420140266418},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5690221190452576},{"id":"https://openalex.org/keywords/lead","display_name":"Lead (geology)","score":0.5399347543716431},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4524688422679901},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.15816763043403625},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.09240847826004028},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08606937527656555}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6423915028572083},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.6404028534889221},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5876420140266418},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5690221190452576},{"id":"https://openalex.org/C2777093003","wikidata":"https://www.wikidata.org/wiki/Q6508345","display_name":"Lead (geology)","level":2,"score":0.5399347543716431},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4524688422679901},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.15816763043403625},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09240847826004028},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08606937527656555},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822035","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822035","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2024 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321881","display_name":"Shanghai Municipal Education Commission","ror":"https://ror.org/05tewj457"},{"id":"https://openalex.org/F4320322999","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1522037109","https://openalex.org/W1991188255","https://openalex.org/W2008708467","https://openalex.org/W2030090172","https://openalex.org/W2102245393","https://openalex.org/W2108067237","https://openalex.org/W2113832037","https://openalex.org/W2999044305","https://openalex.org/W3106745904","https://openalex.org/W3167575787","https://openalex.org/W3177828909","https://openalex.org/W4220685469","https://openalex.org/W4224939843","https://openalex.org/W4318071656","https://openalex.org/W4327550249","https://openalex.org/W4362471278","https://openalex.org/W4367052125","https://openalex.org/W4375858802","https://openalex.org/W4385245566","https://openalex.org/W4387966974","https://openalex.org/W4389472984","https://openalex.org/W4403546608","https://openalex.org/W4404447386","https://openalex.org/W4404755712","https://openalex.org/W6631190155","https://openalex.org/W6782527804","https://openalex.org/W6809747699","https://openalex.org/W6810245500"],"related_works":["https://openalex.org/W4255463199","https://openalex.org/W4281691423","https://openalex.org/W2411039299","https://openalex.org/W1856410221","https://openalex.org/W2081900870","https://openalex.org/W2318949977","https://openalex.org/W2334139353","https://openalex.org/W4251174968","https://openalex.org/W4243014959","https://openalex.org/W2966686650"],"abstract_inverted_index":{"Deep":[0],"learning":[1,61,114,164],"has":[2,17],"become":[3],"a":[4,34,59,72,91,138,158],"crucial":[5],"tool":[6],"in":[7,21,30,53,127],"studying":[8],"proteins.":[9],"While":[10],"the":[11,22,31,134,153],"significance":[12],"of":[13,86],"modeling":[14],"protein":[15,96,124,168],"structure":[16,45,82,129,169],"been":[18],"discussed":[19],"extensively":[20],"literature,":[23],"amino":[24,50,80],"acid":[25,51,81],"types":[26,52],"are":[27],"typically":[28],"included":[29],"input":[32],"as":[33],"default":[35],"operation":[36],"for":[37,133,161],"many":[38],"inference":[39],"tasks.":[40],"This":[41,156],"study":[42],"demonstrates":[43],"with":[44,98,148],"alignment":[46,75],"task":[47,94],"that":[48],"embedding":[49],"some":[54],"cases":[55],"may":[56],"not":[57],"help":[58],"deep":[60,163],"model":[62],"learn":[63],"better":[64],"representation.":[65,83],"To":[66],"this":[67],"end,":[68],"we":[69],"propose":[70],"ProtLOCA,":[71],"local":[73,128,144],"geometry":[74],"method":[76,108],"based":[77,103],"solely":[78],"on":[79,95,104],"The":[84],"effectiveness":[85],"ProtLOCA":[87,132],"is":[88],"examined":[89],"by":[90,116],"global":[92],"structure-matching":[93],"pairs":[97],"an":[99],"independent":[100],"test":[101],"dataset":[102],"CATH":[105],"labels.":[106],"Our":[107],"outperforms":[109],"existing":[110],"sequence-and":[111],"structure-based":[112],"representation":[113],"methods":[115,165],"more":[117],"quickly":[118],"and":[119],"accurately":[120],"matching":[121],"structurally":[122],"consistent":[123],"domains.":[125],"Furthermore,":[126],"pairing":[130],"tasks,":[131],"first":[135],"time":[136],"provides":[137],"valid":[139],"solution":[140],"to":[141,166,170],"highlight":[142],"common":[143],"structures":[145,151],"among":[146],"proteins":[147],"different":[149],"overall":[150],"but":[152],"same":[154],"function.":[155,172],"suggests":[157],"new":[159],"possibility":[160],"using":[162],"analyze":[167],"infer":[171]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
