{"id":"https://openalex.org/W4406238135","doi":"https://doi.org/10.1109/bibm62325.2024.10822117","title":"Secondary Structure-Guided Novel Protein Sequence Generation with Latent Graph Diffusion","display_name":"Secondary Structure-Guided Novel Protein Sequence Generation with Latent Graph Diffusion","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406238135","doi":"https://doi.org/10.1109/bibm62325.2024.10822117"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822117","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822117","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":"conference-paper","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/A5102766584","display_name":"Yutong Hu","orcid":"https://orcid.org/0000-0001-5339-3782"},"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":"Yutong Hu","raw_affiliation_strings":["Shanghai Jiao Tong University,Shanghai,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Shanghai,China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101964468","display_name":"Yang Tan","orcid":"https://orcid.org/0009-0004-7261-1705"},"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,Shanghai,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Shanghai,China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031625303","display_name":"Andi Han","orcid":"https://orcid.org/0000-0003-4655-655X"},"institutions":[{"id":"https://openalex.org/I4210126580","display_name":"RIKEN Center for Advanced Intelligence Project","ror":"https://ror.org/03ckxwf91","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210126580"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Andi Han","raw_affiliation_strings":["Riken AIP,Tokyo,Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Riken AIP,Tokyo,Japan","institution_ids":["https://openalex.org/I4210126580"]}]},{"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,Michigan,USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Michigan,Michigan,USA","institution_ids":["https://openalex.org/I27837315"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000680377","display_name":"Liang Hong","orcid":"https://orcid.org/0000-0003-0107-336X"},"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,Shanghai,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Shanghai,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,Shanghai,China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Jiao Tong University,Shanghai,China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":3.8249,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.93762416,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":null,"issue":null,"first_page":"31","last_page":"41"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9976000189781189,"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":0.9976000189781189,"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":0.9932000041007996,"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":0.9771000146865845,"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":0.638278603553772},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5554917454719543},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4839199185371399},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.248601496219635},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.06864705681800842},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.06595593690872192}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.638278603553772},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5554917454719543},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4839199185371399},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.248601496219635},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.06864705681800842},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.06595593690872192}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822117","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822117","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":[{"display_name":"Zero hunger","id":"https://metadata.un.org/sdg/2","score":0.47999998927116394}],"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":44,"referenced_works":["https://openalex.org/W2016589492","https://openalex.org/W2102245393","https://openalex.org/W3106745904","https://openalex.org/W3133458480","https://openalex.org/W3135130381","https://openalex.org/W3146944767","https://openalex.org/W4205773061","https://openalex.org/W4236236547","https://openalex.org/W4255594044","https://openalex.org/W4281898027","https://openalex.org/W4283698551","https://openalex.org/W4296032638","https://openalex.org/W4312933868","https://openalex.org/W4317212859","https://openalex.org/W4327550249","https://openalex.org/W4366520892","https://openalex.org/W4368374143","https://openalex.org/W4375858802","https://openalex.org/W4383957026","https://openalex.org/W4385245566","https://openalex.org/W4386708656","https://openalex.org/W4387966974","https://openalex.org/W4388024559","https://openalex.org/W4388694364","https://openalex.org/W4388979610","https://openalex.org/W4391849760","https://openalex.org/W4394892342","https://openalex.org/W4402396688","https://openalex.org/W6755207826","https://openalex.org/W6760045743","https://openalex.org/W6769627184","https://openalex.org/W6779823529","https://openalex.org/W6780145172","https://openalex.org/W6790561777","https://openalex.org/W6798447524","https://openalex.org/W6810245500","https://openalex.org/W6854154219","https://openalex.org/W6854177335","https://openalex.org/W6856409742","https://openalex.org/W6860844339","https://openalex.org/W6865088576","https://openalex.org/W6870615235","https://openalex.org/W6874234396","https://openalex.org/W6874933702"],"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":{"Designing":[0],"protein":[1,101,114,127,135],"sequences":[2,194],"with":[3,30,83,122,207],"restrictions":[4],"or":[5,29],"conditions":[6],"is":[7,40,132,222],"an":[8,158],"important":[9],"research":[10],"topic":[11],"in":[12,65,72,143,189],"biology.":[13],"Many":[14],"powerful":[15],"deep":[16],"generative":[17],"models":[18,125,179],"have":[19],"been":[20],"proposed":[21],"to":[22,26,47,138,211],"create":[23],"proteins":[24,46,52,82,155,206],"belonging":[25],"specific":[27,208],"families":[28],"determined":[31],"backbone":[32],"structures.":[33],"However,":[34],"the":[35,54,59,67,73,77,140,148,166,171,213],"amount":[36],"of":[37,69,94,100,106,150,161,173,204,216],"homologous":[38],"data":[39],"not":[41],"always":[42],"sufficient":[43],"for":[44,117],"any":[45],"train":[48],"a":[49,88,112],"model,":[50],"and":[51,92,103,126,163,180,192],"from":[53],"same":[55],"family":[56],"may":[57],"lack":[58],"necessary":[60],"structural":[61,151],"similarity,":[62],"posing":[63],"challenges":[64],"ensuring":[66,157],"presence":[68],"crucial":[70],"structures":[71,137,210],"generated":[74,154],"proteins.":[75],"On":[76],"other":[78],"hand,":[79],"when":[80],"generating":[81,190,205],"fixed":[84],"backbone,":[85],"there":[86],"exists":[87],"trade-off":[89],"between":[90],"reliability":[91],"flexibility":[93],"sequence":[95,120,167],"generation,":[96],"necessitating":[97],"prior":[98],"specification":[99],"length":[102],"precise":[104],"positions":[105],"amino":[107,118],"acids.":[108],"This":[109],"work":[110],"introduces":[111],"flexible":[113],"generation":[115,121,131],"method":[116,175],"acid":[119],"latent":[123],"diffusion":[124],"language":[128,178],"models.":[129],"The":[130,219],"conditioned":[133],"on":[134,153],"secondary":[136,209],"address":[139],"practical":[141],"considerations":[142],"bioengineering":[144],"better.":[145],"It":[146],"enables":[147],"imposition":[149],"constraints":[152],"while":[156],"adequate":[159],"level":[160],"novelty":[162],"diversity":[164],"at":[165,225],"level.":[168],"We":[169],"compare":[170],"performance":[172],"our":[174,217],"against":[176],"popular":[177],"structure-based":[181],"methods":[182],"using":[183],"quantifiable":[184],"metrics,":[185],"demonstrating":[186],"its":[187],"superiority":[188],"diverse":[191],"novel":[193],"that":[195],"exhibit":[196],"high":[197],"foldability.":[198],"Furthermore,":[199],"we":[200],"provide":[201],"case":[202],"studies":[203],"analyze":[212],"biological":[214],"significance":[215],"method.":[218],"source":[220],"code":[221],"publicly":[223],"available":[224],"https://github.com/riacd/CPDiffusion-SS.":[226]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}