{"id":"https://openalex.org/W4406260829","doi":"https://doi.org/10.1109/bibm62325.2024.10822652","title":"ProXplore: A GPU-Enhanced Protein Discovery Engine","display_name":"ProXplore: A GPU-Enhanced Protein Discovery Engine","publication_year":2024,"publication_date":"2024-12-03","ids":{"openalex":"https://openalex.org/W4406260829","doi":"https://doi.org/10.1109/bibm62325.2024.10822652"},"language":"en","primary_location":{"id":"doi:10.1109/bibm62325.2024.10822652","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822652","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/A5101848528","display_name":"Zequn Sun","orcid":"https://orcid.org/0000-0003-4177-9199"},"institutions":[{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zewen Sun","raw_affiliation_strings":["University of Chinese Academy of Sciences"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Chinese Academy of Sciences","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055477377","display_name":"Peiheng Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Peiheng Zhang","raw_affiliation_strings":["CAS,Institute of Intelligent Computing Technology,Suzhou"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAS,Institute of Intelligent Computing Technology,Suzhou","institution_ids":["https://openalex.org/I4210090176"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110712757","display_name":"Xianchun Fu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xingzhuo Fu","raw_affiliation_strings":["University of Chinese Academy of Sciences"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Chinese Academy of Sciences","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100453921","display_name":"Xueqi Li","orcid":"https://orcid.org/0000-0002-1477-9276"},"institutions":[{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xueqi Li","raw_affiliation_strings":["CAS,State Key Lab of Processors, Institute of Computing Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CAS,State Key Lab of Processors, Institute of Computing Technology","institution_ids":["https://openalex.org/I4210090176"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"4276","last_page":"4283"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9919999837875366,"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":0.9919999837875366,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9542999863624573,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9509999752044678,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6843058466911316}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6843058466911316}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm62325.2024.10822652","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm62325.2024.10822652","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":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1596947964","https://openalex.org/W1984794455","https://openalex.org/W2059136964","https://openalex.org/W2618265628","https://openalex.org/W2963457143","https://openalex.org/W2980200167","https://openalex.org/W3081168214","https://openalex.org/W3212854871","https://openalex.org/W4205773061","https://openalex.org/W4212863848","https://openalex.org/W4288066876","https://openalex.org/W6713134421","https://openalex.org/W6778883912"],"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":{"Language":[0],"models":[1,56,75],"have":[2,12],"achieved":[3],"unprecedented":[4],"success":[5],"in":[6,41,50,63,66,126,146,157],"natural":[7,29],"language":[8,30,55,81],"processing":[9],"tasks":[10],"and":[11,101,107,130,166,174],"recently":[13],"been":[14],"adapted":[15],"for":[16,72,79,170],"biological":[17],"sequences.":[18],"However,":[19],"GPUs":[20],"still":[21],"encounter":[22],"significant":[23,64,155],"performance":[24,164],"bottlenecks":[25,165],"when":[26],"running":[27],"BERT-style":[28],"models.":[31],"Moreover,":[32],"due":[33],"to":[34,45,60,110],"the":[35,121,150],"vastly":[36],"greater":[37],"number":[38],"of":[39,123],"tokens":[40],"protein":[42,80,127,171],"sequences":[43,129],"compared":[44],"human":[46,58],"languages":[47,59],"(as":[48],"illustrated":[49],"Figure":[51],"1),":[52],"directly":[53],"transferring":[54],"from":[57],"proteins":[61],"results":[62,138],"changes":[65],"runtime":[67],"behavior.":[68],"Consequently,":[69],"optimizations":[70],"designed":[71],"short-input":[73],"BERT":[74],"are":[76],"less":[77],"effective":[78],"models.In":[82],"this":[83],"paper,":[84],"we":[85,119],"propose":[86],"a":[87,143,154],"novel":[88],"GPU-based":[89],"cross-layer":[90],"optimization":[91],"strategy.":[92],"From":[93,115],"an":[94,116],"architectural":[95],"perspective,":[96,118],"our":[97],"approach":[98],"leverages":[99],"intra-":[100],"inter-operator":[102],"parallelism,":[103],"multilevel":[104],"data":[105],"computation":[106],"warp":[108],"parallelism":[109],"fully":[111],"utilize":[112],"GPU":[113],"features.":[114],"algorithmic":[117],"address":[120],"issue":[122],"varying":[124],"lengths":[125],"input":[128],"reduce":[131],"memory":[132],"overhead":[133],"through":[134],"padding":[135],"removal.":[136],"Experimental":[137],"demonstrate":[139],"that":[140],"ProXplore":[141],"achieves":[142],"1.8\u00d7":[144],"increase":[145],"inference":[147],"speed":[148],"on":[149],"TAPE":[151],"benchmark":[152],"without":[153],"loss":[156],"prediction":[158],"accuracy.":[159],"This":[160],"improvement":[161],"effectively":[162],"overcomes":[163],"provides":[167],"substantial":[168],"benefits":[169],"sequence":[172],"analysis":[173],"other":[175],"bioinformatics":[176],"applications.":[177]},"counts_by_year":[],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
