{"id":"https://openalex.org/W4386764197","doi":"https://doi.org/10.1109/dac56929.2023.10247915","title":"UpPipe: A Novel Pipeline Management on In-Memory Processors for RNA-seq Quantification","display_name":"UpPipe: A Novel Pipeline Management on In-Memory Processors for RNA-seq Quantification","publication_year":2023,"publication_date":"2023-07-09","ids":{"openalex":"https://openalex.org/W4386764197","doi":"https://doi.org/10.1109/dac56929.2023.10247915"},"language":"en","primary_location":{"id":"doi:10.1109/dac56929.2023.10247915","is_oa":false,"landing_page_url":"https://doi.org/10.1109/dac56929.2023.10247915","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 60th ACM/IEEE Design Automation Conference (DAC)","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/A5056850965","display_name":"Liang-Chi Chen","orcid":"https://orcid.org/0000-0003-2579-4305"},"institutions":[{"id":"https://openalex.org/I91807558","display_name":"National Cheng Kung University","ror":"https://ror.org/01b8kcc49","country_code":"TW","type":"education","lineage":["https://openalex.org/I91807558"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Liang-Chi Chen","raw_affiliation_strings":["National Cheng Kung University,Department of CSIE,Tainan,Taiwan R.O.C","Department of CSIE, National Cheng Kung University, Tainan, Taiwan R.O.C"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Cheng Kung University,Department of CSIE,Tainan,Taiwan R.O.C","institution_ids":["https://openalex.org/I91807558"]},{"raw_affiliation_string":"Department of CSIE, National Cheng Kung University, Tainan, Taiwan R.O.C","institution_ids":["https://openalex.org/I91807558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044099250","display_name":"Chien-Chung Ho","orcid":"https://orcid.org/0000-0003-3460-8674"},"institutions":[{"id":"https://openalex.org/I91807558","display_name":"National Cheng Kung University","ror":"https://ror.org/01b8kcc49","country_code":"TW","type":"education","lineage":["https://openalex.org/I91807558"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Chien-Chung Ho","raw_affiliation_strings":["National Cheng Kung University,Department of CSIE,Tainan,Taiwan R.O.C","Department of CSIE, National Cheng Kung University, Tainan, Taiwan R.O.C"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"National Cheng Kung University,Department of CSIE,Tainan,Taiwan R.O.C","institution_ids":["https://openalex.org/I91807558"]},{"raw_affiliation_string":"Department of CSIE, National Cheng Kung University, Tainan, Taiwan R.O.C","institution_ids":["https://openalex.org/I91807558"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073534245","display_name":"Yuan-Hao Chang","orcid":"https://orcid.org/0000-0002-1282-2111"},"institutions":[{"id":"https://openalex.org/I4210098366","display_name":"Institute of Information Science, Academia Sinica","ror":"https://ror.org/00z83z196","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210098366","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yuan-Hao Chang","raw_affiliation_strings":["Academia Sinica,Institute of Information Science,Taipei,Taiwan R.O.C","Institute of Information Science, Academia Sinica, Taipei, Taiwan R.O.C"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Academia Sinica,Institute of Information Science,Taipei,Taiwan R.O.C","institution_ids":["https://openalex.org/I4210098366"]},{"raw_affiliation_string":"Institute of Information Science, Academia Sinica, Taipei, Taiwan R.O.C","institution_ids":["https://openalex.org/I4210098366"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":22.8619,"has_fulltext":false,"cited_by_count":17,"citation_normalized_percentile":{"value":0.99642813,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"1","last_page":"6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9926000237464905,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9926000237464905,"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.9753999710083008,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12326","display_name":"Network Packet Processing and Optimization","score":0.9708999991416931,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.8137308359146118},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7677160501480103},{"id":"https://openalex.org/keywords/overhead","display_name":"Overhead (engineering)","score":0.6747750043869019},{"id":"https://openalex.org/keywords/auxiliary-memory","display_name":"Auxiliary memory","score":0.48352718353271484},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.45879265666007996},{"id":"https://openalex.org/keywords/memory-management","display_name":"Memory management","score":0.4475187659263611},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.4138319790363312},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.3531789481639862},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3391377925872803},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.3102021813392639},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.15156254172325134},{"id":"https://openalex.org/keywords/semiconductor-memory","display_name":"Semiconductor memory","score":0.12769201397895813}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.8137308359146118},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7677160501480103},{"id":"https://openalex.org/C2779960059","wikidata":"https://www.wikidata.org/wiki/Q7113681","display_name":"Overhead (engineering)","level":2,"score":0.6747750043869019},{"id":"https://openalex.org/C82687282","wikidata":"https://www.wikidata.org/wiki/Q66221","display_name":"Auxiliary memory","level":2,"score":0.48352718353271484},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.45879265666007996},{"id":"https://openalex.org/C176649486","wikidata":"https://www.wikidata.org/wiki/Q2308807","display_name":"Memory management","level":3,"score":0.4475187659263611},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.4138319790363312},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.3531789481639862},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3391377925872803},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.3102021813392639},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.15156254172325134},{"id":"https://openalex.org/C98986596","wikidata":"https://www.wikidata.org/wiki/Q1143031","display_name":"Semiconductor memory","level":2,"score":0.12769201397895813}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/dac56929.2023.10247915","is_oa":false,"landing_page_url":"https://doi.org/10.1109/dac56929.2023.10247915","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2023 60th ACM/IEEE Design Automation Conference (DAC)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9","score":0.5199999809265137}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321041","display_name":"Academia Sinica","ror":"https://ror.org/05bxb3784"},{"id":"https://openalex.org/F4320331164","display_name":"National Science and Technology Council","ror":"https://ror.org/00wnb9798"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W2065128082","https://openalex.org/W2140729960","https://openalex.org/W2144560237","https://openalex.org/W2161397498","https://openalex.org/W2323326409","https://openalex.org/W2982008795","https://openalex.org/W3175594783","https://openalex.org/W3211961913","https://openalex.org/W4214923637","https://openalex.org/W4285121610","https://openalex.org/W4297098423","https://openalex.org/W4304699827","https://openalex.org/W6797721083"],"related_works":["https://openalex.org/W2072336782","https://openalex.org/W2104196725","https://openalex.org/W261562921","https://openalex.org/W2063776575","https://openalex.org/W2051837050","https://openalex.org/W166631249","https://openalex.org/W4230105825","https://openalex.org/W2543553956","https://openalex.org/W2526409495","https://openalex.org/W2353759903"],"abstract_inverted_index":{"RNA":[0,24],"sequence":[1],"quantification":[2,17,37,112],"is":[3,18,38,70,150],"an":[4],"important":[5],"analysis":[6],"method":[7],"to":[8,19,26,79,89,106,136,154,179],"measure":[9],"transcript":[10],"abundances.":[11],"A":[12],"key":[13],"overhead":[14],"in":[15],"RNA-seq":[16,36,111],"map":[20],"a":[21,76,125,174],"set":[22],"of":[23,35,45,110,118,141,146,168,185],"reads":[25],"multiple":[27],"reference":[28],"transcripts,":[29],"i.e.,":[30,52],"transcriptome.":[31],"Besides,":[32],"the":[33,42,57,61,72,81,108,116,133,138,144,151,159,166,181],"performance":[34,109],"strictly":[39],"limited":[40,182],"by":[41,93,113],"excessive":[43],"amounts":[44],"data":[46,96],"movement":[47,97],"between":[48,98],"CPU":[49,99],"and":[50,100,172],"memory,":[51],"memory":[53,82],"wall":[54,83],"problem":[55],"on":[56,132,158,177],"conventional":[58],"architecture.":[59],"As":[60],"first":[62,152],"publicly":[63],"commercial":[64],"processing-in-memory":[65],"(PIM)":[66],"system,":[67],"UPMEM":[68],"DPU,":[69],"proposed,":[71],"PIM":[73],"gradually":[74],"becomes":[75],"promising":[77],"solution":[78],"overcome":[80],"problem.":[84],"DPUs":[85,186],"show":[86],"great":[87],"potential":[88],"accelerate":[90],"data-intensive":[91],"workloads":[92],"minimizing":[94],"off-chip":[95],"memory.":[101],"Thus,":[102],"this":[103,149],"paper":[104],"aims":[105],"improve":[107],"fully":[114],"exploiting":[115],"strengths":[117],"DPU.":[119,142],"To":[120,143],"achieve":[121],"that,":[122],"we":[123],"propose":[124],"novel":[126],"DPU-aware":[127],"pipeline":[128,156],"design":[129,171],"\"UpPipe\"":[130],"built":[131],"software":[134],"layer":[135],"address":[137],"hardware":[139,183],"constraints":[140],"best":[145],"our":[147,169],"knowledge,":[148],"work":[153],"enable":[155],"management":[157],"DPU":[160],"system.":[161],"The":[162],"evaluation":[163],"results":[164],"demonstrate":[165],"feasibility":[167],"proposed":[170],"provide":[173],"comprehensive":[175],"study":[176],"how":[178],"utilize":[180],"resources":[184],"efficiently.":[187]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-29T14:22:42.915294","created_date":"2025-10-10T00:00:00"}
