{"id":"https://openalex.org/W4386764039","doi":"https://doi.org/10.1109/dac56929.2023.10247956","title":"MeG<sup>2</sup>: In-Memory Acceleration for Genome Graphs Analysis","display_name":"MeG<sup>2</sup>: In-Memory Acceleration for Genome Graphs Analysis","publication_year":2023,"publication_date":"2023-07-09","ids":{"openalex":"https://openalex.org/W4386764039","doi":"https://doi.org/10.1109/dac56929.2023.10247956"},"language":"en","primary_location":{"id":"doi:10.1109/dac56929.2023.10247956","is_oa":false,"landing_page_url":"https://doi.org/10.1109/dac56929.2023.10247956","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/A5052025786","display_name":"Yu Huang","orcid":"https://orcid.org/0000-0002-3927-1102"},"institutions":[{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]},{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yu Huang","raw_affiliation_strings":["Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074","Zhejiang Lab, Hangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074","institution_ids":["https://openalex.org/I47720641"]},{"raw_affiliation_string":"Zhejiang Lab, Hangzhou, China","institution_ids":["https://openalex.org/I4210123185"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023600493","display_name":"Long Zheng","orcid":"https://orcid.org/0000-0001-7903-2061"},"institutions":[{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]},{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Long Zheng","raw_affiliation_strings":["Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074","Zhejiang Lab, Hangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074","institution_ids":["https://openalex.org/I47720641"]},{"raw_affiliation_string":"Zhejiang Lab, Hangzhou, China","institution_ids":["https://openalex.org/I4210123185"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115053629","display_name":"Haifeng Liu","orcid":"https://orcid.org/0000-0003-3319-254X"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haifeng Liu","raw_affiliation_strings":["Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101333369","display_name":"Zhuoran Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhuoran Zhou","raw_affiliation_strings":["Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101564451","display_name":"Dan Chen","orcid":"https://orcid.org/0000-0003-4158-5239"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dan Chen","raw_affiliation_strings":["Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010485648","display_name":"Pengcheng Yao","orcid":"https://orcid.org/0000-0003-4701-2239"},"institutions":[{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]},{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengcheng Yao","raw_affiliation_strings":["Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074","Zhejiang Lab, Hangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074","institution_ids":["https://openalex.org/I47720641"]},{"raw_affiliation_string":"Zhejiang Lab, Hangzhou, China","institution_ids":["https://openalex.org/I4210123185"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115599465","display_name":"Qinggang Wang","orcid":"https://orcid.org/0000-0002-9951-3345"},"institutions":[{"id":"https://openalex.org/I4210123185","display_name":"Zhejiang Lab","ror":"https://ror.org/02m2h7991","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210123185"]},{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qinggang Wang","raw_affiliation_strings":["Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074","Zhejiang Lab, Hangzhou, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074","institution_ids":["https://openalex.org/I47720641"]},{"raw_affiliation_string":"Zhejiang Lab, Hangzhou, China","institution_ids":["https://openalex.org/I4210123185"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022398389","display_name":"Xiaofei Liao","orcid":"https://orcid.org/0000-0001-6302-813X"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaofei Liao","raw_affiliation_strings":["Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074","institution_ids":["https://openalex.org/I47720641"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5022262922","display_name":"Hai Jin","orcid":"https://orcid.org/0000-0002-3934-7605"},"institutions":[{"id":"https://openalex.org/I47720641","display_name":"Huazhong University of Science and Technology","ror":"https://ror.org/00p991c53","country_code":"CN","type":"education","lineage":["https://openalex.org/I47720641"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hai Jin","raw_affiliation_strings":["Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Huazhong University of Science and Technology,National Engineering Research Center for Big Data Technology and System/Services Computing Technology and System Lab/Cluster and Grid Computing Laboratory,Wuhan,China,430074","institution_ids":["https://openalex.org/I47720641"]}]}],"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":3,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"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":0.9976999759674072,"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":0.9976999759674072,"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":0.9919999837875366,"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/T11478","display_name":"Caching and Content Delivery","score":0.9746999740600586,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7002520561218262},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.41880229115486145},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.41678228974342346},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.33667024970054626},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3352069854736328},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14190244674682617},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12367534637451172}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7002520561218262},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.41880229115486145},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.41678228974342346},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.33667024970054626},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3352069854736328},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14190244674682617},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12367534637451172},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/dac56929.2023.10247956","is_oa":false,"landing_page_url":"https://doi.org/10.1109/dac56929.2023.10247956","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":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W26356079","https://openalex.org/W2034861439","https://openalex.org/W2766489088","https://openalex.org/W2789843538","https://openalex.org/W2888300707","https://openalex.org/W2965998663","https://openalex.org/W3042963200","https://openalex.org/W3088400220","https://openalex.org/W3088711112","https://openalex.org/W3105003914","https://openalex.org/W3189166979","https://openalex.org/W3201830280","https://openalex.org/W4280509186","https://openalex.org/W4281647104","https://openalex.org/W4308083600","https://openalex.org/W4308479188","https://openalex.org/W6601068097"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"Genome":[0],"graphs":[1,50,95,179],"analysis":[2,51,180,224],"has":[3],"emerged":[4],"as":[5,15],"an":[6],"effective":[7],"means":[8],"to":[9,17,31,92,133,155],"enable":[10],"mapping":[11],"DNA":[12],"fragments":[13],"(known":[14],"reads)":[16],"the":[18,23,33,41,58,64,70,105,121,129,135,140,145,152,157,162,173],"reference":[19,26],"genome.":[20],"It":[21],"replaces":[22],"traditional":[24],"linear":[25],"with":[27,104,128,151],"a":[28,86],"graph-based":[29],"representation":[30],"augment":[32],"genetic":[34],"variations":[35],"and":[36,63,73,111,143,176,188,204],"diversity":[37],"information,":[38],"significantly":[39],"improving":[40],"quality":[42],"of":[43,48,107,125,148],"genotyping.":[44],"The":[45],"in-depth":[46],"characterization":[47],"genome":[49,94,178,222],"uncovers":[52],"that":[53,167,211],"it":[54],"is":[55,101],"bottlenecked":[56],"by":[57,182,199],"irregular":[59,136],"seed":[60],"index":[61],"access":[62,123,138],"intensive":[65,158],"alignment":[66,163],"operation,":[67],"stressing":[68],"both":[69,108],"memory":[71,137],"system":[72],"computing":[74],"resources.Based":[75],"on":[76],"these":[77],"observations,":[78],"we":[79],"propose":[80],"MeG":[81,97,116,168,212],"<sup":[82,98,117,169,213],"xmlns:mml=\"http://www.w3.org/1998/Math/MathML\"":[83,99,118,170,214],"xmlns:xlink=\"http://www.w3.org/1999/xlink\">2</sup>":[84,100,119,171,215],",":[85],"lightweight,":[87],"commodity":[88],"DRAM-compliant,":[89],"processing-in-memory":[90],"architecture":[91],"accelerate":[93],"analysis.":[96],"specifically":[102],"integrated":[103],"capabilities":[106],"near-memory":[109,126],"processing":[110,127],"bitwise":[112],"in-situ":[113,149],"computation.":[114],"Specifically,":[115],"leverages":[120],"low":[122],"latency":[124],"index-centric":[130],"offload":[131],"mechanism":[132],"alleviate":[134],"in":[139,161],"seeding":[141],"procedure,":[142],"harnesses":[144],"row-parallel":[146],"capacity":[147],"computation":[150],"distance-aware":[153],"technique":[154],"exploit":[156],"computational":[159],"parallelism":[160],"process.":[164],"Results":[165],"show":[166],"outperforms":[172],"CPU-,":[174],"GPU-,":[175],"ASIC-based":[177],"solutions":[181],"502\u00d7":[183],"(30.2\u00d7),":[184],"272\u00d7":[185],"(15.1\u00d7":[186],"),":[187],"5.5\u00d7":[189],"(8.3\u00d7)":[190],"for":[191],"short":[192],"(long)":[193],"reads,":[194],"while":[195],"reducing":[196],"energy":[197],"consumption":[198],"1628\u00d7":[200],"(85.6\u00d7),":[201],"1443\u00d7":[202],"(77.1\u00d7),":[203],"7.8\u00d7":[205],"(11.7\u00d7),":[206],"respectively.":[207],"We":[208],"also":[209],"demonstrate":[210],"offers":[216],"significant":[217],"improvements":[218],"over":[219],"existing":[220],"PIM-based":[221],"sequence":[223],"accelerators.":[225]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
