{"id":"https://openalex.org/W2118936983","doi":"https://doi.org/10.1145/1542275.1542329","title":"Single-particle 3d reconstruction from cryo-electron microscopy images on GPU","display_name":"Single-particle 3d reconstruction from cryo-electron microscopy images on GPU","publication_year":2009,"publication_date":"2009-06-08","ids":{"openalex":"https://openalex.org/W2118936983","doi":"https://doi.org/10.1145/1542275.1542329","mag":"2118936983"},"language":"en","primary_location":{"id":"doi:10.1145/1542275.1542329","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1542275.1542329","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 23rd international conference on Supercomputing","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/A5104072170","display_name":"Guangming Tan","orcid":null},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guangming Tan","raw_affiliation_strings":["Chinese Academy of Science, Beijing, China","[Chinese Academy of Science, Beijing, China]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chinese Academy of Science, Beijing, China","institution_ids":[]},{"raw_affiliation_string":"[Chinese Academy of Science, Beijing, China]","institution_ids":["https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053834265","display_name":"Ziyu Guo","orcid":"https://orcid.org/0000-0002-4792-1398"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ziyu Guo","raw_affiliation_strings":["Chinese Academy of Science, Beijing, China","[Chinese Academy of Science, Beijing, China]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chinese Academy of Science, Beijing, China","institution_ids":[]},{"raw_affiliation_string":"[Chinese Academy of Science, Beijing, China]","institution_ids":["https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052120417","display_name":"Mingyu Chen","orcid":"https://orcid.org/0000-0002-7264-0731"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Mingyu Chen","raw_affiliation_strings":["Chinese Academy of Science, Beijing, China","[Chinese Academy of Science, Beijing, China]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chinese Academy of Science, Beijing, China","institution_ids":[]},{"raw_affiliation_string":"[Chinese Academy of Science, Beijing, China]","institution_ids":["https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110216462","display_name":"Meng Dan","orcid":null},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dan Meng","raw_affiliation_strings":["Chinese Academy of Science, Beijing, China","[Chinese Academy of Science, Beijing, China]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Chinese Academy of Science, Beijing, China","institution_ids":[]},{"raw_affiliation_string":"[Chinese Academy of Science, Beijing, China]","institution_ids":["https://openalex.org/I19820366"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I19820366"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"380","last_page":"389"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T10857","display_name":"Advanced Electron Microscopy Techniques and Applications","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1315","display_name":"Structural 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/T12039","display_name":"Electron and X-Ray Spectroscopy Techniques","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/2508","display_name":"Surfaces, Coatings and Films"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11183","display_name":"Advanced X-ray Imaging Techniques","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/3108","display_name":"Radiation"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8011224865913391},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.7688840627670288},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.6642332077026367},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.661716878414154},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.48549845814704895},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4671333134174347},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.4243260324001312},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.1473693549633026}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8011224865913391},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.7688840627670288},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.6642332077026367},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.661716878414154},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.48549845814704895},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4671333134174347},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.4243260324001312},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.1473693549633026},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/1542275.1542329","is_oa":false,"landing_page_url":"https://doi.org/10.1145/1542275.1542329","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 23rd international conference on Supercomputing","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.668.3610","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.668.3610","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://asg.ict.ac.cn/tgm/ics067-tan.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321133","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W138765943","https://openalex.org/W178909140","https://openalex.org/W1508511955","https://openalex.org/W1986431220","https://openalex.org/W1992851788","https://openalex.org/W1999752372","https://openalex.org/W2001024934","https://openalex.org/W2006158980","https://openalex.org/W2010580757","https://openalex.org/W2019708326","https://openalex.org/W2044213522","https://openalex.org/W2048982317","https://openalex.org/W2053974706","https://openalex.org/W2063186542","https://openalex.org/W2068654340","https://openalex.org/W2077580539","https://openalex.org/W2114983120","https://openalex.org/W2140092984","https://openalex.org/W2143169490","https://openalex.org/W4386313974","https://openalex.org/W6607203845"],"related_works":["https://openalex.org/W2983282793","https://openalex.org/W2317245370","https://openalex.org/W4249323025","https://openalex.org/W198851386","https://openalex.org/W2030310580","https://openalex.org/W947442053","https://openalex.org/W1980160788","https://openalex.org/W1973046741","https://openalex.org/W2148915962","https://openalex.org/W2283866686"],"abstract_inverted_index":{"Single-particle":[0],"3D":[1,29],"reconstruction":[2],"from":[3],"cryo-electron":[4],"microscopy":[5],"(cryo-EM)":[6],"images":[7],"is":[8,22],"a":[9,27,58,85,94],"kernel":[10],"application":[11],"of":[12,20,44,97,118],"biological":[13],"molecules":[14],"analysis,":[15],"as":[16],"the":[17,37,45,73,101,111],"computational":[18,39],"requirement":[19],"which":[21,92],"now":[23],"beyond":[24],"PetaFlop":[25],"for":[26],"high-resolution":[28],"structure.":[30],"In":[31],"this":[32],"paper,":[33],"we":[34,56,79],"quantitatively":[35],"analyze":[36],"workload,":[38],"intensity":[40],"and":[41,67,121],"memory":[42,65,76,119],"performance":[43],"application,":[46],"parallelize":[47],"it":[48],"on":[49,84],"an":[50],"emerging":[51],"multicore":[52],"architecture":[53],"GPU-CUDA.":[54],"Further":[55],"apply":[57],"percolation":[59,113],"technique":[60],"to":[61,71,90,100],"decouple":[62],"computation":[63],"with":[64],"operations":[66],"orchestrate":[68],"thread-data":[69],"mapping":[70],"reduce":[72],"overhead":[74],"off-chip":[75],"operations.":[77],"Finally":[78],"tested":[80],"our":[81],"optimization":[82],"strategy":[83],"popular":[86],"open-source":[87],"package":[88],"EMAN":[89],"GPU-CUDA,":[91],"achieves":[93],"relative":[95],"speedup":[96],"about":[98],"10X":[99],"original":[102],"CPU-only":[103],"EMAN.":[104],"The":[105],"experimental":[106],"results":[107],"also":[108],"show":[109],"that":[110],"proposed":[112],"programming":[114],"greatly":[115],"improves":[116],"utilization":[117],"bandwidth":[120],"floating-point":[122],"units.":[123]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}