{"id":"https://openalex.org/W3192166791","doi":"https://doi.org/10.1109/fpl53798.2021.00024","title":"Communication-avoiding micro-architecture to compute Xcorr scores for peptide identification","display_name":"Communication-avoiding micro-architecture to compute Xcorr scores for peptide identification","publication_year":2021,"publication_date":"2021-08-01","ids":{"openalex":"https://openalex.org/W3192166791","doi":"https://doi.org/10.1109/fpl53798.2021.00024","mag":"3192166791","pmid":"https://pubmed.ncbi.nlm.nih.gov/35440952"},"language":"en","primary_location":{"id":"doi:10.1109/fpl53798.2021.00024","is_oa":false,"landing_page_url":"https://doi.org/10.1109/fpl53798.2021.00024","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 31st International Conference on Field-Programmable Logic and Applications (FPL)","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://export.arxiv.org/pdf/2108.00147","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5084886863","display_name":"Sumesh Kumar","orcid":null},"institutions":[{"id":"https://openalex.org/I19700959","display_name":"Florida International University","ror":"https://ror.org/02gz6gg07","country_code":"US","type":"education","lineage":["https://openalex.org/I19700959"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sumesh Kumar","raw_affiliation_strings":["Knight Foundation School of Computing and Information Sciences, Florida International University (FIU), Miami, FL USA 33199","Florida International University (FIU),Knight Foundation School of Computing and Information Sciences,Miami,FL,USA,33199"],"affiliations":[{"raw_affiliation_string":"Knight Foundation School of Computing and Information Sciences, Florida International University (FIU), Miami, FL USA 33199","institution_ids":[]},{"raw_affiliation_string":"Florida International University (FIU),Knight Foundation School of Computing and Information Sciences,Miami,FL,USA,33199","institution_ids":["https://openalex.org/I19700959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102729196","display_name":"Fahad Saeed","orcid":"https://orcid.org/0000-0002-3410-9552"},"institutions":[{"id":"https://openalex.org/I19700959","display_name":"Florida International University","ror":"https://ror.org/02gz6gg07","country_code":"US","type":"education","lineage":["https://openalex.org/I19700959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fahad Saeed","raw_affiliation_strings":["Knight Foundation School of Computing and Information Sciences, Florida International University (FIU), Miami, FL USA 33199","Florida International University"],"affiliations":[{"raw_affiliation_string":"Knight Foundation School of Computing and Information Sciences, Florida International University (FIU), Miami, FL USA 33199","institution_ids":[]},{"raw_affiliation_string":"Florida International University","institution_ids":["https://openalex.org/I19700959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5084886863"],"corresponding_institution_ids":["https://openalex.org/I19700959"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.07889357,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"2021","issue":null,"first_page":"99","last_page":"103"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9998999834060669,"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/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9984999895095825,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9929999709129333,"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":0.8097387552261353},{"id":"https://openalex.org/keywords/dram","display_name":"Dram","score":0.5916444063186646},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.48447299003601074},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.476046085357666},{"id":"https://openalex.org/keywords/cache","display_name":"Cache","score":0.4630691111087799},{"id":"https://openalex.org/keywords/exploit","display_name":"Exploit","score":0.44791871309280396},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.389525443315506},{"id":"https://openalex.org/keywords/embedded-system","display_name":"Embedded system","score":0.37421590089797974},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.33152711391448975},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.2732805609703064}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8097387552261353},{"id":"https://openalex.org/C7366592","wikidata":"https://www.wikidata.org/wiki/Q1255620","display_name":"Dram","level":2,"score":0.5916444063186646},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.48447299003601074},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.476046085357666},{"id":"https://openalex.org/C115537543","wikidata":"https://www.wikidata.org/wiki/Q165596","display_name":"Cache","level":2,"score":0.4630691111087799},{"id":"https://openalex.org/C165696696","wikidata":"https://www.wikidata.org/wiki/Q11287","display_name":"Exploit","level":2,"score":0.44791871309280396},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.389525443315506},{"id":"https://openalex.org/C149635348","wikidata":"https://www.wikidata.org/wiki/Q193040","display_name":"Embedded system","level":1,"score":0.37421590089797974},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.33152711391448975},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.2732805609703064},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1109/fpl53798.2021.00024","is_oa":false,"landing_page_url":"https://doi.org/10.1109/fpl53798.2021.00024","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 31st International Conference on Field-Programmable Logic and Applications (FPL)","raw_type":"proceedings-article"},{"id":"pmid:35440952","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35440952","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Conference on Field-programmable Logic and Applications : [proceedings]. International Conference on Field-Programmable Logic and Applications","raw_type":null},{"id":"mag:3192166791","is_oa":true,"landing_page_url":"http://export.arxiv.org/pdf/2108.00147","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:9015013","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9015013","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"TEST","raw_type":"Text"},{"id":"doi:10.48550/arxiv.2108.00147","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2108.00147","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"mag:3192166791","is_oa":true,"landing_page_url":"http://export.arxiv.org/pdf/2108.00147","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1968044788","https://openalex.org/W1973333402","https://openalex.org/W1979231364","https://openalex.org/W1985560593","https://openalex.org/W2016605939","https://openalex.org/W2023096047","https://openalex.org/W2023655541","https://openalex.org/W2026465178","https://openalex.org/W2034601083","https://openalex.org/W2085467029","https://openalex.org/W2130706354","https://openalex.org/W2152998178","https://openalex.org/W2476382785","https://openalex.org/W2502602747","https://openalex.org/W2527036487","https://openalex.org/W2607310450","https://openalex.org/W2763395976","https://openalex.org/W2918401251","https://openalex.org/W3003896859","https://openalex.org/W3090870634"],"related_works":["https://openalex.org/W3207382677","https://openalex.org/W2122048769","https://openalex.org/W2891489843","https://openalex.org/W2584219348","https://openalex.org/W2004709743","https://openalex.org/W3142643768","https://openalex.org/W2780829033","https://openalex.org/W2253289281","https://openalex.org/W1483010078","https://openalex.org/W2896857054","https://openalex.org/W2907387573","https://openalex.org/W2551619187","https://openalex.org/W2103880112","https://openalex.org/W2952112274","https://openalex.org/W2905658624","https://openalex.org/W2226815576","https://openalex.org/W2802636586","https://openalex.org/W3042659887","https://openalex.org/W2584275757","https://openalex.org/W2082023298"],"abstract_inverted_index":{"Database":[0],"algorithms":[1,22],"play":[2],"a":[3,125,148,190,195],"crucial":[4],"part":[5],"in":[6,103],"systems":[7],"biology":[8],"studies":[9],"by":[10,27,84,135],"identifying":[11],"proteins":[12],"from":[13],"mass":[14],"spectrometry":[15,53],"data.":[16],"Many":[17],"of":[18,34,50,66,77,91,173],"these":[19,97],"database":[20],"search":[21,60],"incur":[23],"huge":[24],"computational":[25],"costs":[26,87,99],"computing":[28],"similarity":[29,133],"scores":[30],"for":[31],"each":[32],"pair":[33],"sparse":[35],"experimental":[36],"spectrum":[37,41],"and":[38,79,93,111,140,147,164,170],"candidate":[39],"theoretical":[40],"vectors.":[42],"Modern":[43],"MS":[44],"instrumentation":[45],"techniques":[46],"which":[47],"are":[48,100],"capable":[49],"generating":[51],"high-resolution":[52],"data":[54],"require":[55],"comparison":[56],"against":[57],"an":[58],"enormous":[59],"space,":[61],"further":[62],"emphasizing":[63],"the":[64,74,85,181],"need":[65],"efficient":[67,137,158],"accelerators.":[68],"Recent":[69],"research":[70],"has":[71],"shown":[72],"that":[73,180],"overall":[75],"cost":[76,169],"scoring,":[78],"deducing":[80],"peptides":[81],"is":[82],"dominated":[83],"communication":[86,98],"between":[88],"different":[89],"hierarchies":[90],"memory":[92,117],"processing":[94,174],"units.":[95],"However,":[96],"seldom":[101],"considered":[102],"accelerator-based":[104],"architectures":[105],"leading":[106],"to":[107,115,129,143,153,166],"inefficient":[108],"DRAM":[109,145],"accesses,":[110,146],"poor":[112],"data-utilization":[113],"due":[114],"irregular":[116],"access":[118],"patterns.":[119],"In":[120],"this":[121],"paper,":[122],"we":[123],"propose":[124],"novel":[126],"communication-avoiding":[127],"micro-architecture":[128,183],"compute":[130],"cross-correlation":[131],"based":[132],"score":[134],"utilizing":[136],"local":[138],"cache,":[139],"peptide":[141,150],"pre-fetching":[142],"minimize":[144,167],"custom-designed":[149],"broadcast":[151],"bus":[152,159],"allow":[154],"input":[155],"reuse.":[156],"An":[157],"arbitration":[160],"scheme":[161],"was":[162],"designed,":[163],"implemented":[165],"synchronization":[168],"exploit":[171],"parallelism":[172],"elements.":[175],"Our":[176],"simulation":[177],"results":[178],"show":[179],"proposed":[182],"performs":[184],"on":[185,194],"average":[186],"24x":[187],"better":[188],"than":[189],"CPU":[191],"implementation":[192],"running":[193],"3.6":[196],"GHz":[197],"Intel":[198],"i7-4970":[199],"processor":[200],"with":[201],"16GB":[202],"memory.":[203]},"counts_by_year":[],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
