{"id":"https://openalex.org/W4310514724","doi":"https://doi.org/10.48550/arxiv.2211.16422","title":"Massively Parallel Open Modification Spectral Library Searching with Hyperdimensional Computing","display_name":"Massively Parallel Open Modification Spectral Library Searching with Hyperdimensional Computing","publication_year":2022,"publication_date":"2022-11-15","ids":{"openalex":"https://openalex.org/W4310514724","doi":"https://doi.org/10.48550/arxiv.2211.16422"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2211.16422","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2211.16422","pdf_url":"https://arxiv.org/pdf/2211.16422","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":"","raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2211.16422","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5036244247","display_name":"Jaeyoung Kang","orcid":"https://orcid.org/0000-0003-1483-0278"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kang, Jaeyoung","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100407819","display_name":"Weihong Xu","orcid":"https://orcid.org/0000-0001-8521-7644"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xu, Weihong","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053271927","display_name":"Wout Bittremieux","orcid":"https://orcid.org/0000-0002-3105-1359"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bittremieux, Wout","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5025573294","display_name":"Tajana Rosing","orcid":"https://orcid.org/0000-0002-6954-997X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rosing, Tajana","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12808","display_name":"Ferroelectric and Negative Capacitance Devices","score":0.9373999834060669,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12808","display_name":"Ferroelectric and Negative Capacitance Devices","score":0.9373999834060669,"subfield":{"id":"https://openalex.org/subfields/2208","display_name":"Electrical and Electronic Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.787177562713623},{"id":"https://openalex.org/keywords/massively-parallel","display_name":"Massively parallel","score":0.6973404288291931},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6021182537078857},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5421655178070068},{"id":"https://openalex.org/keywords/parallelism","display_name":"Parallelism (grammar)","score":0.44959181547164917},{"id":"https://openalex.org/keywords/binary-number","display_name":"Binary number","score":0.440187007188797},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3959559500217438},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3873673379421234},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12739551067352295}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.787177562713623},{"id":"https://openalex.org/C190475519","wikidata":"https://www.wikidata.org/wiki/Q544384","display_name":"Massively parallel","level":2,"score":0.6973404288291931},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6021182537078857},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5421655178070068},{"id":"https://openalex.org/C2781172179","wikidata":"https://www.wikidata.org/wiki/Q853109","display_name":"Parallelism (grammar)","level":2,"score":0.44959181547164917},{"id":"https://openalex.org/C48372109","wikidata":"https://www.wikidata.org/wiki/Q3913","display_name":"Binary number","level":2,"score":0.440187007188797},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3959559500217438},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3873673379421234},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12739551067352295},{"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},{"id":"https://openalex.org/C94375191","wikidata":"https://www.wikidata.org/wiki/Q11205","display_name":"Arithmetic","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2211.16422","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2211.16422","pdf_url":"https://arxiv.org/pdf/2211.16422","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":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2211.16422","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2211.16422","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":"Preprint"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2211.16422","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2211.16422","pdf_url":"https://arxiv.org/pdf/2211.16422","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":"","raw_type":"text"},"sustainable_development_goals":[{"display_name":"Affordable and clean energy","id":"https://metadata.un.org/sdg/7","score":0.8700000047683716}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2023839151","https://openalex.org/W1774183074","https://openalex.org/W2057488824","https://openalex.org/W2334687145","https://openalex.org/W2178011914","https://openalex.org/W4235962491","https://openalex.org/W2061778832","https://openalex.org/W1513001507","https://openalex.org/W2257153718","https://openalex.org/W3134702077"],"abstract_inverted_index":{"Mass":[0],"spectrometry,":[1],"commonly":[2],"used":[3],"for":[4],"protein":[5],"identification,":[6],"generates":[7],"a":[8,19,44],"massive":[9,112],"number":[10],"of":[11,25],"spectra":[12],"that":[13,86,130],"need":[14],"to":[15,32,46,78,136,155],"be":[16,120],"matched":[17],"against":[18],"large":[20],"database.":[21],"In":[22,65],"reality,":[23],"most":[24],"them":[26,96],"remain":[27],"unidentified":[28],"or":[29],"mismatched":[30],"due":[31],"unexpected":[33],"post-translational":[34],"modifications.":[35],"Open":[36],"modification":[37],"search":[38,62,153,157],"(OMS)":[39],"has":[40],"been":[41],"proposed":[42],"as":[43],"strategy":[45],"improve":[47],"the":[48,61,104,111,145],"identification":[49],"rate":[50],"by":[51],"considering":[52],"every":[53],"possible":[54],"change":[55],"in":[56,107],"spectra,":[57],"but":[58],"it":[59],"expands":[60],"space":[63],"exponentially.":[64],"this":[66],"work,":[67],"we":[68],"propose":[69],"HyperOMS,":[70],"which":[71],"redesigns":[72],"OMS":[73,106,148],"based":[74],"on":[75,123,132],"hyperdimensional":[76],"computing":[77,125],"cope":[79],"with":[80,90,97],"such":[81],"challenges.":[82],"Unlike":[83],"existing":[84],"algorithms":[85],"represent":[87],"spectral":[88],"data":[89],"floating":[91],"point":[92],"numbers,":[93],"HyperOMS":[94,118,131],"encodes":[95],"high":[98],"dimensional":[99],"binary":[100],"vectors":[101],"and":[102,114,139],"performs":[103],"efficient":[105,143],"high-dimensional":[108],"space.":[109],"With":[110],"parallelism":[113],"simple":[115],"boolean":[116],"operations,":[117],"can":[119],"efficiently":[121],"handled":[122],"parallel":[124],"platforms.":[126],"Experimental":[127],"results":[128],"show":[129],"GPU":[133],"is":[134],"up":[135],"$17\\times$":[137],"faster":[138],"$6.4\\times$":[140],"more":[141],"energy":[142],"than":[144],"state-of-the-art":[146],"GPU-based":[147],"tool":[149],"while":[150],"providing":[151],"comparable":[152],"quality":[154],"competing":[156],"tools.":[158]},"counts_by_year":[{"year":2023,"cited_by_count":1}],"updated_date":"2026-07-01T06:00:48.157686","created_date":"2022-12-11T00:00:00"}
