{"id":"https://openalex.org/W4313525688","doi":"https://doi.org/10.1109/bibm55620.2022.9995222","title":"Understanding Performance Portability of Bioinformatics Applications in SYCL on an NVIDIA GPU","display_name":"Understanding Performance Portability of Bioinformatics Applications in SYCL on an NVIDIA GPU","publication_year":2022,"publication_date":"2022-12-06","ids":{"openalex":"https://openalex.org/W4313525688","doi":"https://doi.org/10.1109/bibm55620.2022.9995222"},"language":"en","primary_location":{"id":"doi:10.1109/bibm55620.2022.9995222","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm55620.2022.9995222","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.osti.gov/servlets/purl/1909099","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101790023","display_name":"Zheming Jin","orcid":"https://orcid.org/0000-0002-7197-780X"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Zheming Jin","raw_affiliation_strings":["Oak Ridge National Laboratory"],"affiliations":[{"raw_affiliation_string":"Oak Ridge National Laboratory","institution_ids":["https://openalex.org/I1289243028"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061838490","display_name":"Jeffrey S. Vetter","orcid":"https://orcid.org/0000-0002-2449-6720"},"institutions":[{"id":"https://openalex.org/I1289243028","display_name":"Oak Ridge National Laboratory","ror":"https://ror.org/01qz5mb56","country_code":"US","type":"facility","lineage":["https://openalex.org/I1289243028","https://openalex.org/I1330989302","https://openalex.org/I39565521","https://openalex.org/I4210159294"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey S. Vetter","raw_affiliation_strings":["Oak Ridge National Laboratory"],"affiliations":[{"raw_affiliation_string":"Oak Ridge National Laboratory","institution_ids":["https://openalex.org/I1289243028"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5101790023"],"corresponding_institution_ids":["https://openalex.org/I1289243028"],"apc_list":null,"apc_paid":null,"fwci":7.4953,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":{"value":0.98583792,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":null,"issue":null,"first_page":"2190","last_page":"2195"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.995199978351593,"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/T10885","display_name":"Gene expression and cancer classification","score":0.995199978351593,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9915000200271606,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9846000075340271,"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/software-portability","display_name":"Software portability","score":0.9340095520019531},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.9104216694831848},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7800354957580566},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.6198985576629639},{"id":"https://openalex.org/keywords/general-purpose-computing-on-graphics-processing-units","display_name":"General-purpose computing on graphics processing units","score":0.5582039952278137},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.47646641731262207},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.43065306544303894},{"id":"https://openalex.org/keywords/computer-architecture","display_name":"Computer architecture","score":0.32565751671791077},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3203306794166565},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.22055649757385254},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.15381336212158203},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1106971800327301}],"concepts":[{"id":"https://openalex.org/C63000827","wikidata":"https://www.wikidata.org/wiki/Q3080428","display_name":"Software portability","level":2,"score":0.9340095520019531},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.9104216694831848},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7800354957580566},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.6198985576629639},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.5582039952278137},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.47646641731262207},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.43065306544303894},{"id":"https://openalex.org/C118524514","wikidata":"https://www.wikidata.org/wiki/Q173212","display_name":"Computer architecture","level":1,"score":0.32565751671791077},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3203306794166565},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.22055649757385254},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.15381336212158203},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1106971800327301}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/bibm55620.2022.9995222","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm55620.2022.9995222","pdf_url":null,"source":{"id":"https://openalex.org/S4363607730","display_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},{"id":"pmh:oai:osti.gov:1909099","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1909099","pdf_url":"https://www.osti.gov/servlets/purl/1909099","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:osti.gov:1909099","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1909099","pdf_url":"https://www.osti.gov/servlets/purl/1909099","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"sustainable_development_goals":[{"score":0.5,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320316892","display_name":"UT-Battelle","ror":"https://ror.org/04nza6677"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4313525688.pdf","grobid_xml":"https://content.openalex.org/works/W4313525688.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W599934088","https://openalex.org/W780656674","https://openalex.org/W1868492295","https://openalex.org/W1906046253","https://openalex.org/W1989909503","https://openalex.org/W2016939324","https://openalex.org/W2041724468","https://openalex.org/W2080592089","https://openalex.org/W2080914619","https://openalex.org/W2121604817","https://openalex.org/W2144663944","https://openalex.org/W2155503253","https://openalex.org/W2160004708","https://openalex.org/W2253428983","https://openalex.org/W2762584814","https://openalex.org/W2787181861","https://openalex.org/W3019518753","https://openalex.org/W3020054090","https://openalex.org/W3094070534","https://openalex.org/W3103832161","https://openalex.org/W3138529574","https://openalex.org/W3209449653","https://openalex.org/W4200216396","https://openalex.org/W4200582832","https://openalex.org/W4225270014","https://openalex.org/W4225271295","https://openalex.org/W4225548362","https://openalex.org/W4248294582","https://openalex.org/W4288421628"],"related_works":["https://openalex.org/W3020739840","https://openalex.org/W2913998709","https://openalex.org/W4386875822","https://openalex.org/W3177128669","https://openalex.org/W1963859303","https://openalex.org/W2364044215","https://openalex.org/W2389600408","https://openalex.org/W240129890","https://openalex.org/W3048701459","https://openalex.org/W2149078538"],"abstract_inverted_index":{"Our":[0],"goal":[1],"is":[2],"to":[3,29,56],"have":[4],"a":[5,15],"better":[6],"understanding":[7],"of":[8,11,59],"performance":[9,33,41,44],"portability":[10],"SYCL":[12,61],"kernels":[13,23],"on":[14,34],"GPU.":[16],"Toward":[17],"this":[18],"goal,":[19],"we":[20],"migrate":[21],"representative":[22],"in":[24],"bioinformatics":[25],"applications":[26],"from":[27],"CUDA":[28],"SYCL,":[30],"evaluate":[31],"their":[32],"an":[35],"NVIDIA":[36],"GPU,":[37],"and":[38,46],"explain":[39],"the":[40,51,57,60],"gaps":[42],"through":[43],"profiling":[45],"analyses.":[47],"We":[48],"hope":[49],"that":[50],"findings":[52],"provide":[53],"valuable":[54],"feedback":[55],"development":[58],"ecosystem.":[62]},"counts_by_year":[{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":7}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
